An ontology of phenotypic qualities (properties, attributes or characteristics). PATO - the Phenotype And Trait Ontology quality 1.2 2021-11-05 definition IAO:0000116 uberon editor_note true editor_note editor note editor note term replaced by term replaced by If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL is a defining property chain axiom If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. is a defining property chain axiom where second argument is reflexive 'anterior end of organism' is-opposite-of 'posterior end of organism' 'increase in temperature' is-opposite-of 'decrease in temperature' x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x). RO:0002604 quality is_opposite_of true true is_opposite_of is opposite of is_opposite_of Abnormal/normal slim Absent/present slim Attribute slim cell_quality Disposition slim Human phenotype slim Pathology slim Relational slim: types of quality that require an additional entity in order to exist Scalar slim Value slim http://purl.org/dc/elements/1.1/contributor uberon dc-contributor true dc-contributor contributor http://purl.org/dc/elements/1.1/creator uberon dc-creator true dc-creator creator subset_property consider has_alternative_id has_broad_synonym database_cross_reference has_exact_synonym has_narrow_synonym has_obo_format_version has_obo_namespace has_related_synonym in_subset shorthand is part of is part of my brain is part of my body (continuant parthood, two material entities) my brain is part of my body (continuant parthood, two material entities) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) this day is part of this year (occurrent parthood) this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole a core relation that holds between a part and its whole Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of part_of BFO:0000050 external protein quality uberon part_of part_of part of part of part_of http://www.obofoundry.org/ro/#OBO_REL:part_of has part has part my body has part my brain (continuant parthood, two material entities) my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) this year has part this day (occurrent parthood) Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. a core relation that holds between a whole and its part a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part has_part BFO:0000051 chebi_ontology external protein quality uberon has_part false has_part We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'. has part has part has_part preceded by X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X) x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 is preceded by takes place after uberon preceded_by preceded_by preceded by preceded by preceded_by is preceded by SIO:000249 takes place after Allen:precedes precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. BFO:0000063 uberon precedes precedes precedes precedes b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t BFO:0000066 occurs_in occurs in occurs in [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t BFO:0000067 uberon contains_process contains_process contains process contains process x anterior to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail. x anterior_to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail: bearer cjm 2009-07-31T02:15:46Z BSPO:0000096 uberon anterior_to anterior_to anterior to anterior_to x anterior to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail. BSPO:cjm x anterior_to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail: bearer http://orcid.org/0000-0002-6601-2165 x distal to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal). x distal_to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal). BSPO:0000097 uberon distal_to distal_to distal to distal_to x distal to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal). BSPO:cjm x distal_to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal). http://orcid.org/0000-0002-6601-2165 x dorsal to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly). x dorsal_to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly). BSPO:0000098 uberon dorsal_to dorsal_to dorsal to dorsal_to x dorsal to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly). BSPO:cjm x dorsal_to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly). http://orcid.org/0000-0002-6601-2165 x posterior to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail. x posterior_to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail. BSPO:0000099 caudal_to uberon posterior_to posterior_to posterior to posterior_to x posterior to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail. BSPO:cjm x posterior_to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail. http://orcid.org/0000-0002-6601-2165 x proximal to y iff x is closer to the point of attachment with the body than y. x proximal_to y iff x is closer to the point of attachment with the body than y. BSPO:0000100 uberon proximal_to proximal_to proximal to proximal_to x proximal to y iff x is closer to the point of attachment with the body than y. BSPO:cjm x proximal_to y iff x is closer to the point of attachment with the body than y. http://orcid.org/0000-0002-6601-2165 x ventral to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly). x ventral_to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly). BSPO:0000102 uberon ventral_to ventral_to ventral to ventral_to x ventral to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly). BSPO:cjm x ventral_to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly). http://orcid.org/0000-0002-6601-2165 Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines. BSPO:0000107 uberon deep_to deep_to deep to deep_to Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines. BSPO:cjm Near the outer surface of the organism. Thus, skin is superficial to the muscle layer. BSPO:0000108 uberon superficial_to superficial_to superficial to superficial_to Near the outer surface of the organism. Thus, skin is superficial to the muscle layer. BSPO:cjm X in left side of Y <=> if Y is subdivided into two left and right portions, X is part of the left portion. X in_left_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the left portion. BSPO:0000120 uberon in_left_side_of in_left_side_of in left side of in_left_side_of https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern X in left side of Y <=> if Y is subdivided into two left and right portions, X is part of the left portion. BSPO:PATO_mtg_2009 X in_left_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the left portion. BSPO:PATO_mtg_2009 X in right side of Y <=> if Y is subdivided into two left and right portions, X is part of the right portion. X in_right_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the right portion. BSPO:0000121 uberon in_right_side_of in_right_side_of in right side of in_right_side_of https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern X in right side of Y <=> if Y is subdivided into two left and right portions, X is part of the right portion. BSPO:PATO_mtg_2009 X in_right_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the right portion. BSPO:PATO_mtg_2009 X posterior side of Y <=> if Y is subdivided into two anterior and posterior portions, X is part of the posterior portion. X posterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the posterior portion. BSPO:0000122 uberon in_posterior_side_of in_posterior_side_of in posterior side of in_posterior_side_of X posterior side of Y <=> if Y is subdivided into two anterior and posterior portions, X is part of the posterior portion. BSPO:PATO_mtg_2009 X posterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the posterior portion. BSPO:PATO_mtg_2009 X anterior side of Y <=> if Y is subdivided into two anterior and posterior portions, X is part of the anterior portion. X anterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the anterior portion. BSPO:0000123 uberon in_anterior_side_of in_anterior_side_of in anterior side of in_anterior_side_of X anterior side of Y <=> if Y is subdivided into two anterior and posterior portions, X is part of the anterior portion. BSPO:PATO_mtg_2009 X anterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the anterior portion. BSPO:PATO_mtg_2009 X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion. x in proximal side of y <=> if y is subdivided into two proximal and distal portions, y is part of the proximal portion. BSPO:0000124 uberon in_proximal_side_of in_proximal_side_of in proximal side of in_proximal_side_of X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion. BSPO:PATO_mtg_2009 x in proximal side of y <=> if y is subdivided into two proximal and distal portions, y is part of the proximal portion. BSPO:PATO_mtg_2009 X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion. x in distal side of y <=> if y is subdivided into two proximal and distal portions, y is part of the distal portion. BSPO:0000125 uberon in_distal_side_of in_distal_side_of in distal side of in_distal_side_of X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion. BSPO:PATO_mtg_2009 x in distal side of y <=> if y is subdivided into two proximal and distal portions, y is part of the distal portion. BSPO:PATO_mtg_2009 X in lateral side of Y <=> if X is in left side of Y or X is in right side of Y. X is often, but not always a paired structure X in_lateral_side_of Y <=> if X is in_left_side_of Y or X is in_right_side_of Y. X is often, but not always a paired structure BSPO:0000126 uberon in_lateral_side_of in_lateral_side_of in lateral side of in_lateral_side_of https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern X in lateral side of Y <=> if X is in left side of Y or X is in right side of Y. X is often, but not always a paired structure UBERON:cjm X in_lateral_side_of Y <=> if X is in_left_side_of Y or X is in_right_side_of Y. X is often, but not always a paired structure https://orcid.org/0000-0002-6601-2165 X proximalmost part of Y <=> X is in proximal side of Y and X is adjacent to the proximal boundary of Y X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y BSPO:0001106 uberon proximalmost_part_of proximalmost_part_of proximalmost part of proximalmost_part_of X proximalmost part of Y <=> X is in proximal side of Y and X is adjacent to the proximal boundary of Y https://orcid.org/0000-0002-6601-2165 X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y https://orcid.org/0000-0002-6601-2165 This relation holds when both the deep_to and ajdacent_to relationship similarly hold. x immediately deep to y iff x deep_to y and x is contiguous with y. BSPO:0001107 uberon immediately_deep_to immediately_deep_to immediately deep to immediately_deep_to This relation holds when both the deep_to and ajdacent_to relationship similarly hold. http://orcid.org/0000-0002-6601-2165 x immediately deep to y iff x deep_to y and x is contiguous with y. BSPO:curators X distalmost part of Y <=> X is in distal side of Y and X is adjacent to the distal boundary of Y X distalmost_part_of Y <=> X is part_of Y and X is adjacent_to the distal boundary of Y BSPO:0001108 uberon distalmost_part_of distalmost_part_of distalmost part of distalmost_part_of X distalmost part of Y <=> X is in distal side of Y and X is adjacent to the distal boundary of Y https://orcid.org/0000-0002-6601-2165 X distalmost_part_of Y <=> X is part_of Y and X is adjacent_to the distal boundary of Y https://orcid.org/0000-0002-6601-2165 X intersects median plane of iff X crosses the midine plane of Y. X intersects_median_plane of iff X crosses the midine plane of Y. BSPO:0005001 uberon intersects_midsagittal_plane_of intersects_midsagittal_plane_of intersects midsagittal plane of intersects_midsagittal_plane_of x immediately superficial to y iff x superficial to y and x is contiguous with y. BSPO:0015014 uberon immediately_superficial_to immediately_superficial_to immediately superficial to immediately_superficial_to x immediately superficial to y iff x superficial to y and x is contiguous with y. BSPO:curators X dorsal side of Y <=> if Y is subdivided into two dorsal and ventral portions, X is part of the dorsal portion. BSPO:0015101 uberon in_dorsal_side_of in_dorsal_side_of in dorsal side of in_dorsal_side_of X dorsal side of Y <=> if Y is subdivided into two dorsal and ventral portions, X is part of the dorsal portion. BSPO:cjm inheres in this fragility is a characteristic of this vase this red color is a characteristic of this apple a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. inheres_in Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of inheres in bearer of this apple is bearer of this red color this vase is bearer of this fragility Inverse of characteristic_of A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. bearer_of is bearer of RO:0000053 uberon bearer_of bearer_of bearer of bearer of has characteristic participates in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in RO:0000056 uberon participates_in participates_in participates in participates_in has participant this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant this catalysis function is a function of this enzyme a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. function_of is function of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. function of this red color is a quality of this apple a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence A quality inheres in its bearer at all times for which the quality exists. is quality of quality_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. quality of this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. is role of role_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. role of this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. has_function has function this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. has_quality RO:0000086 uberon has_quality has_quality has quality this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. has_role has role has role a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence has disposition inverse of has disposition This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. disposition of a relation between two independent continuants, the location and the target, in which the target is entirely within the location RO:0001015 uberon location_of location_of location of location_of contained in RO:0001019 uberon contains contains contains contains a relation between two independent continuants, the target and the location, in which the target is entirely within the location RO:0001025 uberon located_in located_in located in located_in This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity RO:0002000 uberon boundary_of boundary_of 2D boundary of a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity RO:0002002 uberon has_boundary has_boundary has 2D boundary has boundary RO:0002005 nerve supply uberon innervated_by innervated_by http://code.google.com/p/obo-relations/issues/detail?id=6 innervated_by nerve supply FMA:85999 David Osumi-Sutherland has synaptic terminal of X outer_layer_of Y iff: . X :continuant that bearer_of some PATO:laminar . X part_of Y . exists Z :surface . X has_boundary Z . Z boundary_of Y has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000 RO:0002007 uberon bounding_layer_of bounding_layer_of A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. bounding layer of bounding layer of A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. dos 2017-05-24T09:30:46Z has regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. dos 2017-05-24T09:31:01Z By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. has negative regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. dos 2017-05-24T09:31:17Z By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. has positive regulatory component activity dos 2017-05-24T09:44:33Z A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. has component activity w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. dos 2017-05-24T09:49:21Z has component process dos 2017-09-17T13:52:24Z Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. directly regulated by Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. GOC:dos Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. dos 2017-09-17T13:52:38Z directly negatively regulated by Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. GOC:dos Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. dos 2017-09-17T13:52:47Z directly positively regulated by Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. GOC:dos A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. dos 2017-09-22T14:14:36Z This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. has effector activity A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. GOC:dos before or simultaneous with Relation between occurrents, shares start and end boundaries. RO:0002082 coincides_with is_equal_to uberon simultaneous_with simultaneous_with simultaneous with Relation between occurrents, shares start and end boundaries. Allen:is_equal_to https://orcid.org/0000-0002-6601-2165 David Osumi-Sutherland X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) David Osumi-Sutherland starts_at_end_of A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]. RO:0002087 directly preceded by is directly preceded by is immediately preceded by starts_at_end_of uberon immediately_preceded_by immediately_preceded_by X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by immediately_preceded_by A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]. SIO:000251 is immediately preceded by SIO:000251 David Osumi-Sutherland ends_at_start_of meets X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes Relation between a neuron and an anatomical structure that its soma is part of. David Osumi-Sutherland <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) has soma location Relation between a neuron and some structure its axon forms (chemical) synapses in. Chris Mungall David Osumi-Sutherland David Osumi-Sutherland <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y))) axon synapses in Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. Chris Mungall David Osumi-Sutherland synapsed in http://purl.obolibrary.org/obo/BFO_0000051 some ( http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)) has postsynaptic terminal in Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. synapses in <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) has presynaptic terminal in A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input. David Osumi-Sutherland has synapse in <http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) has synaptic terminal in A overlaps B if they share some part in common. x overlaps y if and only if there exists some z such that x has part z and z part of y x overlaps y iff they have some part in common. BFO_0000051 some (BFO_0000050 some ?Y) http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) RO:0002131 uberon overlaps overlaps overlaps overlaps x overlaps y iff they have some part in common. BSPO:cjm true Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. T innervates some R Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. RO:0002134 uberon innervates innervates http://code.google.com/p/obo-relations/issues/detail?id=6 innervates X continuous_with Y if and only if X and Y share a fiat boundary. RO:0002150 uberon continuous_with continuous_with continuous with continuous_with S only_in_taxon T iff: S SubClassOf in_taxon only T x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z. RO:0002160 uberon only_in_taxon only_in_taxon only in taxon S only_in_taxon T iff: S SubClassOf in_taxon only T PMID:20973947 x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. RO:0002162 uberon in_taxon in_taxon in taxon Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship. a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b RO:0002170 uberon connected_to connected_to Connection does not imply overlaps. connected to connected to Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship. http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship. c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system. this is currently used for both structural relationships (such as between a valve and the chamber it connects) and abstract relationships (anatomical lines and the entities they connect) RO:0002176 uberon connects connects connects connects Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship. http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. RO:0002177 uberon attaches_to_part_of attaches_to_part_of attached to part of attaches_to_part_of true true Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy. relation between an artery and the structure is supplies with blood. RO:0002178 arterial supply of uberon supplies supplies source: FMA supplies arterial supply of FMA:86003 Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure. RO:0002179 drains blood from drains from uberon drains drains source: Wikipedia drains drains w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. RO:0002180 uberon has_component has_component has component has component has_component x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y Chris Mungall Chris Mungall David Osumi-Sutherland David Osumi-Sutherland Melissa Haendel Terry Meehan Terry Meehan RO:0002202 uberon develops_from develops_from This is the transitive form of the develops from relation develops from develops from develops_from inverse of develops from Chris Mungall David Osumi-Sutherland Terry Meehan RO:0002203 uberon develops_into develops_into develops into develops_into Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. RO:0002207 uberon directly_develops_from directly_develops_from directly develops from inverse of directly develops from directly develops into process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit Chris Mungall David Hill Tanya Berardini GO Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false RO:0002211 regulates regulates regulates Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. Chris Mungall negatively regulates (process to process) RO:0002212 negatively_regulates negatively regulates negatively regulates Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. Chris Mungall positively regulates (process to process) RO:0002213 positively_regulates positively regulates positively regulates mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. Chris Mungall has function realized in For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". RO:0002215 protein uberon capable_of false capable_of capable of capable of capable_of c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. Chris Mungall has function in RO:0002216 uberon capable_of_part_of capable_of_part_of capable of part of capable of part of true x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y RO:0002219 uberon surrounded_by surrounded_by surrounded by surrounded_by x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y https://orcid.org/0000-0002-6601-2165 x adjacent to y if and only if x and y share a boundary. x adjacent_to y iff: x and y share a boundary RO:0002220 uberon adjacent_to adjacent_to adjacent to adjacent to adjacent_to inverse of surrounded by inverse of surrounded_by RO:0002221 uberon surrounds surrounds surrounds surrounds inverse of surrounded_by https://orcid.org/0000-0002-6601-2165 Chris Mungall Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to Relation between occurrents, shares a start boundary with. inverse of starts with RO:0002223 uberon starts starts starts starts Relation between occurrents, shares a start boundary with. Allen:starts https://orcid.org/0000-0002-6601-2165 x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. RO:0002224 uberon starts_with starts_with starts with starts with x develops from part of y if and only if there exists some z such that x develops from z and z is part of y RO:0002225 uberon develops_from_part_of develops_from_part_of develops from part of x develops_in y if x is located in y whilst x is developing RO:0002226 uberon develops_in develops_in This relation take from EHDAA2 - precise semantics yet to be defined develops in Relation between occurrents, shares an end boundary with. inverse of ends with RO:0002229 finishes uberon ends ends ends ends Relation between occurrents, shares an end boundary with. Allen:starts ZFS:finishes https://orcid.org/0000-0002-6601-2165 x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. RO:0002230 uberon ends_with ends_with ends with ends with x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y has start location x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y has end location p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. Chris Mungall consumes has input p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p. has output Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y Chris Mungall RO:0002254 uberon has_developmental_contribution_from has_developmental_contribution_from has developmental contribution from has developmental contribution from inverse of has developmental contribution from Chris Mungall RO:0002255 uberon developmentally_contributes_to developmentally_contributes_to developmentally contributes to t1 developmentally_induced_by t2 if there is a process of organ induction (GO:0001759) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor tissue type T to T', where T' develops_from T. t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor anatomical structure type T to T', where T' develops_from T RO:0002256 uberon developmentally_induced_by developmentally_induced_by sources for developmentally_induced_by relationships in Uberon: Developmental Biology, Gilbert, 8th edition, figure 6.5(F) developmentally induced by developmentally_induced_by t1 developmentally_induced_by t2 if there is a process of organ induction (GO:0001759) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor tissue type T to T', where T' develops_from T. GO:0001759 Inverse of developmentally induced by developmentally induces Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false Chris Mungall In general you should not use this relation to make assertions - use one of the more specific relations below this one RO:0002258 uberon developmentally_preceded_by developmentally_preceded_by This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from developmentally preceded by A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. acts upstream of A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. affects acts upstream of or within x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else RO:0002285 uberon developmentally_replaces developmentally_replaces developmentally replaces developmentally_replaces Inverse of developmentally preceded by Chris Mungall developmentally succeeded by part of developmental precursor of cjm holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect cjm holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y causally upstream of, negative effect q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. Because part_of is transitive, inheres in is a sub-relation of characteristic of part of Chris Mungall inheres in part of characteristic of part of true RO:0002322 adapted_for uberon confers_advantage_in confers_advantage_in confers advantage in A mereological relationship or a topological relationship Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships mereotopologically related to A relationship that holds between entities participating in some developmental process (GO:0032502) Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development developmentally related to a particular instances of akt-2 enables some instance of protein kinase activity Chris Mungall catalyzes executes has is catalyzing is executing This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. enables A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. Chris Mungall This is a grouping relation that collects relations used for the purpose of connecting structure and function RO:0002328 uberon functionally_related_to functionally_related_to functionally related to this relation holds between c and p when c is part of some c', and c' is capable of p. Chris Mungall false RO:0002329 uberon part_of_structure_that_is_capable_of part_of_structure_that_is_capable_of part of structure that is capable of true c involved_in p if and only if c enables some process p', and p' is part of p Chris Mungall actively involved in enables part of involved in inverse of enables Chris Mungall enabled by inverse of regulates Chris Mungall regulated by (processual) regulated by inverse of negatively regulates Chris Mungall negatively regulated by inverse of positively regulates Chris Mungall positively regulated by is member of is a mereological relation between a item and a collection. RO:0002350 uberon member_of member_of member of member of has member is a mereological relation between a collection and an item. RO:0002351 uberon has_member has_member has member has member inverse of has input Chris Mungall RO:0002352 uberon input_of input_of input of inverse of has output RO:0002353 uberon output_of output_of output of output of a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a RO:0002371 uberon attaches_to attaches_to attached to attaches_to m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. RO:0002373 uberon has_muscle_insertion has_muscle_insertion The insertion is the point of attachment of a muscle that moves the most when the muscle shortens, or the most distal end of limb muscles has muscle insertion We need to import uberon muscle into RO to use as a stricter domain constraint m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. Wikipedia:Insertion_(anatomy) A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. in branching relationship with x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. RO:0002376 uberon drains into tributary_of tributary_of tributary of tributary_of drains into dbpowl:drainsTo x spatially_coextensive_with y if and inly if x and y have the same location spatially coextensive with x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y we need to check if FMA branch_of implies part_of. the relation we intend to use here should - for example, see vestibulocochlear nerve RO:0002380 uberon branching_part_of branching_part_of branching part of branching_part_of x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). Chris Mungall has developmental potential involving x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y Chris Mungall RO:0002385 uberon has_potential_to_developmentally_contribute_to has_potential_to_developmentally_contribute_to has potential to developmentally contribute to x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y has potential to developmentally induce x has the potential to develop into y iff x develops into y or if x is capable of developing into y x has the potential to develop into y iff x develops into y or if x is capable of developing into y Chris Mungall RO:0002387 uberon has_potential_to_develop_into has_potential_to_develop_into has potential to develop into has potential to develop into x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y Chris Mungall RO:0002388 uberon has_potential_to_directly_develop_into has_potential_to_directly_develop_into has potential to directly develop into inverse of upstream of Chris Mungall causally downstream of Chris Mungall immediately causally downstream of This relation groups causal relations between material entities and causal relations between processes This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain Chris Mungall causally upstream of p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. Chris Mungall immediately causally upstream of p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) affects causally upstream of or within inverse of causally upstream of or within Chris Mungall causally downstream of or within c involved in regulation of p if c is involved in some p' and p' regulates some p Chris Mungall involved in regulation of c involved in regulation of p if c is involved in some p' and p' positively regulates some p Chris Mungall involved in positive regulation of c involved in regulation of p if c is involved in some p' and p' negatively regulates some p Chris Mungall involved in negative regulation of c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union Chris Mungall involved in or reguates involved in or involved in regulation of c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. is active in true c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. GOC:cjm GOC:dos p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. RO:0002433 uberon contributes_to_morphology_of contributes_to_morphology_of contributes to morphology of A relationship that holds between two entities in which the processes executed by the two entities are causally connected. Considering relabeling as 'pairwise interacts with' This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. Chris Mungall Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. in pairwise interaction with interacts with http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ http://purl.obolibrary.org/obo/MI_0914 An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. Chris Mungall binds molecularly binds with molecularly interacts with http://purl.obolibrary.org/obo/MI_0915 Axiomatization to GO to be added later Chris Mungall An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. phosphorylates The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. Chris Mungall Vasundra Touré molecularly controls directly regulates activity of The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. Chris Mungall Vasundra Touré directly inhibits molecularly decreases activity of directly negatively regulates activity of The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. Chris Mungall Vasundra Touré directly activates molecularly increases activity of directly positively regulates activity of Chris Mungall This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. helper property (not for use in curation) x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. x composed_primarily_of y iff: more than half of the mass of x is made from parts of y RO:0002473 uberon RO:0002473 composed_primarily_of composed_primarily_of composed primarily of p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. has part that occurs in true Chris Mungall is kinase activity relation between physical entity and a process or stage Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s. x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y). RO:0002488 begins_to_exist_during uberon RO:0002488 existence_starts_during existence_starts_during existence starts during Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s. https://orcid.org/0000-0002-6601-2165 Relation between continuant and occurrent, such that c comes into existence at the start of p. x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y). RO:0002489 uberon existence_starts_with existence_starts_with existence starts with Relation between continuant and occurrent, such that c comes into existence at the start of p. https://orcid.org/0000-0002-6601-2165 x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y)) existence overlaps x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y) RO:0002491 uberon existence_starts_and_ends_during existence_starts_and_ends_during existence starts and ends during Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely. x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y). RO:0002492 ceases_to_exist_during uberon RO:0002492 existence_ends_during existence_ends_during existence ends during Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely. https://orcid.org/0000-0002-6601-2165 Relation between continuant and occurrent, such that c ceases to exist at the end of p. x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y). RO:0002493 uberon existence_ends_with existence_ends_with existence ends with Relation between continuant and occurrent, such that c ceases to exist at the end of p. https://orcid.org/0000-0002-6601-2165 x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships RO:0002494 transforms from uberon transformation_of transformation_of transformation of transforms from SIO:000657 x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t RO:0002495 direct_transformation_of immediately transforms from uberon immediate_transformation_of immediate_transformation_of immediate transformation of direct_transformation_of https://orcid.org/0000-0002-6601-2165 immediately transforms from SIO:000658 x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). RO:0002496 uberon existence_starts_during_or_after existence_starts_during_or_after existence starts during or after x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends. RO:0002497 uberon existence_ends_during_or_before existence_ends_during_or_before existence ends during or before A relationship between a material entity and a process where the material entity has some causal role that influences the process causal agent in process p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between processes Chris Mungall depends on The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between entities A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision. RO:0002551 uberon has sekeletal support has supporting framework has_skeleton has_skeleton has skeleton This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional. A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision. http://orcid.org/0000-0002-6601-2165 Chris Mungall causally influenced by (entity-centric) causally influenced by Chris Mungall interaction relation helper property http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ Chris Mungall molecular interaction relation helper property The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). Chris Mungall Vasundra Touré causally influences (entity-centric) causally influences A relation that holds between elements of a musculoskeletal system or its analogs. biomechanically related to inverse of branching part of RO:0002569 uberon has_branching_part has_branching_part has branching part x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. RO:0002571 uberon lumen_of lumen_of lumen of s is luminal space of x iff s is lumen_of x and s is an immaterial entity RO:0002572 uberon luminal_space_of luminal_space_of luminal space of inverse of has skeleton RO:0002576 uberon skeleton_of skeleton_of skeleton of Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. Chris Mungall directly regulates (processual) directly regulates gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p Chris Mungall has part structure that is capable of A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. Chris Mungall causal relation between material entity and a process pyrethroid -> growth Holds between c and p if and only if c is capable of some activity a, and a regulates p. capable of regulating Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. capable of negatively regulating renin -> arteriolar smooth muscle contraction Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. capable of positively regulating Inverse of 'causal agent in process' process has causal agent Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2. directly positively regulates (process to process) directly positively regulates Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2. directly negatively regulates (process to process) directly negatively regulates a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. RO:0003000 uberon produces produces produces produces a produced_by b iff some process that occurs_in b has_output a. RO:0003001 uberon produced_by produced_by produced by produced by produced_by Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. cjm 2018-01-25T23:20:13Z enables subfunction cjm 2018-01-26T23:49:30Z acts upstream of or within, positive effect cjm 2018-01-26T23:49:51Z acts upstream of or within, negative effect c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive cjm 2018-01-26T23:53:14Z acts upstream of, positive effect c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative cjm 2018-01-26T23:53:22Z acts upstream of, negative effect cjm 2018-03-13T23:55:05Z causally upstream of or within, negative effect cjm 2018-03-13T23:55:19Z causally upstream of or within, positive effect The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. Vasundra Touré regulates activity of quality correlates_with correlates_with q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. quality decreased_in_magnitude_relative_to This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'. decreased_in_magnitude_relative_to q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. PATOC:CJM q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. quality different_in_magnitude_relative_to different_in_magnitude_relative_to q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. PATOC:CJM q1 directly_associated_with q2 iff q1 is dependent on q2, and the magnitude of q1 increases if the magnitude of q2 is increased, or the magnitude of q1 decreases if the magnitude of q2 is decreased. The relationship is not necessarily linear. cjm 2009-08-26T02:50:08Z quality directly_associated_with Example: 'Lewy bodies increased number related to dystrophic neurite increased number' (from annotation of PMID:8740227 in http://ccdb.ucsd.edu/1.0/NDPO.owl#ndpo_404). Here the increase in the number of lewy bodies is directly_associated_with the increase in the number of dystrophic neurites. Association is weaker than correlation or proportionality. These relations may be later added to PATO. directly_associated_with q1 directly_associated_with q2 iff q1 is dependent on q2, and the magnitude of q1 increases if the magnitude of q2 is increased, or the magnitude of q1 decreases if the magnitude of q2 is decreased. The relationship is not necessarily linear. PATOC:cjm Wikipedia:Association_(statistics) s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2. quality has_cross_section Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round. has_cross_section s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2. PATOC:CJM quality has_dividend_entity has_dividend_entity quality has_dividend_quality has_dividend_quality quality has_divisor_entity has_divisor_entity quality has_divisor_quality has_divisor_quality quality has_ratio_quality has_ratio_quality quality has_relative_magnitude has_relative_magnitude q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. quality increased_in_magnitude_relative_to This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'. increased_in_magnitude_relative_to q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. PATOC:CJM q1 inversely_associated_with q2 iff q1 is dependent on q2, and the magnitude of q1 decreases if the magnitude of q2 is increased, or the magnitude of q1 increases if the magnitude of q2 is decreased. The relationship is not necessarily linear. cjm 2009-08-26T02:50:24Z quality inversely_associated_with Association is weaker than correlation or proportionality. These relations may be later added to PATO. inversely_associated_with q1 inversely_associated_with q2 iff q1 is dependent on q2, and the magnitude of q1 decreases if the magnitude of q2 is increased, or the magnitude of q1 increases if the magnitude of q2 is decreased. The relationship is not necessarily linear. PATOC:cjm Wikipedia:Association_(statistics) pato.ontology is_magnitude_of is_magnitude_of pato.ontology is_measurement_of is_measurement_of pato.ontology is_unit_of is_unit_of quality realized_by realized_by q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e. quality reciprocal_of There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality. reciprocal_of q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e. PATOC:CJM q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. quality similar_in_magnitude_relative_to similar_in_magnitude_relative_to q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. PATOC:CJM monadic_form_of quality singly_occurring_form_of PATO divides qualities between normal (monadic, singly-occurring) qualities and relational qualities. Relational qualities stand in the 'towards' relation with respect to some additional entity. For example, The sensitivity of an eye towards red light. In some cases we want to represent a quality such as 'protruding' in both monadic and relational branches. We use this relation to link them. singly_occurring_form_of quality towards Relation binding a relational quality or disposition to the relevant type of entity. towards x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y. uberon anteriorly_connected_to anteriorly connected to x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y. http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern carries uberon channel_for channel for uberon channels_from channels_from uberon channels_into channels_into x is a conduit for y iff y passes through the lumen of x. uberon conduit_for conduit for x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y. uberon distally_connected_to distally connected to x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y. http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern uberon extends_fibers_into extends_fibers_into Relationship between a fluid and a material entity, where the fluid is the output of a realization of a filtration role that inheres in the material entity. uberon filtered_through Relationship between a fluid and a filtration barrier, where the portion of fluid arises as a transformation of another portion of fluid on the other side of the barrier, with larger particles removed filtered through a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s add to RO uberon indirectly_supplies indirectly_supplies x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y. uberon posteriorly_connected_to posteriorly connected to x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y. http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern uberon protects protects x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y. uberon proximally_connected_to proximally connected to x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y. http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern c site_of p if c is the bearer of a disposition that is realized by a process that has p as part uberon capable_of_has_part site_of site_of uberon subdivision_of placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B subdivision of Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. uberon synapsed_by synapsed by . uberon transitively_anteriorly_connected_to transitively anteriorly connected to . http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern uberon transitively_connected_to transitively_connected to . uberon transitively_distally_connected_to transitively distally connected to . http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern . uberon transitively_proximally_connected_to transitively proximally connected to . http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern entity An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. continuant An entity that has temporal parts and that happens, unfolds or develops through time. occurrent A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. independent continuant An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. process disposition A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. realizable entity quality A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. specifically dependent continuant A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. role object object function An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. material entity material entity anatomical entity connected anatomical structure material anatomical entity biological entity electron hyaluronic acid glycan glycosaminoglycan aminoglycan molecular entity chemical entity group nitrogen atom nonmetal atom organic sulfate oxygen atom oxygen molecular entity sulfuric ester sulfates sulfur atom sulfur molecular entity carbon atom fundamental particle oxoacid derivative atom atomic nucleus nucleon heteroorganic entity pnictogen pnictogen molecular entity chalcogen chalcogen molecular entity carbon group element atom main group element atom sulfur oxoacid derivative p-block element atom main group molecular entity carbon group molecular entity p-block molecular entity biomacromolecule macromolecule organonitrogen compound ester sulfated glycosaminoglycan carbohydrate sulfate lepton baryon fermion subatomic particle composite particle hadron nuclear particle polyatomic entity organochalcogen compound organooxygen compound mucopolysaccharide heteroatomic molecular entity sulfuric acid derivative mineral phosphate mineral organic amino compound organic molecular entity nitrogen molecular entity apatite hydroxylapatite chemical substance carbohydrate derivative polysaccharide derivative exopolysaccharide carbohydrates and carbohydrate derivatives A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. CALOHA:TS-2035 FMA:68646 GO:0005623 KUPO:0000002 VHOG:0001533 WBbt:0004017 XAO:0003012 cell CL:0000000 The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). cell cell A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). CARO:0000013 cell in vivo cell CL:0000003 To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12). native cell Any fibroblast that is deriived from the neural crest. cell CL:0000005 fibroblast neural crest derived neuronal receptor cell (sensu Animalia) cell CL:0000006 neuronal receptor cell A cell found in the embryo before the formation of all the gem layers is complete. cell CL:0000007 early embryonic cell (metazoa) Cell that is part of the migratory cranial neural crest population. Migratory cranial neural crest cells develop from premigratory cranial neural crest cells and have undergone epithelial to mesenchymal transition and delamination. cell CL:0000008 migratory cranial neural crest cell Cell that is part of the migratory trunk neural crest population. Migratory trunk neural crest cells develop from premigratory trunk neural crest cells and have undergone epithelial to mesenchymal transition and delamination. cell CL:0000011 migratory trunk neural crest cell germline stem cell cell CL:0000014 germ line stem cell A smooth muscle cell derived from the neural crest. cell CL:0000027 smooth muscle cell neural crest derived cell CL:0000029 neuron neural crest derived FBbt:00005145 cell CL:0000030 glioblast A cell that will develop into a neuron often after a migration phase. CL:0000337 BTO:0000930 FMA:70563 neuroblast cell CL:0000031 neuroblast (sensu Vertebrata) A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells. CALOHA:TS-2086 FMA:63368 cell CL:0000034 stem cell A stem cell that self-renews as well as give rise to a single mature cell type. FMA:70569 unipotent stem cell unipotential stem cell cell CL:0000035 single fate stem cell cell CL:0000036 epithelial fate stem cell A stem cell from which all cells of the lymphoid and myeloid lineages develop, including blood cells and cells of the immune system. Hematopoietic stem cells lack cell markers of effector cells (lin-negative). Lin-negative is defined by lacking one or more of the following cell surface markers: CD2, CD3 epsilon, CD4, CD5 ,CD8 alpha chain, CD11b, CD14, CD19, CD20, CD56, ly6G, ter119. BTO:0000725 CALOHA:TS-0448 FMA:70337 FMA:86475 VHOG:0001485 HSC blood forming stem cell hemopoietic stem cell cell colony forming unit hematopoietic CL:0000037 Markers differ between species, and two sets of markers have been described for mice. HSCs are reportedly CD34-positive, CD45-positive, CD48-negative, CD150-positive, CD133-positive, and CD244-negative. hematopoietic stem cell A progenitor cell committed to the erythroid lineage. BTO:0004911 cell BFU-E CFU-E blast forming unit erythroid burst forming unit erythroid colony forming unit erythroid erythroid stem cell CL:0000038 erythroid progenitor cell A cell that is within the developmental lineage of gametes and is able to pass along its genetic material to offspring. cell CL:0000039 Originally this term had some plant germ line cell children. germ line cell Neural stem cell is characterized as an undifferentiated cell that originates from the neuroectoderm and has the capacity both to perpetually self-renew without differentiating and to generate multiple types of lineage-restricted progenitors. BTO:0002881 CALOHA:TS-2360 FMA:86684 NSC neural stem cell cell CL:0000047 neuronal stem cell A stem cell that can give rise to multiple lineages of cells. FMA:84789 multi-fate stem cell multifate stem cell multipotent cell multipotent stem cell cell CL:0000048 multi fate stem cell A progenitor cell committed to myeloid lineage, including the megakaryocyte and erythroid lineages. BTO:0004730 CMP common myeloid precursor cell CFU-GEMM CFU-S colony forming unit granulocyte, erythrocyte, macrophage, and megakaryocyte multipotential myeloid stem cell myeloid stem cell pluripotent stem cell (bone marrow) CL:0000049 This cell type is intended to be compatible with any vertebrate common myeloid progenitor. For mammalian CMP known to be CD34-positive, please use the term 'common myeloid progenitor, CD34-positive' (CL_0001059). common myeloid progenitor A progenitor cell committed to the megakaryocyte and erythroid lineages. CFU-EM CFU-MegE MEP Meg/E progenitor colony forming unit erythroid megakaryocyte megakaryocyte/erythrocyte progenitor megakaryocyte/erythroid progenitor cell cell CL:0000050 MEPs are reportedly CD19-negative, CD34-negative, CD45RA-negative, CD110-positive, CD117-positive, and SCA1-negative and reportedly express the transcription factors GATA-1 and NF-E2. megakaryocyte-erythroid progenitor cell A stem cell from which all cells of the body can form. FMA:84790 totipotential stem cell cell CL:0000052 totipotent stem cell A precursor cell with a limited number of potential fates. BTO:0000125 FMA:84782 blast cell cell CL:0000055 define using PATO mulit-potent or oligopotent? non-terminally differentiated cell A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair. BTO:0000222 CALOHA:TS-0650 FBbt:00005083 FMA:70335 VHOG:0001529 cell CL:0000056 myoblast A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped. BTO:0000452 CALOHA:TS-0362 FMA:63877 VHOG:0001482 cell CL:0000057 These cells may be vimentin-positive, fibronectin-positive, fsp1-positive, MMP-1-positive, collagen I-positive, collagen III-positive, and alpha-SMA-negative. fibroblast Skeletogenic cell that is typically non-terminally differentiated, secretes an avascular, GAG rich matrix; is not buried in cartilage tissue matrix, retains the ability to divide, located adjacent to cartilage tissue (including within the perichondrium), and develops from prechondroblast (and thus prechondrogenic) cell. BTO:0003607 FMA:66783 chrondoplast cell CL:0000058 chondroblast A cell that has a filiform extrusion of the cell surface. VHOG:0001532 XAO:0000031 cell CL:0000064 ciliated cell A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina. BTO:0000414 CALOHA:TS-2026 CARO:0000077 FBbt:00000124 FMA:66768 WBbt:0003672 epitheliocyte cell CL:0000066 epithelial cell An epithelial cell that has a cilia. FMA:70605 cell CL:0000067 ciliated epithelial cell An epithelial cell that is part of a duct. cell CL:0000068 duct epithelial cell An endothelial cell that lines the vasculature. cuboidal endothelial cell of vascular tree cell CL:0000071 blood vessel endothelial cell A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube. cell CL:0000075 columnar/cuboidal epithelial cell CALOHA:TS-1249 cell CL:0000076 squamous epithelial cell A flattened epithelial cell of mesenchymal origin that lines the serous cavity. FMA:66773 mesotheliocyte cell CL:0000077 mesothelial cell cell CL:0000079 stratified epithelial cell A cell which moves among different tissues of the body, via blood, lymph, or other medium. cell CL:0000080 circulating cell A cell found predominately in the blood. FMA:62844 cell CL:0000081 blood cell An epithelial cell of the lung. BTO:0004299 lung epithelial cell cell CL:0000082 epithelial cell of lung cell CL:0000095 neuron associated cell A specialized epithelial cell involved in sensory perception. Restricted to special sense organs of the olfactory, gustatory, and vestibulocochlear receptor systems; contain sensory cells surrounded by supportive, non-receptive cells. neuroepithelial cell BTO:0004301 cell CL:0000098 The term "neuroepithelial cell" is used to describe both this cell type and neurecto-epithelial cell (CL:0000710). sensory epithelial cell Most generally any neuron which is not motor or sensory. Interneurons may also refer to neurons whose axons remain within a particular brain region as contrasted with projection neurons which have axons projecting to other brain regions. BTO:0003811 FBbt:00005125 FMA:67313 WBbt:0005113 cell CL:0000099 interneuron An efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes or inhibits movement. BTO:0000312 FMA:83617 WBbt:0005409 motoneuron cell CL:0000100 motor neuron Any neuron having a sensory function; an afferent neuron conveying sensory impulses. BTO:0001037 FBbt:00005124 FMA:84649 WBbt:0005759 cell CL:0000101 sensory neuron FMA:72552 cell of surface ectoderm surface ectoderm cell cell CL:0000114 surface ectodermal cell An endothelial cell comprises the outermost layer or lining of anatomical structures and can be squamous or cuboidal. In mammals, endothelial cell has vimentin filaments and is derived from the mesoderm. BTO:0001176 CALOHA:TS-0278 FMA:66772 endotheliocyte cell CL:0000115 From FMA: 9.07.2001: Endothelial cell has always been classified as a kind of epithelial cell, specifically a squamous cell but that is not true. First, endothelial cell can either be squamous or cuboidal (e.g. high-endothelial cell) and secondly, it has different embryological derivation (mesodermal) than a true epithelial cell (ectodermal and endodermal). The basis for present classification is the fact that it comprises the outermost layer or lining of anatomical structures (location-based) but a better structural basis for the differentia is the cytoskeleton of the cell. Endothelial cell has vimentin filaments while an epithelial cell has keratin filaments. [Onard]. endothelial cell cell CL:0000117 CNS neuron (sensu Vertebrata) cell CL:0000123 neuron associated cell (sensu Vertebrata) A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons. BTO:0002606 CALOHA:TS-0415 FMA:54536 neuroglial cell cell neuroglia CL:0000125 glial cell Ectoderm destined to be nervous tissue. neurectoderm cell cell CL:0000133 neurectodermal cell A connective tissue cell that normally gives rise to other cells that are organized as three-dimensional masses. In humans, this cell type is CD73-positive, CD90-positive, CD105-positive, CD45-negative, CD34-negative, and MHCII-negative. They may further differentiate into osteoblasts, adipocytes, myocytes, neurons, or chondroblasts in vitro. Originally described as residing in the bone marrow, this cell type is now known to reside in many, if not all, adult organs. CL:0002452 BTO:0002625 BTO:0003298 FMA:70546 BMSC bone marrow stromal cells colony-forming unit-fibroblast marrow stromal cells cell CFU-F MSC mesenchymal precursor cell mesenchymal progenitor cells mesenchymal stem cell mesenchymal stromal cell mesenchymal stromal cells stem cells, mesenchymal CL:0000134 Many but not all mesenchymal cells derive from the mesoderm. MSCs are reportedly CD3-negative, CD4-negative, CD5-negative, CD8-negative, CD11a-negative, CD11b-negative, CD14-negative, CD19-negative, CD29-positive, CD31-negative, CD34-negative, CD38-negative, CD40-negative, CD44-positive, CD45-negative, CD49-positive, CD54-positive, CD66b-negative, CD79a-negative, CD80-negative, CD102-positive, CD106-positive, CD117-positive, CD121a-positive, CD121b-positive, CD123-positive, CD124-positive, CD133-negative, CD146-positive, CD166-positive, CD271-positive, B220-negative, Gr1-negative, MHCI-positive, MHCII-negative, SSEA4-negative, sca1-positive, Ter119-negative, and glycophorin A-negative. Cultured MSCs are capable of producing stem cell factor, IL7, IL8, IL11, TGF-beta, cofilin, galectin-1, laminin-receptor 1, cyclophilin A, and MMP-2. mesenchymal stem cell https://github.com/obophenotype/cell-ontology/issues/474 A fat-storing cell found mostly in the abdominal cavity and subcutaneous tissue of mammals. Fat is usually stored in the form of triglycerides. CL:0000450 BTO:0000443 CALOHA:TS-0012 FMA:63880 adipocyte adipose cell cell CL:0000136 fat cell Skeletogenic cell that is terminally differentiated, secretes an avascular, GAG-rich matrix, is embedded in cartilage tissue matrix, retains the ability to divide, and develops from a chondroblast cell. BTO:0000249 CALOHA:TS-0138 FMA:66782 cartilage cell cell CL:0000138 chondrocyte A pigment cell is a cell that contains pigment granules. VHOG:0001678 chromatocyte chromatophore cell CL:0000147 pigment cell A pigment cell derived from the neural crest. Contains melanin-filled pigment granules, which gives a brown to black appearance. CL:0000572 BTO:0000847 CALOHA:TS-0613 FMA:70545 VHOG:0001679 melanophore cell CL:0000148 melanocyte pigment cell cell CL:0000149 visual pigment cell A specialized epithelial cell that is capable of synthesizing and secreting certain biomolecules. CALOHA:TS-2085 FMA:86494 cell CL:0000150 glandular epithelial cell A cell that specializes in controlled release of one or more substances. BTO:0003659 FMA:86916 cell CL:0000151 secretory cell A cell of an exocrine gland; i.e. a gland that discharges its secretion via a duct. FMA:16014 cell CL:0000152 exocrine cell A cell that secretes glycosaminoglycans. GAG secreting cell hyaluronic acid secreting cell cell CL:0000153 glycosaminoglycan secreting cell cell CL:0000159 seromucus secreting cell cell CL:0000161 acid secreting cell A cell of an endocrine gland, ductless glands that secrete substances which are released directly into the circulation and which influence metabolism and other body functions. FMA:83809 endocrinocyte cell CL:0000163 endocrine cell An endocrine cell that is located in the epithelium of the gastrointestinal tract or in the pancreas. BTO:0003865 FMA:62930 cell CL:0000164 enteroendocrine cell An endocrine cell that has the specialized function to produce and secrete hormones in response to neuronal signals. BTO:0002691 FMA:83810 neurosecretory cell cell CL:0000165 neuroendocrine cell cell CL:0000167 peptide hormone secreting cell A cell that secretes glucagon. FMA:84045 glucagon-secreting cell cell CL:0000170 glucagon secreting cell cell CL:0000172 somatostatin secreting cell cell CL:0000174 steroid hormone secreting cell A cell whose primary function is to shorten. cell CL:0000183 contractile cell A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns. BTO:0000888 BTO:0000902 CALOHA:TS-2032 FBbt:00005074 FMA:67328 WBbt:0003675 muscle fiber myocyte cell CL:0000187 muscle cell A somatic cell located in skeletal muscle. BTO:0004392 CALOHA:TS-2158 FMA:9727 skeletal muscle cell cell CL:0000188 cell of skeletal muscle A non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels. They develop from specialized myoblasts (smooth muscle myoblast). CL:0000191 BTO:0004576 CALOHA:TS-2159 FMA:14072 SMCs myocytes, smooth muscle smooth muscle fiber non-striated muscle cell cell CL:0000192 smooth muscle cell A cell that is capable of detection of a stimulus involved in sensory perception. receptor cell cell CL:0000197 sensory receptor cell A cell specialized to detect chemical substances and relay that information centrally in the nervous system. Chemoreceptors may monitor external stimuli, as in taste and olfaction, or internal stimuli, such as the concentrations of oxygen and carbon dioxide in the blood. cell CL:0000206 chemoreceptor cell A cell type found in the spherical or ovoid clusters of receptor cells found mainly in the epithelium of the tongue and constituting the end organs of the sense of taste. FMA:67910 taste bud cell cell CL:0000209 taste receptor cell A cell specialized to detect and transduce light. BTO:0001060 CALOHA:TS-0868 FBbt:00004211 FMA:86740 cell CL:0000210 photoreceptor cell A cell whose function is determined by the generation or the reception of an electric signal. cell CL:0000211 electrically active cell A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism. boundary cell cell CL:0000213 lining cell A meso-epithelial cell that lies between the cartilaginous fibers in the synovial membrane of a joint and produces hyaluronic acid. BTO:0003652 CALOHA:TS-0995 FMA:66786 synoviocyte hyaluronic acid secreting cell cell CL:0000214 synovial cell A cell whose primary function is to prevent the transport of stuff across compartments. cell CL:0000215 barrier cell A cell that moves by its own activities. cell CL:0000219 motile cell A cell of the outer of the three germ layers of the embryo. FMA:72549 ectoderm cell cell CL:0000221 ectodermal cell A cell of the middle germ layer of the embryo. FMA:72554 mesoblast mesoderm cell cell CL:0000222 mesodermal cell A cell of the inner of the three germ layers of the embryo. FMA:72555 endoderm cell cell CL:0000223 endodermal cell A cell with more than one nucleus. AEO:0000203 WBbt:0008074 syncitium syncytial cell syncytium cell CL:0000228 multinucleate cell A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen. BTO:0000424 CALOHA:TS-0290 FMA:81100 RBC red blood cell cell CL:0000232 erythrocyte cell CL:0000237 keratinizing barrier epithelial cell cell CL:0000240 stratified squamous epithelial cell A modified epidermal cell located in the stratum basale. They are found mostly in areas where sensory perception is acute. Merkel cells are closely associated with an expanded terminal bulb of an afferent myelinated nerve fiber. FMA:70548 Merkel's cell cell CL:0000242 Merkel cell cell CL:0000255 eukaryotic cell cell CL:0000287 eye photoreceptor cell A cell whose primary function is to provide structural support, to provide strength and physical integrity to the organism. cell CL:0000293 structural cell FBbt:00004193 lens cell cell CL:0000306 crystallin accumulating cell cell CL:0000311 keratin accumulating cell An epidermal cell which synthesizes keratin and undergoes a characteristic change as it moves upward from the basal layers of the epidermis to the cornified (horny) layer of the skin. Successive stages of differentiation of the keratinocytes forming the epidermal layers are basal cell, spinous or prickle cell, and the granular cell. CL:0002185 BTO:0000667 CALOHA:TS-0500 FMA:62879 keratinized cell of epidermis malpighian cell cell CL:0000312 Keratinocytes are reportedly CDw210a-negative, CDw210b-positive, CD281-positive, CD282-positive, CD285-positive, IL22Ra1-positive, Human keratinocytes are reportedly capable of secreting BD-2, BD-3, hCAP-18, CXCL1, CXCL5, CXCL8, elafin, MMP-3, NGAL, PDGF-A, S100A7, S100A8, and S100A9. Transcription factors: STAT3-positive. keratinocyte Columnar glandular cell with irregular nucleus, copious granular endoplasmic reticulum and supranuclear granules. Secretes a watery fluid containing proteins known as serous fluid. BTO:0003687 FMA:62511 serous cell cell CL:0000313 serous secreting cell A cell that is specialised to accumulate a particular substance(s). cell CL:0000325 stuff accumulating cell cell CL:0000327 extracellular matrix secreting cell cell CL:0000329 oxygen accumulating cell A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body. FMA:86667 cell CL:0000333 migratory neural crest cell A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors. cell CL:0000335 mesenchyme condensation cell An early neural cell developing from the early ependymal cell of the neural tube. FMA:70564 spongioblast cell CL:0000339 glioblast (sensu Vertebrata) A cell of the sclera of the eye. cell CL:0000347 scleral cell A cell of the choroid of the eye. cell CL:0000348 choroidal cell of the eye cell CL:0000349 extraembryonic cell A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation. cell CL:0000352 epiblast cell A multifate stem cell found in skeletal muscle than can differentiate into many different cell types, including muscle. Distinct cell type from satellite cell. FMA:86767 cell CL:0000355 Multi-potency demonstrated ex vivo. At the time of writing, it is unclear whether the endogenous population differentiates into multiple cell types in vivo. multi-potent skeletal muscle stem cell cell CL:0000357 stratified epithelial stem cell A smooth muscle cell assocatiated with the vasculature. VSMC vascular smooth muscle cell cell CL:0000359 vascular associated smooth muscle cell An epithelial cell of the integument (the outer layer of an organism). CL:1000396 BTO:0001470 CALOHA:TS-0283 FMA:62411 cell of epidermis epithelial cell of skin cell CL:0000362 epidermal cell Diploid cell produced by the fusion of sperm cell nucleus and egg cell. zygote BTO:0000854 EHDAA2:0004546 FMA:72395 cell CL:0000365 animal zygote FBbt:00005130 cell CL:0000381 neurosecretory neuron A cell whose function is determined by its response to an electric signal. cell CL:0000393 electrically responsive cell cell CL:0000402 CNS interneuron A cell that initiates an electrical signal and passes that signal to another cell. cell CL:0000404 electrically signaling cell cell CL:0000447 carbohydrate secreting cell cell CL:0000457 biogenic amine secreting cell A cell type that secretes 5-Hydroxytryptamine (serotonin). 5-HT secreting cell 5-Hydroxytryptamine secreting cell cell CL:0000458 serotonin secreting cell A cell capable of producting norepiniphrine. Norepiniphrine is a catecholamine with multiple roles including as a hormone and a neurotransmitter. In addition, epiniphrine is synthesized from norepiniphrine by the actions of the phenylethanolamine N-methyltransferase enzyme. noradrenaline secreting cell norepinephrin secreting cell norepinephrine secreting cell cell CL:0000459 noradrenergic cell A photoreceptor cell that detects visible light. cell CL:0000488 visible light photoreceptor cell A connective tissue cell of an organ found in the loose connective tissue. These are most often associated with the uterine mucosa and the ovary as well as the hematopoietic system and elsewhere. BTO:0002064 FMA:83624 cell CL:0000499 stromal cell A precursor cell destined to differentiate into cardiac muscle cell. CL:0000714 FMA:84797 cardiac muscle progenitor cell cardiomyocyte progenitor cell cell CL:0000513 cardiac muscle myoblast A precursor cell destined to differentiate into smooth muscle myocytes. FMA:84798 myoblast, smooth muscle cell satellite cell CL:0000514 smooth muscle myoblast A myoblast that differentiates into skeletal muscle fibers. FMA:84799 skeletal myoblast cell CL:0000515 skeletal muscle myoblast A neuron which conveys sensory information centrally from the periphery. FMA:87653 input neuron cell CL:0000526 afferent neuron A neuron which sends impulses peripherally to activate muscles or secretory cells. output neuron cell CL:0000527 efferent neuron cell CL:0000530 primary neuron cell CL:0000531 primary sensory neuron The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. BTO:0000938 CALOHA:TS-0683 FBbt:00005106 FMA:54527 VHOG:0001483 WBbt:0003679 nerve cell cell CL:0000540 These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma. neuron neuron A cell that originates from the neural crest and differentiates into a pigment cell. BTO:0003217 FMA:83377 cell CL:0000541 Derived from UBERON:0002342 neural crest. melanoblast An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. This cell is CD71-positive, has both a nucleus and a nucleolus, and lacks hematopoeitic lineage markers. FMA:83518 rubriblast cell pronormoblast CL:0000547 proerythroblast cell CL:0000548 animal cell A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. This cell is CD71-positive and lacks hematopoeitic lineage markers. FMA:83505 basophilic normoblast early erythroblast early normoblast prorubricyte cell CL:0000549 basophilic erythroblast A nucleated, immature erythrocyte in which the nucleus occupies a relatively smaller part of the cell than in its precursor, the basophilic erythroblast. The cytoplasm is beginning to acquire hemoglobin and thus is no longer a purely basophilic, but takes on acidophilic aspects, which becomes progressively more marked as the cell matures. The chromatin of the nucleus is arranged in coarse, deeply staining clumps. This cell is CD71-positive and lacks hematopoeitic lineage markers. FMA:83506 intermediate erythroblast intermediate normoblast polychromatic erythroblast polychromatic normoblast polychromatophilic normoblast rubricyte cell CL:0000550 polychromatophilic erythroblast The final stage of the nucleated, immature erythrocyte, before nuclear loss. Typically the cytoplasm is described as acidophilic, but it still shows a faint polychromatic tint. The nucleus is small and initially may still have coarse, clumped chromatin, as in its precursor, the polychromatophilic erythroblast, but ultimately it becomes pyknotic, and appears as a deeply staining, blue-black, homogeneous structureless mass. The nucleus is often eccentric and sometimes lobulated. FMA:84646 acidophilic erythroblast eosinophilic erythroblast late erythoblast orthochromatic normoblast pyknotic eto enrythroblast cell CL:0000552 orthochromatic erythroblast An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds. BTO:0001173 CALOHA:TS-0864 cell CL:0000558 reticulocyte A mesenchymal stem cell capable of developing into blood vessel endothelium. angioblast chondroplast cell CL:0000566 These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive. angioblastic mesenchymal cell One of the two photoreceptor cell types in the vertebrate retina. In cones the photopigment is in invaginations of the cell membrane of the outer segment. Cones are less sensitive to light than rods, but they provide vision with higher spatial and temporal acuity, and the combination of signals from cones with different pigments allows color vision. BTO:0001036 CALOHA:TS-0866 FMA:67748 cell CL:0000573 retinal cone cell An epithelial cell of the cornea. CL:1000431 BTO:0004298 CALOHA:TS-0173 FMA:70551 epithelial cell of cornea cell CL:0000575 corneal epithelial cell The reproductive cell in multicellular organisms. BTO:0000535 VHOG:0001534 WBbt:0006796 cell CL:0000586 germ cell A steroid hormone secreting cell that secretes androgen. cell CL:0000593 androgen secreting cell One of the two photoreceptor cell types of the vertebrate retina. In rods the photopigment is in stacks of membranous disks separate from the outer cell membrane. Rods are more sensitive to light than cones, but rod mediated vision has less spatial and temporal resolution than cone vision. BTO:0001024 CALOHA:TS-0870 FMA:67747 cell CL:0000604 retinal rod cell A cell whose primary function is to support other cell types. BTO:0002315 cell CL:0000630 supportive cell Undifferentiated; mitotic stem cell for other epithelial cell types; rounded or elliptical with little cytoplasm and few organelles; contain cytokeratin intermediate filament. BTO:0000939 FMA:62516 cell CL:0000646 basal cell An extracellular matrix secreting cell that secretes collagen. cell CL:0000667 collagen secreting cell A primordial germ cell is a diploid germ cell precursors that transiently exist in the embryo before they enter into close association with the somatic cells of the gonad and become irreversibly committed as germ cells. FMA:70567 gonocyte primitive germ cell cell CL:0000670 primordial germ cell A non-terminally differentiated cell that is capable of developing into a muscle cell. cell CL:0000680 muscle precursor cell A cell that stores and secretes pancreatic polypeptide hormone. FMA:62938 FMA:83409 type F enteroendocrine cell cell CL:0000696 PP cell Epithelial cells derived from neural plate and neural crest. neuroepithelial cell BTO:0004301 FMA:70557 cell CL:0000710 The term "neuroepithelial cell" is used to describe both this cell type and sensory epithelial cell (CL:0000098). neurecto-epithelial cell A stem cell that can give rise to cell types of the body other than those of the germ-line. CALOHA:TS-2086 FMA:63368 cell CL:0000723 somatic stem cell Muscle cell which has as its direct parts myofilaments organized into sarcomeres. BTO:0002916 CALOHA:TS-2157 FMA:86936 cell CL:0000737 striated muscle cell The set of neurons that receives neural inputs via bipolar, horizontal and amacrine cells. The axons of these cells make up the optic nerve. BTO:0001800 FMA:67765 RGC gangliocyte ganglion cell of retina cell CL:0000740 retinal ganglion cell Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. In mammals, the contractile fiber resembles those of skeletal muscle but are only one third as large in diameter, are richer in sarcoplasm, and contain centrally located instead of peripheral nuclei. FMA:83808 cardiocyte BTO:0001539 CALOHA:TS-0115 FMA:14067 cardiac muscle fiber cardiac myocyte cardiomyocyte heart muscle cell cell CL:0000746 This class encompasses the muscle cells responsible for heart* contraction in both vertebrates and arthropods. The ultrastucture of a wide range of arthropod heart cells has been examined including spiders, horseshoe crabs, crustaceans (see Sherman, 1973 and refs therein) and insects (see Lehmacher et al (2012) and refs therein). According to these refs, the cells participating in heart contraction in all cases are transversely striated. Insects hearts additionally contain ostial cells, also transversely striated muscle cells, but which do not participate in heart contraction. cardiac muscle cell A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage. BTO:0001441 CALOHA:TS-0647 cell CL:0000763 myeloid cell A immature or mature cell in the lineage leading to and including erythrocytes. CL:0002156 CALOHA:TS-0290 FMA:62845 FMA:83516 erythropoietic cell cell CL:0000764 Note that in FMA erythropoietic cells are types of nucleated erythrocytes and thus don't include erythrocytes. erythroid lineage cell A nucleated precursor of an erythrocyte that lacks hematopoietic lineage markers. BTO:0001571 CALOHA:TS-0289 FMA:83504 normoblast cell CL:0000765 erythroblast A hematopoietic multipotent progenitor cell is multipotent, but not capable of long-term self-renewal. These cells are characterized as lacking lineage cell surface markers and being CD34-positive in both mice and humans. BTO:0000725 CALOHA:TS-0448 MPP hemopoietic progenitor cell cell CL:0000837 Markers differ between mouse and human. hematopoietic multipotent progenitor cell A progenitor cell restricted to the myeloid lineage. myeloid progenitor cell BTO:0004730 CALOHA:TS-2099 FMA:70339 cell CL:0000839 Note that this is a class of cell types, not an identified single cell type. myeloid lineage restricted progenitor cell A cell of a hematopoietic lineage. BTO:0000574 CALOHA:TS-2017 FMA:70366 FMA:83598 haematopoietic cell haemopoietic cell hemopoietic cell cell CL:0000988 hematopoietic cell A connective tissue cell found in bone. adiehl 2011-11-16T04:28:16Z cell CL:0001035 bone cell A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells. tmeehan 2010-01-06T03:43:20Z cell CL:0002031 hematopoietic lineage restricted progenitor cell A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. tmeehan 2010-01-06T03:43:27Z cell CL:0002032 This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060). hematopoietic oligopotent progenitor cell An enteroendocrine cell that produces glucagon. tmeehan 2010-09-10T10:48:54Z FMA:62939 cell CL:0002067 type A enteroendocrine cell Specialized cardiac myocyte that is subendocardially interspersed with the regular cardiac muscle cell. They are uninucleate cylindrical cells, associated end-to-end in long rows, continue from the node to the atrioventricular bundle; relatively short compared to ordinary myocytes but are nearly twice their diameter. tmeehan 2010-06-28T08:36:15Z BTO:0001032 FMA:14146 Purkinje cell fiber Purkinje muscle cell myocytus conducens cardiacus cell CL:0002068 Purkinje myocyte A specialized cardiac myocyte in the sinoatrial and atrioventricular nodes. The cell is slender and fusiform confined to the nodal center, circumferentially arranged around the nodal artery. tmeehan 2010-06-29T11:41:37Z pacemaker cell BTO:0004190 FMA:67101 P cell cardiac pacemaker cell myocytus nodalis cell CL:0002072 nodal myocyte Specialized cardiac myocyte which is in the internodal tract and atrioventricular node. The cell is more slender than ordinary atrial myocytes and has more myofibrils than nodal myocytes. tmeehan 2010-06-29T02:39:32Z FMA:67142 cell CL:0002073 transitional myocyte The myoendocrine cellis a specialized myocyte localized mainly in the right and left atrial appendages, and also scattered within other areas of the atria and along the conductive system in the ventricular septum. The most conspicuous feature distinguishing myoendocrine cells from other atrial myoctyes is the presence of membane-bounded secretory granules (these granules contain precursor of cardiodilatins or atrial natriuretic polypeptides). tmeehan 2010-06-29T11:50:47Z FMA:67111 cell CL:0002074 myocardial endocrine cell An epithelial cell derived from endoderm. tmeehan 2010-06-29T03:38:14Z FMA:69075 cell CL:0002076 endo-epithelial cell An epithelial cell derived from ectoderm. tmeehan 2010-06-29T03:38:22Z FMA:69074 cell CL:0002077 ecto-epithelial cell Epithelial cell derived from mesoderm or mesenchyme. tmeehan 2010-06-29T03:49:14Z FMA:69076 epithelial mesenchymal cell cell CL:0002078 meso-epithelial cell A cardiac myocyte that is an excitable cells in the myocardium, specifically in the conducting system of heart. tmeehan 2010-07-21T01:33:38Z FMA:67968 cell CL:0002086 specialized cardiac myocyte A cell found in the bone marrow. This can include fibroblasts, macrophages, adipocytes, osteoblasts, osteoclasts, endothelial cells and hematopoietic cells. tmeehan 2010-07-22T04:48:15Z BTO:0004850 FMA:83621 cell CL:0002092 MH consider whether bone marrow cells are bone cells in the structural sense vs. being part of bone organ sense. bone marrow cell A cell in the hilum of the ovary that produces androgens. tmeehan 2010-08-23T11:18:18Z FMA:18710 hilar cell of ovary cell CL:0002095 hilus cell of ovary A stomal cell of the ovary tmeehan 2010-08-23T12:10:31Z FMA:72299 ovarian stromal cell cell CL:0002132 stromal cell of ovary An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels. tmeehan 2010-08-24T02:06:40Z BTO:0001854 CALOHA:TS-1106 FMA:67755 vascular endothelial cell cubodial endothelial cell of vascular tree cell CL:0002139 These cells are reportedly CD31-positive, CD34-positive, CD144-positive, TAL1-positive. endothelial cell of vascular tree An endothelial cell found in capillaries. tmeehan 2010-08-24T10:15:00Z BTO:0004956 CALOHA:TS-0112 FMA:67756 cell CL:0002144 capillary endothelial cell Epithelial cells derived from general body ectoderm and ectoderm placodes. tmeehan 2010-08-26T08:31:08Z FMA:70556 cell CL:0002159 general ecto-epithelial cell A keratinized cell located in the hard palate or gingiva. tmeehan 2010-08-26T02:51:30Z cell CL:0002170 keratinized cell of the oral mucosa An epithelial cell found in the lining of the stomach. tmeehan 2010-08-25T03:22:08Z CL:1000399 FMA:62948 cell CL:0002178 epithelial cell of stomach A mucous cell in the epithelium of the stomach. tmeehan 2010-08-25T03:38:51Z CL:1000404 FMA:63464 cell CL:0002180 mucous cell of stomach A stomach epithelial cell that is olumnar in form with a few short apical microvilli; relatively undifferentiated mitotic cell from which other types of gland are derived; few in number, situated in the isthmus region of the gland and base of the gastric pit. tmeehan 2010-08-25T03:57:08Z CL:1000400 FMA:62953 cell CL:0002183 stem cell of gastric gland A basally situated, mitotically active, columnar-shaped keratinocyte attached to the basement membrane. tmeehan 2010-08-26T03:12:49Z CL:1000439 FMA:70571 cell CL:0002187 basal cell of epidermis A cell comprising the transparent, biconvex body separating the posterior chamber and vitreous body, and constituting part of the refracting mechanism of the mammalian eye. tmeehan 2010-09-07T10:38:03Z FMA:70950 cell CL:0002222 vertebrate lens cell A cell of the cuboidal epithelium that covers the lens. The cells of the lens epithelium regulate most of the homeostatic functions of the lens. As ions, nutrients, and liquid enter the lens from the aqueous humor, Na+/K+ ATPase pumps in the lens epithelial cells pump ions out of the lens to maintain appropriate lens osmolarity and volume, with equatorially positioned lens epithelium cells contributing most to this current. The activity of the Na+/K+ ATPases keeps water and current flowing through the lens from the poles and exiting through the equatorial regions. The cells of the lens epithelium also serve as the progenitors for new lens fibers. It constantly lays down fibers in the embryo, fetus, infant, and adult, and continues to lay down fibers for lifelong growth. tmeehan 2010-09-07T10:45:47Z FMA:67559 cell CL:0002224 lens epithelial cell A fibroblast in the bone marrow. tmeehan 2010-09-07T02:25:18Z FMA:84377 cell CL:0002240 marrow fibroblast A cell containing at least one nucleus. tmeehan 2010-09-07T03:32:33Z FMA:67513 cell CL:0002242 nucleate cell A hematopoeitic stem cell found in the blood. Normally found in very limited numbers in the peripheral circulation (less than 0.1% of all nucleated cells). tmeehan 2010-09-07T03:57:09Z BTO:0002669 FMA:86711 PBSC cell CL:0002246 peripheral blood stem cell An epithelial cell of the musculomembranous digestive tube extending from the mouth to the anus. tmeehan 2010-09-08T09:26:53Z cell CL:0002251 epithelial cell of alimentary canal An epithelial cell of the esophagus. tmeehan 2010-09-08T09:28:20Z CL:1000402 FMA:63071 cell CL:0002252 epithelial cell of esophagus An epithelial cell of the large intestine. tmeehan 2010-09-08T09:28:22Z CL:1000292 BTO:0004297 FMA:256157 cell epithelial cell of colon CL:0002253 epithelial cell of large intestine An endothelial cell found in the mucosa associated with the facial skeleton. tmeehan 2010-09-14T10:40:12Z CL:1000446 FMA:70627 cell CL:0002261 endothelial cell of viscerocranial mucosa An endothelial cell that lines any of the venous cavities through which blood passes in various glands and organs such as the spleen and liver. tmeehan 2010-09-14T10:57:26Z CL:1000403 FMA:63134 cell CL:0002262 endothelial cell of sinusoid A type of enteroendocrine cell found in the stomach that secretes glucagon. tmeehan 2010-09-10T10:54:42Z FMA:83411 cell CL:0002264 type A cell of stomach An epithelial cell of a skin gland. tmeehan 2010-09-14T12:00:07Z FMA:70657 epithelial cell of gland of skin cell CL:0002308 epithelial cell of skin gland A cell that is part of the nervous system. tmeehan 2010-09-15T01:34:57Z CALOHA:TS-2040 FMA:70333 cell CL:0002319 neural cell A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone. tmeehan 2010-09-15T03:01:54Z CL:1000406 CALOHA:TS-2096 FMA:63875 cell CL:0002320 connective tissue cell A cell of the embryo. tmeehan 2010-09-15T03:39:21Z CALOHA:TS-0263 FMA:82840 FMA:82841 WBbt:0007028 cell CL:0002321 embryonic cell (metazoa) A fat cell derived from a neural crest cell. tmeehan 2010-09-20T02:25:25Z cell CL:0002333 neural crest derived fat cell An endothelial cell that lines the oral cavitiy including the mucosa of the gums, the palate, the lip, and the cheek. tmeehan 2010-09-20T02:52:54Z cell CL:0002336 buccal mucosa cell An endothelial cell that lines the intracavitary lumen of the heart, separating the circulating blood from the underlying myocardium. This cell type releases a number of vasoactive substances including prostacyclin, nitrous oxide and endothelin. tmeehan 2010-09-21T04:33:05Z CL:1000475 FMA:75621 endocardial endothelial cell endothelial cell of endocardium cell CL:0002350 endocardial cell A hematopoietic stem cell that exists during embryogenesis. tmeehan 2010-09-22T09:05:13Z cell CL:0002352 gestational hematopoietic stem cell A keratocyte is a specialized fibroblast residing in the cornea stroma that has a flattened, dendritic cell located between the lamellae with a large flattened nucleus and lengthy processes which communicate with neighboring cells. This corneal layer, representing about 85-90% of corneal thickness, is built up from highly regular collagenous lamellae and extracellular matrix components. Keratocytes play the major role in keeping it transparent, healing its wounds, and synthesizing its components. This cell type secretes collagen I, V, VI, and keratin sulfate. tmeehan 2010-09-22T01:57:40Z corneal fibroblast corneal keratocyte cell CL:0002363 keratocyte An endo-epithelial cell of the respiratory tract. tmeehan 2010-09-23T04:38:49Z BTO:0004533 airway epithelial cell cell CL:0002368 respiratory epithelial cell A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell). tmeehan 2010-09-24T09:44:42Z BTO:0001268 FMA:72300 WBbt:0008378 cell CL:0002371 somatic cell A transversely striated, synctial muscle cell, formed by the fusion of myoblasts. tmeehan 2010-09-24T01:13:01Z CL:0000369 myotubule single cell sarcomere cell CL:0002372 myotube The cell type from which oligodendrocytes develop. This cell originates from multiple structures within the developing brain including the medial ganglion eminence and the lateral ganglionic eminence. These cells migrate throughout the central nervous system and persist into adulthood where they play an important role in remyelination of injured neurons. tmeehan 2010-11-10T02:51:34Z cell CL:0002453 oligodendrocyte precursor cell A melanocyte that produces pigment in the dermis. tmeehan 2010-12-03T03:17:05Z cell CL:0002482 dermal melanocyte A melanocyte that produces pigment in the epithelium. tmeehan 2010-12-03T03:17:14Z cell CL:0002484 The text defintion reference to the MP term appears to reference an epidermal melanocyte term. This term represents any melanocyte in any epithelium. epithelial melanocyte A melanocyte of the retina. This cell type is distinct from pigmented retinal epithelium. tmeehan 2010-12-03T03:25:32Z cell CL:0002485 retinal melanocyte A cell located in the heart, including both muscle and non muscle cells. tmeehan 2010-12-07T09:37:22Z BTO:0001539 CALOHA:TS-0115 FMA:83808 FMA:84791 heart cell cell CL:0002494 From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart. cardiocyte A cell of the adventitial layer of ductal structures such as the uterer, defent duct, biliary duct, etc tmeehan 2010-12-07T04:03:56Z BTO:0002441 FMA:84639 cell CL:0002503 adventitial cell A smooth muscle cell of the intestine. tmeehan 2011-01-17T03:39:38Z intestinal smooth muscle cell cell CL:0002504 enteric smooth muscle cell A fat cell that is part of subcutaneous adipose tissue. tmeehan 2011-02-21T02:51:22Z subcutaneous adipocyte cell CL:0002521 subcutaneous fat cell A smooth muscle cell of the aorta. tmeehan 2011-02-28T01:42:12Z BTO:0004577 cell CL:0002539 aortic smooth muscle cell A mesenchymal stem cell that is part of the bone marrow. tmeehan 2011-02-28T01:47:47Z cell CL:0002540 mesenchymal stem cell of the bone marrow An endothelial cell that is part of the vein. tmeehan 2011-02-28T03:48:11Z CL:1000393 FMA:62104 KUPO:0001099 endothelial cell of vein venous endothelial cell cell CL:0002543 vein endothelial cell An endothelial progenitor cell that participates in angiogenesis during development. tmeehan 2011-02-28T04:20:39Z cell CL:0002546 See CL:0002619. embryonic blood vessel endothelial progenitor cell A fibroblast of the aortic adventitia. tmeehan 2011-02-28T04:43:41Z cell CL:0002547 fibroblast of the aortic adventitia A fibroblast that is part of the heart. tmeehan 2011-02-28T04:57:44Z cardiac fibroblast cell CL:0002548 fibroblast of cardiac tissue tmeehan 2011-02-28T05:05:33Z cell CL:0002551 fibroblast of dermis A fibroblast that is part of lung. tmeehan 2011-02-28T05:11:03Z BTO:0000764 CALOHA:TS-0575 cell CL:0002553 fibroblast of lung A fibroblast of pulmonary artery. tmeehan 2011-02-28T05:22:27Z cell CL:0002557 fibroblast of pulmonary artery An epithelial cell of the intestine. tmeehan 2011-03-01T05:18:31Z cell CL:0002563 intestinal epithelial cell A mesenchymal stem cell of adipose tissue. tmeehan 2011-03-01T09:57:17Z cell CL:0002570 mesenchymal stem cell of adipose A mesenchymal stem cell of the vertebrae. tmeehan 2011-03-01T10:40:27Z cell CL:0002572 vertebral mesenchymal stem cell A glial cell that ensheathes axons of neuron in the peripheral nervous system and are necessary for their maintainance and function. tmeehan 2011-03-02T01:19:27Z BTO:0001220 CALOHA:TS-0898 cell CL:0002573 Schwann cell A blood vessel endothelial cell that is part of the retina. tmeehan 2011-03-06T03:28:27Z cell CL:0002585 retinal blood vessel endothelial cell A smooth muscle cell of the bachiocephalic vasculature. tmeehan 2011-03-06T05:00:58Z cell CL:0002589 smooth muscle cell of the brachiocephalic vasculature A vascular associated smooth muscle cell of the brain vasculature. tmeehan 2011-03-06T05:01:20Z cell CL:0002590 smooth muscle cell of the brain vasculature A smooth muscle of the pulmonary artery. tmeehan 2011-03-06T05:01:28Z BTO:0003336 cell CL:0002591 smooth muscle cell of the pulmonary artery Smooth muscle cell of the carotid artery. tmeehan 2011-03-06T05:01:56Z cell CL:0002596 smooth muscle cell of the carotid artery A smooth muscle cell of the esophagus. tmeehan 2011-03-06T05:48:17Z cell CL:0002599 smooth muscle cell of the esophagus A fibroblast of skin. tmeehan 2011-03-14T12:31:49Z BTO:0001255 CALOHA:TS-0935 cell CL:0002620 skin fibroblast tmeehan 2011-06-21T12:29:31Z cell CL:0002632 epithelial cell of lower respiratory tract An epithelial cell of the anal column. tmeehan 2011-07-08T12:11:38Z cell CL:0002634 epithelial cell of anal column An epithelial cell of the anal canal that is keratinized. This cell type is found towards the lower, rectal end of the anal canal. tmeehan 2011-07-08T02:08:40Z cell CL:0002637 keratinized epithelial cell of the anal canal A glandular epithelial cell of the esophagus. tmeehan 2011-07-08T03:55:57Z FMA:86548 cell CL:0002657 glandular cell of esophagus A glandular epithelial cell of the large intestine. tmeehan 2011-07-08T04:03:01Z FMA:87194 cell CL:0002658 glandular cell of the large intestine A glandular epithelial cell that is part of the stomach. tmeehan 2011-07-11T01:20:35Z CALOHA:TS-1284 FMA:86554 cell CL:0002659 glandular cell of stomach A myocardial endocrine cell that is part of the atrium. tmeehan 2011-07-11T02:45:39Z FMA:83389 cell CL:0002663 myocardial endocrine cell of atrium A multi-fate stem cell that can give rise to different retinal cell types including rod and cone cells. tmeehan 2011-08-16T02:38:01Z cell CL:0002672 retinal progenitor cell A neuroblast derived from a neural crest cell. tmeehan 2011-08-22T09:24:15Z cell CL:0002676 neural crest derived neuroblast A PP cell found in intestine. tmeehan 2011-09-27T11:59:01Z cell CL:0002680 PP cell of intestine A CNS interneuron located in the spinal cord. cell CL:0005000 Is_a interneuron, part_of UBERON:0002240. spinal cord interneuron Cell that has the potential to form a skeletal cell type (e.g. cells in periosteum, cells in marrow) and produce extracellular matrix (often mineralized) and skeletal tissue (often mineralized). haendel 2012-06-15T02:51:27Z scleroblast cell CL:0007001 Needs logical definition. Should be capable_of skeletal system morphogenesis? or skeletal tissue development? needs to be added to GO. NOTES:a cell type of the early embryo (see also: mesenchymal cells) that will give rise to mineralized connective tissue. Scleroblasts can differentiate into osteoblasts (bone-forming cells), chondroblasts (cartilage-forming cells), odontoblasts (dentin-forming cells), ameloblasts (enamel-forming cells). The mesenchymal cells developing into osteoblasts and chondroblasts are derived from the mesoderm. Those developing into odontoblasts are neural crest cells. Those developing into ameloblasts are derived from the ectoderm. (http://www.copewithcytokines.de/cope.cgi?key=scleroblasts) skeletogenic cell Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells. haendel 2012-06-27T08:27:35Z cell CL:0007004 premigratory neural crest cell Skeletogenic cell that has the potential to develop into a chondroblast; and arises from neural crest, meseosdermal and notochordal and connective tissue cells. haendel 2012-06-27T10:44:01Z cell CL:0007009 prechondroblast Any muscle cell in which the fibers are not organised into sarcomeres. CL:0008000 non-striated muscle cell Any hematopoietic cell that is a precursor of some other hematopoietic cell type. CL:0008001 hematopoietic precursor cell A transversely striated, synctial cell of skeletal muscle. It is formed when proliferating myoblasts exit the cell cycle, differentiate and fuse. CL:0008002 skeletal muscle fiber A muscle cell that is part of some visceral muscle CL:0008007 visceral muscle cell A non-polarised cell precursor cell that is part of some mesenchyme, is associated with the cell matrix but is not connected to other cells and is capable of migration. mesenchyme cell CL:0008019 mesenchymal cell Mural cells are pericytes and the vascular smooth muscle cells (vSMCs) of the microcirculation. dos 2020-02-29T17:33:55Z CL:0008034 mural cell dos 2020-02-29T17:37:00Z CL:0008035 microcirculation associated smooth muscle cell A sensory neuron of the spinal nerve that senses body position and sends information about how much the muscle is stretched to the spinal cord. spinal sensory neuron CL:0009000 sensory neuron of spinal nerve Any cell in the retina, the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates. PMID:10702418 cell CL:0009004 retinal cell A stromal cell found in the lamina propria of the large intestine. http://orcid.org/0000-0002-2825-0621 CL:0009021 stromal cell of lamina propria of large intestine A mesothelial cell that is part of the large intestine. http://orcid.org/0000-0002-2825-0621 CL:0009025 mesothelial cell of large intestine A stromal cell that is part_of a bone marrow. GOC:cjm bone marrow stromal cell CL:0010001 stromal cell of bone marrow CL:0010006 cardiac blood vessel endothelial cell CL:0010008 cardiac endothelial cell camera type eye photoreceptor cell CL:0010009 camera-type eye photoreceptor cell A zygote in a plant or an animal. CL:0010017 zygote CL:0010020 cardiac glial cell cell CL:0010021 cardiac myoblast CL:0010022 cardiac neuron A cell in the area of mesoderm in the neurulating embryo that flanks and forms simultaneously with the neural tube. The cells of this region give rise to somites. paraxial mesoderm cell somitic mesoderm cell presomitic mesoderm cell CL:0011007 paraxial cell A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells. cell CL:0011012 neural crest cell A mesothelial cell that is part of the epicardium. http://orcid.org/0000-0001-5208-3432 CL:0011019 mesothelial cell of epicardium A fibroblast that is part of upper back skin. http://orcid.org/0000-0001-5208-3432 CL:0011021 fibroblast of upper back skin A fibroblast that is part of skin of back. http://orcid.org/0000-0001-5208-3432 CL:0011022 fibroblast of skin of back A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses. http://orcid.org/0000-0001-5208-3432 CL:0011026 progenitor cell Any fibroblast that is part of skeletal muscle tissue. http://orcid.org/0000-0001-5208-3432 skeleton muscle fibroblast CL:0011027 skeletal muscle fibroblast Epithelial cell that is part of the colon epithelium. colonic epithelial cell CL:0011108 colon epithelial cell A cell that, by division or terminal differentiation, can give rise to other cell types. CL:0011115 Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell. precursor cell A smooth muscle cell that is part of any blood vessel. 2020-07-21T12:42:48Z smooth muscle cell of blood vessel CL:0019018 blood vessel smooth muscle cell CL:1000042 forebrain neuroblast CL:1000222 stomach neuroendocrine cell CL:1000223 lung neuroendocrine cell CL:1000271 lung ciliated cell CL:1000272 lung secretory cell A smooth muscle cell that is part of the large intestine. FMA:15653 non-striated muscle fiber of large intestine cell CL:1000279 smooth muscle cell of large intestine A smooth muscle cell that is part of the colon. FMA:15663 non-striated muscle fiber of colon cell CL:1000280 smooth muscle cell of colon A smooth muscle cell that is part of the sigmoid colon. FMA:17521 non-striated muscle fiber of sigmoid colon cell CL:1000285 smooth muscle cell of sigmoid colon A smooth muscle cell that is part of the rectum. FMA:17522 non-striated muscle fiber of rectum smooth muscle fiber of rectum cell CL:1000286 smooth muscle cell of rectum A fibroblast that is part of the areolar connective tissue. FMA:261279 cell CL:1000303 fibroblast of areolar connective tissue A fibroblast that is part of the tunica adventitia of artery. FMA:261285 cell CL:1000306 fibroblast of tunica adventitia of artery A fibroblast that is part of the dense regular elastic tissue. FMA:261287 cell CL:1000307 fibroblast of dense regular elastic tissue A fat cell that is part of the epicardial fat. FMA:261293 adipocyte of epicardial fat epicardial fat cell cell CL:1000309 epicardial adipocyte A fat cell that is part of the epicardial fat of right ventricle. FMA:261297 epicardial adipocyte of right ventricle epicardial fat cell of right ventricle cell CL:1000310 adipocyte of epicardial fat of right ventricle A fat cell that is part of the epicardial fat of left ventricle. FMA:261300 epicardial adipocyte of left ventricle epicardial fat cell of left ventricle cell CL:1000311 adipocyte of epicardial fat of left ventricle A transitional myocyte that is part of the interatrial septum. FMA:263152 cell CL:1000361 transitional myocyte of interatrial septum A transitional myocyte that is part of the interventricular septum. FMA:263154 cell CL:1000362 transitional myocyte of interventricular septum A Purkinje myocyte that is part of the interventricular septum. FMA:263182 cell CL:1000376 Purkinje myocyte of interventricular septum A muscle cell that is part of the sinoatrial node. FMA:67102 SA nodal myocyte SA node cardiac muscle cell myocyte of sinoatrial node sinoatrial node cell sinoatrial node myocyte sinuatrial node myocyte cell CL:1000409 myocyte of sinoatrial node A muscle cell that is part of the atrioventricular node. FMA:67106 AV nodal myocyte AV node cardiac muscle cell AV node cell atrioventricular node cell atrioventricular node myocyte cell CL:1000410 myocyte of atrioventricular node An endothelial cell that is part of the arteriole. FMA:67760 KUPO:0001097 cell CL:1000412 endothelial cell of arteriole A blood vessel endothelial cell that is part of an arterial endothelium. CL:0002542 BTO:0004758 FMA:67761 KUPO:0001095 arterial endothelial cell cell CL:1000413 endothelial cell of artery An endothelial cell that is part of the venule. FMA:67762 cell CL:1000414 endothelial cell of venule A somatic stem cell that is part of the epidermis. FMA:70541 epidermal stem cell cell CL:1000428 stem cell of epidermis A smooth muscle cell that is part of the ciliary body. FMA:70610 smooth muscle cell of ciliary body cell CL:1000443 ciliary muscle cell A mesothelial cell that is part of the anterior chamber of eyeball. FMA:70615 cell CL:1000444 mesothelial cell of anterior chamber of eye A basal cell that is part of the epithelium of esophagus. FMA:70731 basal cell of esophageal epithelium cell CL:1000447 epithelial cell of stratum germinativum of esophagus A mesothelial cell that is part of the parietal peritoneum. FMA:72142 cell CL:1000456 mesothelial cell of parietal peritoneum A mesothelial cell that is part of the visceral peritoneum. FMA:72143 cell CL:1000457 mesothelial cell of visceral peritoneum A melanocyte that is part of the skin of body. CALOHA:TS-2374 FMA:72144 skin melanocyte cell CL:1000458 melanocyte of skin A transitional myocyte that is part of the sinoatrial node. FMA:83384 transitinal myocyte of sinuatrial node cell CL:1000478 transitional myocyte of sinoatrial node A Purkinje myocyte that is part of the atrioventricular node. FMA:83386 cell CL:1000479 Purkinje myocyte of atrioventricular node A myocardial endocrine cell that is part of the interventricular septum. FMA:83390 cell CL:1000482 myocardial endocrine cell of interventricular septum A mesothelial cell that is part of the peritoneum. FMA:86736 peritoneal mesothelial cell cell CL:1000490 mesothelial cell of peritoneum A mesothelial cell that is part of the pleura. FMA:86737 pleural mesothelial cell cell CL:1000491 mesothelial cell of pleura A mesothelial cell that is part of the parietal pleura. FMA:86738 cell CL:1000492 mesothelial cell of parietal pleura A mesothelial cell that is part of the visceral pleura. FMA:86739 cell CL:1000493 mesothelial cell of visceral pleura The various hormone- or neurotransmitter-secreting cells present throughout the mucosa of the intestinal tract. cl CL:1001516 intestinal enteroendocrine cell cl endothelial cell of lung pulmonary vessel endothelial cell CL:1001567 lung endothelial cell BTO:0001141 cl PAEC cell CL:1001568 pulmonary artery endothelial cell A vascular endothelial cell found in colon blood vessels. CALOHA:TS-2397 colon endothelial cells colonic endothelial cell CL:1001572 colon endothelial cell Squamous cell of oral epithelium. CALOHA:TS-1252 oral cavity mucosa squamous cell oral cavity mucosa squamous epithelial cell oral mucosa squamous epithelial cell oral mucosa squamous epithelial cells CL:1001576 oral mucosa squamous cell Glial cell of cerebral cortex. CALOHA:TS-1256 brain cortex glial cell cerebral cortex glial cells cerebrum cortex glial cell CL:1001579 cerebral cortex glial cell Glandular cell of colon epithelium. Example: Goblet cells; enterocytes or absorptive cells; enteroendocrine and M cells. CALOHA:TS-1274 colon glandular cells CL:1001588 colon glandular cell Glandular cell of rectal epithelium. Example: Goblet cell; enterocytes or absorptive cells; enteroendocrine and M cells. CALOHA:TS-1281 rectal glandular cell rectum glandular cells CL:1001595 rectum glandular cell Endothelial cells forming the walls of the capillaries within the cerebral cortex. CALOHA:TS-2372 cerebral cortex endothelial cells endothelial cells of cerebral cortex CL:1001602 cerebral cortex endothelial cell Fibroblast from muscle organ. CALOHA:TS-0643 CL:1001609 muscle fibroblast Hematopoietic cells resident in the bone marrow. Include: hematopoietic stem cells (lymphoid stem cells and myeloid stem cells) and the precursor cells for thrombocytes, erythrocytes, basophils, neutrophils, eosinophils, monocytes and lymphocytes. CALOHA:TS-2109 bone marrow hematopoietic cells bone marrow poietic cells CL:1001610 bone marrow hematopoietic cell Any melanocyte that is part of a epidermis. TermGenie 2014-02-03T23:03:09Z cell CL:2000000 These cells are found primarily, but not exclusively, in primates including humans epidermal melanocyte Any blood vessel endothelial cell that is part of a dermis. TermGenie 2014-06-04T15:12:06Z cell CL:2000010 dermis blood vessel endothelial cell Any skin fibroblast that is part of a skin of abdomen. TermGenie 2014-06-04T15:18:16Z cell CL:2000013 fibroblast of skin of abdomen Any native cell that is part of a cardiac septum. TermGenie 2014-06-24T23:17:07Z cell CL:2000022 cardiac septum cell Any neuron that is part of a central nervous system. TermGenie 2014-06-25T01:17:43Z cell CL:2000029 central nervous system neuron Any fibroblast that is part of a embryo. TermGenie 2014-07-09T00:12:00Z cell CL:2000042 embryonic fibroblast Any cardiac muscle cell that is part of a cardiac ventricle. TermGenie 2014-08-12T20:50:28Z cell CL:2000046 ventricular cardiac muscle cell Any fibroblast that is part of a female gonad. TermGenie 2014-10-07T17:57:42Z cell CL:2000063 http://www.sciencellonline.com/site/productInformation.php?keyword=7330 ovarian fibroblast Any epithelial cell that is part of a female gonad. TermGenie 2014-10-07T17:59:13Z cell CL:2000064 http://www.sciencellonline.com/site/productInformation.php?keyword=7310 ovarian surface epithelial cell Any fibroblast that is part of a cardiac ventricle. TermGenie 2014-10-07T18:35:38Z cell CL:2000066 http://www.sciencellonline.com/site/productInformation.php?keyword=6310 cardiac ventricle fibroblast Any fibroblast that is part of a cardiac atrium. TermGenie 2014-10-07T18:36:54Z cell CL:2000067 http://www.sciencellonline.com/site/productInformation.php?keyword=6320 cardiac atrium fibroblast Any fibroblast that is part of a pericardium. TermGenie 2014-10-07T18:38:06Z cell CL:2000068 http://www.sciencellonline.com/site/productInformation.php?keyword=6430 pericardium fibroblast Any fibroblast that is part of a optic choroid. TermGenie 2014-10-07T18:50:43Z cell CL:2000070 http://www.sciencellonline.com/site/productInformation.php?keyword=6620 optic choroid fibroblast Any migratory neural crest cell that is part of a cardiac neural crest. TermGenie 2014-11-05T01:18:43Z cell CL:2000073 migratory cardiac neural crest cell Any mesenchymal stem cell of adipose that is part of a abdomen. TermGenie 2014-12-02T19:10:34Z cell CL:2000080 mesenchymal stem cell of abdominal adipose Any melanocyte of skin that is part of a skin of face. TermGenie 2014-12-02T19:10:40Z cell CL:2000081 melanocyte of skin of face A ciliated epithelial cell of the esophagus. CellBLAST 2019-02-09T16:40:30Z cell CL:3000000 ciliated epithelial cell of esophagus obsolete aerial habitat environmental system reproduction nuclear chromosome cytoplasmic chromosome chromatin heterochromatin skeletal system development ossification action potential angiogenesis blood vessel development branching involved in blood vessel morphogenesis temperature homeostasis ameboidal-type cell migration gastric acid secretion formation of primary germ layer ectoderm formation endoderm formation mesoderm formation morphogenesis of a branching structure serotonin secretion embryonic epithelial tube formation neural tube formation vasculature development intramembranous ossification morphogenesis of an epithelium regulation of heart rate positive regulation of mesenchymal cell proliferation regulation of respiratory gaseous exchange by nervous system process positive regulation of antimicrobial peptide production leukocyte chemotaxis involved in immune response hematopoietic progenitor cell differentiation immune effector process myeloid cell homeostasis immune system process production of molecular mediator of immune response immune system development leukocyte migration involved in immune response regulation of immune system process negative regulation of immune system process positive regulation of immune system process regulation of leukocyte migration negative regulation of leukocyte migration positive regulation of leukocyte migration regulation of leukocyte chemotaxis negative regulation of leukocyte chemotaxis positive regulation of leukocyte chemotaxis regulation of immune effector process negative regulation of immune effector process positive regulation of immune effector process regulation of production of molecular mediator of immune response negative regulation of production of molecular mediator of immune response positive regulation of production of molecular mediator of immune response regulation of antimicrobial humoral response positive regulation of antimicrobial humoral response antimicrobial peptide production antimicrobial peptide secretion regulation of antimicrobial peptide production negative regulation of antimicrobial peptide production peptide secretion regulation of peptide secretion negative regulation of peptide secretion positive regulation of peptide secretion regulation of antimicrobial peptide secretion negative regulation of antimicrobial peptide secretion positive regulation of antimicrobial peptide secretion regulation of response to biotic stimulus negative regulation of response to biotic stimulus positive regulation of response to biotic stimulus regulation of humoral immune response negative regulation of humoral immune response positive regulation of humoral immune response developmental process involved in reproduction system process muscle system process circulatory system process heart process respiratory system process regulation of extracellular matrix constituent secretion positive regulation of extracellular matrix constituent secretion negative regulation of extracellular matrix constituent secretion molecular process molecular_function catalytic activity transmembrane signaling receptor activity A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome). GO:0008372 NIF_Subcellular:sao1337158144 cell or subcellular entity cellular component cellular_component subcellular entity GO:0005575 Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. cellular_component A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome). GOC:pdt NIF_Subcellular:sao1337158144 subcellular entity NIF_Subcellular:nlx_subcell_100315 extracellular region fibrinogen complex collagen trimer fibrillar collagen trimer collagen type IV trimer basement membrane extracellular space A component of a cell contained within (but not including) the plasma membrane. In eukaryotes it includes the nucleus and cytoplasm. https://github.com/geneontology/go-ontology/issues/17776 Wikipedia:Intracellular internal to cell intracellular protoplasm cellular_component nucleocytoplasm protoplast GO:0005622 intracellular anatomical structure A component of a cell contained within (but not including) the plasma membrane. In eukaryotes it includes the nucleus and cytoplasm. ISBN:0198506732 nucleocytoplasm GOC:mah protoplast GOC:mah A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. NIF_Subcellular:sao1702920020 Wikipedia:Cell_nucleus cell nucleus horsetail nucleus cellular_component GO:0005634 nucleus nucleus A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent. GOC:go_curators horsetail nucleus GOC:al GOC:mah GOC:vw PMID:15030757 The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space). GO:0005636 Wikipedia:Nuclear_envelope cellular_component GO:0005635 nuclear envelope The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space). ISBN:0198547684 chromosome nucleolus The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. Wikipedia:Cytoplasm cellular_component GO:0005737 cytoplasm The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. ISBN:0198547684 A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol. Wikipedia:Vacuole cellular_component vacuolar carboxypeptidase Y GO:0005773 vacuole A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol. GOC:mtg_sensu ISBN:0198506732 vacuolar lumen The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. GO:0005904 juxtamembrane NIF_Subcellular:sao1663586795 Wikipedia:Cell_membrane cell membrane cellular membrane cytoplasmic membrane plasmalemma bacterial inner membrane inner endospore membrane plasma membrane lipid bilayer cellular_component GO:0005886 plasma membrane The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. ISBN:0716731363 cellular membrane NIF_Subcellular:sao6433132645 plasma membrane lipid bilayer GOC:mah cell-cell junction A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body. GO:0072372 FMA:67181 NIF_Subcellular:sao787716553 Wikipedia:Cilium eukaryotic flagellum microtubule-based flagellum primary cilium cellular_component flagellum GO:0005929 Note that we deem cilium and microtubule-based flagellum to be equivalent. In most eukaryotic species, intracellular sub-components of the cilium, such as the ciliary base and rootlet, are located near the plasma membrane. In Diplomonads such as Giardia, instead, the same ciliary parts are located further intracellularly. Also, 'cilium' may be used when axonemal structure and/or motility are unknown, or when axonemal structure is unusual. For all other cases, please refer to children of 'cilium'. Finally, note that any role of ciliary proteins in sensory events should be captured by annotating to relevant biological process terms. cilium A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body. GOC:cilia GOC:curators GOC:kmv GOC:vw ISBN:0198547684 PMID:16824949 PMID:17009929 PMID:20144998 The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins. Wikipedia:Cell_cortex cellular_component cell periphery peripheral cytoplasm GO:0005938 cell cortex The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins. GOC:mah ISBN:0815316194 transport ion transport cation transport serotonin transport extracellular transport lipid transport movement of cell or subcellular component chemotaxis muscle contraction regulation of muscle contraction smooth muscle contraction regulation of smooth muscle contraction striated muscle contraction regulation of striated muscle contraction immune response humoral immune response organelle organization cell communication signal transduction cell-cell signaling chemical synaptic transmission multicellular organism development gamete generation gastrulation ectoderm development nervous system development endoderm development mesoderm development respiratory gaseous exchange by respiratory system digestion excretion sensory perception visual perception sensory perception of sound sensory perception of chemical stimulus behavior learning or memory memory locomotory behavior blood circulation regulation of heart contraction A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. jl 2012-09-19T15:05:24Z GO:0000004 GO:0007582 GO:0044699 Wikipedia:Biological_process biological process physiological process biological_process single organism process single-organism process GO:0008150 Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. biological_process A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. GOC:pdt metabolic process cell population proliferation positive regulation of cell population proliferation negative regulation of cell population proliferation negative regulation of antimicrobial humoral response taste receptor activity response to radiation response to light stimulus detection of external stimulus detection of abiotic stimulus detection of light stimulus detection of visible light detection of chemical stimulus response to external stimulus response to biotic stimulus response to abiotic stimulus anatomical structure morphogenesis embryo development post-embryonic development embryo development ending in birth or egg hatching tissue development negative regulation of metabolic process positive regulation of metabolic process hormone transport regulation of signal transduction positive regulation of signal transduction negative regulation of signal transduction cellular process mesenchymal cell proliferation regulation of mesenchymal cell proliferation gene expression regulation of gene expression regulation of signaling receptor activity regulation of gastrulation positive regulation of macromolecule metabolic process negative regulation of macromolecule metabolic process positive regulation of gene expression negative regulation of gene expression positive regulation of organelle organization negative regulation of organelle organization regulation of cell communication positive regulation of cell communication negative regulation of cell communication negative regulation of norepinephrine secretion positive regulation of norepinephrine secretion regulation of hormone levels lipid localization cellular component assembly involved in morphogenesis A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles. Wikipedia:Endomembrane_system cellular_component GO:0012505 endomembrane system A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles. GOC:lh vesicle membrane regulation of norepinephrine secretion regulation of serotonin secretion negative regulation of serotonin secretion positive regulation of serotonin secretion phasic smooth muscle contraction gas transport oxygen transport peptide transport amine transport monoamine transport organic hydroxy compound transport norepinephrine transport A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. 2014-03-06T11:37:54Z GO:0098589 GO:0098805 Wikipedia:Biological_membrane membrane region region of membrane whole membrane cellular_component GO:0016020 membrane A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. GOC:dos GOC:mah ISBN:0815316194 cellular component organization vesicle organization true kinase activity morphogenesis of embryonic epithelium cell migration negative regulation of angiogenesis transferase activity transferase activity, transferring phosphorus-containing groups stem cell division reproductive behavior regulation of metabolic process transmission of nerve impulse antimicrobial humoral response sexual reproduction neural tube development cellular process involved in reproduction in multicellular organism reproductive process digestive system process regulation of anatomical structure morphogenesis cellular component assembly signal transduction involved in regulation of gene expression regulation of signaling signaling positive regulation of signaling negative regulation of signaling signal release myofibril sarcomere A cellular component that forms a specialized region of connection between two or more cells, or between a cell and the extracellular matrix, or between two membrane-bound components of a cell, such as flagella. Wikipedia:Cell_junction cellular_component GO:0030054 cell junction A cellular component that forms a specialized region of connection between two or more cells, or between a cell and the extracellular matrix, or between two membrane-bound components of a cell, such as flagella. GOC:aruk GOC:bc GOC:mah ISBN:0198506732 PMID:26820516 PMID:28096264 http://www.vivo.colostate.edu/hbooks/cmb/cells/pmemb/junctions_a.html peptide hormone secretion hemopoiesis myeloid cell differentiation cell differentiation extracellular matrix organization erythrocyte differentiation megakaryocyte differentiation regulation of ossification negative regulation of ossification external encapsulating structure regulation of cell migration positive regulation of cell migration negative regulation of cell migration defecation A neuron projection that has a short, tapering, morphology. Dendrites receive and integrate signals from other neurons or from sensory stimuli, and conduct nerve impulses towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body. NIF_Subcellular:sao1211023249 Wikipedia:Dendrite cellular_component GO:0030425 dendrite A neuron projection that has a short, tapering, morphology. Dendrites receive and integrate signals from other neurons or from sensory stimuli, and conduct nerve impulses towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body. GOC:aruk GOC:bc GOC:dos GOC:mah GOC:nln ISBN:0198506732 peristalsis neutrophil chemotaxis leukocyte chemotaxis cytoplasmic vesicle membrane A nonmembrane-bound oligomeric protein complex that participates in bidirectional transport of molecules (cargo) along axonemal microtubules. intraflagellar transport complex intraflagellar transport particle cellular_component IFT complex GO:0030990 Note that we deem cilia and microtubule-based flagella to be equivalent. intraciliary transport particle A nonmembrane-bound oligomeric protein complex that participates in bidirectional transport of molecules (cargo) along axonemal microtubules. GOC:cilia GOC:kmv PMID:14570576 PMID:22118932 PMID:23945166 extracellular matrix A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle. NIF_Subcellular:sao830981606 cellular_component intracellular membrane GO:0031090 organelle membrane A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle. GOC:dos GOC:mah intracellular membrane NIF_Subcellular:sao830981606 cytoplasmic vesicle regulation of nervous system process negative regulation of nervous system process positive regulation of nervous system process Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space. NIF_Subcellular:sao1687101204 cellular_component GO:0031965 nuclear membrane Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space. GOC:mah GOC:pz A double membrane structure enclosing an organelle, including two lipid bilayers and the region between them. In some cases, an organelle envelope may have more than two membranes. cellular_component GO:0031967 organelle envelope A double membrane structure enclosing an organelle, including two lipid bilayers and the region between them. In some cases, an organelle envelope may have more than two membranes. GOC:mah GOC:pz membrane-enclosed lumen A multilayered structure surrounding all or part of a cell; encompasses one or more lipid bilayers, and may include a cell wall layer; also includes the space between layers. cellular_component GO:0031975 envelope A multilayered structure surrounding all or part of a cell; encompasses one or more lipid bilayers, and may include a cell wall layer; also includes the space between layers. GOC:mah GOC:pz nuclear lumen vesicle locomotion involved in locomotory behavior regulation of response to external stimulus negative regulation of response to external stimulus positive regulation of response to external stimulus regulation of lipid transport negative regulation of lipid transport positive regulation of lipid transport regulation of intracellular transport negative regulation of intracellular transport positive regulation of intracellular transport multicellular organismal process developmental process multicellular organism reproduction All of the contents of a plasma membrane bounded cell projection, excluding the plasma membrane surrounding the projection. cellular_component GO:0032838 plasma membrane bounded cell projection cytoplasm All of the contents of a plasma membrane bounded cell projection, excluding the plasma membrane surrounding the projection. GOC:krc GOC:mah All of the contents of a dendrite, excluding the surrounding plasma membrane. dendritic cytoplasm cellular_component GO:0032839 dendrite cytoplasm All of the contents of a dendrite, excluding the surrounding plasma membrane. GOC:mah regulation of localization secretion by cell cellular component morphogenesis A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. GO:0043234 macromolecular complex macromolecule complex protein containing complex protein complex protein-protein complex cellular_component GO:0032991 A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole. protein-containing complex A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. GOC:dos GOC:mah macromolecule localization regulation of organelle organization negative regulation of catecholamine secretion positive regulation of catecholamine secretion erythrocyte homeostasis tube formation tube morphogenesis tube development intracellular signal transduction multicellular organismal signaling steroid hormone secretion androgen secretion direct ossification The region of a neuron that includes the cell body (cell soma) and dendrite(s), but excludes the axon. bf 2014-07-24T10:06:19Z cellular_component GO:0036477 somatodendritic compartment The region of a neuron that includes the cell body (cell soma) and dendrite(s), but excludes the axon. GOC:PARL GOC:pad signaling receptor activity locomotion regulation of locomotion negative regulation of locomotion embryonic cleavage positive regulation of locomotion positive regulation of embryonic development cell migration involved in gastrulation regulation of cell population proliferation response to chemical taxis regulation of membrane potential melanosome homeostatic process amide transport A prolongation or process extending from a cell, e.g. a flagellum or axon. cell process cellular process cellular projection cellular_component GO:0042995 cell projection A prolongation or process extending from a cell, e.g. a flagellum or axon. GOC:jl http://www.cogsci.princeton.edu/~wn/ A prolongation or process extending from a nerve cell, e.g. an axon or dendrite. NIF_Subcellular:sao867568886 neuron process neuron protrusion neuronal cell projection neurite cellular_component nerve fiber GO:0043005 neuron projection A prolongation or process extending from a nerve cell, e.g. an axon or dendrite. GOC:jl http://www.cogsci.princeton.edu/~wn/ neuron protrusion NIF_Subcellular:sao250931889 nerve fiber GOC:dph chordate embryonic development neuronal cell body extracellular structure organization macromolecule metabolic process A small, membranous protrusion from a dendrite that forms a postsynaptic compartment, typically receiving input from a single presynapse. They function as partially isolated biochemical and an electrical compartments. Spine morphology is variable:they can be thin, stubby, mushroom, or branched, with a continuum of intermediate morphologies. They typically terminate in a bulb shape, linked to the dendritic shaft by a restriction. Spine remodeling is though to be involved in synaptic plasticity. NIF_Subcellular:sao1799103720 Wikipedia:Dendritic_spine dendrite spine branched dendritic spine mushroom dendritic spine sessile dendritic spine stubby dendritic spine thin dendritic spine cellular_component GO:0043197 dendritic spine A small, membranous protrusion from a dendrite that forms a postsynaptic compartment, typically receiving input from a single presynapse. They function as partially isolated biochemical and an electrical compartments. Spine morphology is variable:they can be thin, stubby, mushroom, or branched, with a continuum of intermediate morphologies. They typically terminate in a bulb shape, linked to the dendritic shaft by a restriction. Spine remodeling is though to be involved in synaptic plasticity. GOC:nln branched dendritic spine NIF_Subcellular:sao965204139 mushroom dendritic spine NIF_Subcellular:sao876577163 sessile dendritic spine NIF_Subcellular:sao1536532595 stubby dendritic spine NIF_Subcellular:sao317384566 thin dendritic spine NIF_Subcellular:sao1232858786 response to external biotic stimulus Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane. NIF_Subcellular:sao1539965131 Wikipedia:Organelle cellular_component GO:0043226 organelle Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane. GOC:go_curators Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. NIF_Subcellular:sao414196390 membrane-enclosed organelle cellular_component GO:0043227 membrane-bounded organelle Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. GOC:go_curators non-membrane-bounded organelle Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. cellular_component GO:0043229 intracellular organelle Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. GOC:go_curators extracellular organelle Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. intracellular membrane-enclosed organelle cellular_component GO:0043231 intracellular membrane-bounded organelle Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. GOC:go_curators intracellular non-membrane-bounded organelle organelle lumen extracellular non-membrane-bounded organelle regulation of ion transport positive regulation of ion transport negative regulation of ion transport contractile fiber regulation of respiratory gaseous exchange regulation of system process regulation of digestive system process regulation of endocrine process regulation of excretion regulation of respiratory system process cellular component biogenesis regulation of cellular component biogenesis positive regulation of cellular component biogenesis negative regulation of molecular function positive regulation of molecular function cell body A small membranous protrusion, often ending in a bulbous head and attached to the neuron by a narrow stalk or neck. jl 2010-02-05T04:25:10Z spine NIF_Subcellular:sao1145756102 cellular_component GO:0044309 neuron spine A small membranous protrusion, often ending in a bulbous head and attached to the neuron by a narrow stalk or neck. ISBN:0198504888 NIF_Subcellular:sao1145756102 biological process involved in interspecies interaction between organisms cell part obsolete cell part multi-organism reproductive process The junction between an axon of one neuron and a dendrite of another neuron, a muscle fiber or a glial cell. As the axon approaches the synapse it enlarges into a specialized structure, the presynaptic terminal bouton, which contains mitochondria and synaptic vesicles. At the tip of the terminal bouton is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic terminal bouton secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane. NIF_Subcellular:sao914572699 Wikipedia:Chemical_synapse synaptic junction mixed synapse cellular_component electrotonic synapse GO:0045202 synapse The junction between an axon of one neuron and a dendrite of another neuron, a muscle fiber or a glial cell. As the axon approaches the synapse it enlarges into a specialized structure, the presynaptic terminal bouton, which contains mitochondria and synaptic vesicles. At the tip of the terminal bouton is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic terminal bouton secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane. GOC:aruk ISBN:0198506732 PMID:24619342 PMID:29383328 PMID:31998110 mixed synapse NIF_Subcellular:sao1506103497 electrotonic synapse NIF_Subcellular:sao1311109124 external encapsulating structure organization regulation of cell differentiation negative regulation of cell differentiation positive regulation of cell differentiation regulation of myeloid cell differentiation negative regulation of myeloid cell differentiation positive regulation of myeloid cell differentiation regulation of erythrocyte differentiation negative regulation of erythrocyte differentiation positive regulation of erythrocyte differentiation regulation of megakaryocyte differentiation negative regulation of megakaryocyte differentiation positive regulation of megakaryocyte differentiation negative regulation of action potential positive regulation of action potential regulation of angiogenesis positive regulation of angiogenesis positive regulation of ossification negative regulation of heart contraction positive regulation of heart contraction negative regulation of muscle contraction positive regulation of muscle contraction negative regulation of smooth muscle contraction positive regulation of smooth muscle contraction negative regulation of striated muscle contraction positive regulation of striated muscle contraction negative regulation of embryonic development regulation of embryonic development acid secretion hormone secretion regulation of hormone secretion positive regulation of hormone secretion negative regulation of hormone secretion secretion intracellular transport somatic stem cell division norepinephrine secretion mesoderm morphogenesis animal organ development blood vessel morphogenesis positive regulation of biological process negative regulation of biological process positive regulation of behavior negative regulation of behavior positive regulation of cellular process negative regulation of cellular process hematopoietic or lymphoid organ development regulation of post-embryonic development negative regulation of post-embryonic development positive regulation of post-embryonic development regulation of response to stimulus positive regulation of response to stimulus negative regulation of response to stimulus embryonic morphogenesis multicellular organismal reproductive process anatomical structure formation involved in morphogenesis tissue morphogenesis system development branching morphogenesis of an epithelial tube pigment granule anatomical structure development cellular developmental process cell motility multicellular organismal homeostasis homeostasis of number of cells catecholamine secretion regulation of catecholamine secretion regulation of immune response negative regulation of immune response positive regulation of immune response regulation of biological process regulation of developmental process regulation of cellular process regulation of behavior modulation of chemical synaptic transmission negative regulation of synaptic transmission positive regulation of synaptic transmission nervous system process endocrine process cognition response to stimulus leukocyte migration detection of stimulus involved in sensory perception detection of chemical stimulus involved in sensory perception detection of light stimulus involved in visual perception sensory perception of taste detection of chemical stimulus involved in sensory perception of taste regulation of chemotaxis positive regulation of chemotaxis negative regulation of chemotaxis sensory perception of light stimulus sensory perception of mechanical stimulus detection of light stimulus involved in sensory perception regulation of secretion positive regulation of secretion negative regulation of secretion regulation of transport positive regulation of transport negative regulation of transport negative regulation of developmental process positive regulation of developmental process regulation of cellular component organization negative regulation of cellular component organization positive regulation of cellular component organization localization cartilage development establishment of localization regulation of multicellular organismal process positive regulation of multicellular organismal process negative regulation of multicellular organismal process regulation of cellular component movement negative regulation of cellular component movement positive regulation of cellular component movement cell division regulation of cell division detection of stimulus cellular localization establishment of localization in cell localization of cell multi-organism process response to other organism cellular response to stimulus positive regulation of cell division negative regulation of cell division regulation of sensory perception catecholamine transport regulation of amine transport negative regulation of amine transport positive regulation of amine transport regulation of nervous system development negative regulation of nervous system development positive regulation of nervous system development regulation of transmission of nerve impulse negative regulation of transmission of nerve impulse positive regulation of transmission of nerve impulse regulation of cardiac muscle contraction negative regulation of cardiac muscle contraction heart contraction cardiac muscle contraction molecular transducer activity regulation of macromolecule metabolic process cell chemotaxis regulation of cellular localization flight epithelium development positive regulation of cardiac muscle contraction regulation of gastric acid secretion positive regulation of gastric acid secretion negative regulation of gastric acid secretion positive regulation of digestive system process negative regulation of digestive system process epithelial tube morphogenesis regulation of morphogenesis of a branching structure endocrine hormone secretion regulation of cartilage development positive regulation of cartilage development negative regulation of cartilage development morphogenesis of a branching epithelium connective tissue development antimicrobial humoral immune response mediated by antimicrobial peptide The region of the neuronal cytoplasm located in dendritic spines. cellular_component GO:0061846 dendritic spine cytoplasm The region of the neuronal cytoplasm located in dendritic spines. PMID:15673667 collagen-containing extracellular matrix biological regulation regulation of biological quality regulation of molecular function extracellular membrane-bounded organelle intracellular organelle lumen glucagon secretion regulation of glucagon secretion negative regulation of glucagon secretion positive regulation of glucagon secretion anchoring junction somatostatin secretion extracellular matrix constituent secretion cellular response to chemical stimulus organelle assembly granulocyte chemotaxis regulation of granulocyte chemotaxis negative regulation of granulocyte chemotaxis positive regulation of granulocyte chemotaxis mastication organic substance transport organic substance metabolic process nitrogen compound transport cellular component organization or biogenesis The part of a cell encompassing the cell cortex, the plasma membrane, and any external encapsulating structures. mah 2010-10-04T01:51:47Z cellular_component GO:0071944 cell periphery The part of a cell encompassing the cell cortex, the plasma membrane, and any external encapsulating structures. GOC:mah elastic fiber extracellular exosome assembly epithelial tube formation negative regulation of mesenchymal cell proliferation circulatory system development regulation of neutrophil chemotaxis positive regulation of neutrophil chemotaxis negative regulation of neutrophil chemotaxis regulation of peptide transport regulation of muscle system process regulation of somatostatin secretion positive regulation of somatostatin secretion negative regulation of somatostatin secretion regulation of peptide hormone secretion positive regulation of peptide hormone secretion negative regulation of peptide hormone secretion regulation of locomotion involved in locomotory behavior positive regulation of locomotion involved in locomotory behavior negative regulation of locomotion involved in locomotory behavior All of the contents of a cilium, excluding the plasma membrane surrounding the cilium. pr 2011-03-23T01:52:31Z cilium plasm microtubule-based flagellar matrix microtubule-based flagellum matrix cellular_component cilial cytoplasm ciliary cytoplasm cilium cytoplasm microtubule-based flagellar cytoplasm microtubule-based flagellum cytoplasm GO:0097014 Note that we deem cilium and microtubule-based flagellum to be equivalent. Also, researchers consider the composition of both the plasm and the membrane of the cilium to be detectably different from that in the non-ciliary cytosol and plasma membrane (e.g. in terms of calcium ion concentration, membrane lipid composition, and more). For this reason, the term "ciliary plasm" is not linked to "cytoplasm". ciliary plasm All of the contents of a cilium, excluding the plasma membrane surrounding the cilium. GOC:BHF GOC:cilia GOC:dos PMID:17895364 A specialized area of membrane on either the presynaptic or the postsynaptic side of a synapse, the junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell. pr 2011-06-07T11:22:09Z cellular_component GO:0097060 synaptic membrane A specialized area of membrane on either the presynaptic or the postsynaptic side of a synapse, the junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell. GOC:BHF PMID:20410104 The entire complement of dendrites for a neuron, consisting of each primary dendrite and all its branches. pr 2012-12-17T12:31:49Z NIF_Subcellular:sao172297168 cellular_component GO:0097447 dendritic tree The entire complement of dendrites for a neuron, consisting of each primary dendrite and all its branches. GOC:aruk GOC:bc NIF_Subcellular:sao172297168 myeloid leukocyte migration granulocyte migration intracellular vesicle extracellular exosome biogenesis A membrane that is a (regional) part of the plasma membrane. dos 2014-03-06T11:55:32Z region of plasma membrane cellular_component GO:0098590 Note that this term should not be used for direct manual annotation as it should always be possible to choose a more specific subclass. plasma membrane region A membrane that is a (regional) part of the plasma membrane. GOC:dos network-forming collagen trimer banded collagen fibril complex of collagen trimers collagen network basement membrane collagen trimer The part of a synapse that is part of the post-synaptic cell. cellular_component GO:0098794 postsynapse The part of a synapse that is part of the post-synaptic cell. GOC:dos Any protein complex that is part of a membrane. cellular_component GO:0098796 membrane protein complex Any protein complex that is part of a membrane. GOC:dos Any protein complex that is part of the plasma membrane. cellular_component GO:0098797 plasma membrane protein complex Any protein complex that is part of the plasma membrane. GOC:dos regulation of action potential anterograde trans-synaptic signaling supramolecular complex supramolecular polymer regulation of trans-synaptic signaling supramolecular fiber synaptic signaling trans-synaptic signaling trans-synaptic signaling, modulating synaptic transmission Any (proper) part of the cytoplasm of a single cell of sufficient size to still be considered cytoplasm. cellular_component GO:0099568 cytoplasmic region Any (proper) part of the cytoplasm of a single cell of sufficient size to still be considered cytoplasm. GOC:dos signal release from synapse The complete extent of cell cortex that underlies some some region of the plasma membrane. perimembrane region cellular_component GO:0099738 cell cortex region The complete extent of cell cortex that underlies some some region of the plasma membrane. GOC:dos A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. kmv 2019-08-12T18:01:37Z cellular_component GO:0110165 cellular anatomical entity A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. GOC:kmv A prolongation or process extending from a cell and that is bounded by plasma membrane, e.g. a cilium, lamellipodium, or axon. https://github.com/geneontology/go-ontology/issues/13193 krc 2017-03-21T17:26:07Z cellular_component GO:0120025 plasma membrane bounded cell projection A prolongation or process extending from a cell and that is bounded by plasma membrane, e.g. a cilium, lamellipodium, or axon. GOC:krc All of the contents of a plasma membrane bounded neuron projection, excluding the plasma membrane surrounding the projection. krc 2017-11-01T18:58:12Z cellular_component GO:0120111 neuron projection cytoplasm All of the contents of a plasma membrane bounded neuron projection, excluding the plasma membrane surrounding the projection. GOC:ha extracellular vesicle biogenesis export from cell lipid export from cell A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together in the nucleus. pg 2020-09-09T05:12:38Z nuclear complex cellular_component GO:0140513 nuclear protein-containing complex A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together in the nucleus. GOC:pg extracellular regulation of signal transduction extracellular negative regulation of signal transduction gene expression involved in extracellular matrix organization regulation of vasculature development negative regulation of vasculature development regulation of hematopoietic progenitor cell differentiation negative regulation of hematopoietic progenitor cell differentiation positive regulation of hematopoietic progenitor cell differentiation regulation of organelle assembly negative regulation of organelle assembly positive regulation of organelle assembly regulation of intracellular signal transduction negative regulation of intracellular signal transduction positive regulation of intracellular signal transduction regulation of neutrophil migration negative regulation of neutrophil migration positive regulation of neutrophil migration regulation of extracellular matrix organization negative regulation of extracellular matrix organization positive regulation of extracellular matrix organization regulation of blood circulation negative regulation of blood circulation positive regulation of blood circulation regulation of secretion by cell negative regulation of secretion by cell positive regulation of secretion by cell regulation of extracellular exosome assembly negative regulation of extracellular exosome assembly positive regulation of extracellular exosome assembly extracellular vesicle regulation of hemopoiesis negative regulation of hemopoiesis positive regulation of hemopoiesis negative regulation of respiratory gaseous exchange positive regulation of respiratory gaseous exchange positive regulation of vasculature development regulation of somatic stem cell division negative regulation of somatic stem cell division positive regulation of somatic stem cell division regulation of epithelial tube formation negative regulation of epithelial tube formation positive regulation of epithelial tube formation regulation of morphogenesis of an epithelium negative regulation of morphogenesis of an epithelium positive regulation of morphogenesis of an epithelium regulation of blood vessel branching negative regulation of vessel branching positive regulation of blood vessel branching regulation of mesoderm formation negative regulation of mesoderm formation positive regulation of mesoderm formation regulation of lipid localization negative regulation of lipid localization positive regulation of lipid localization neutrophil migration regulation of multicellular organismal development regulation of stem cell division regulation of cell motility negative regulation of cell motility positive regulation of cell motility negative regulation of blood vessel morphogenesis regulation of reproductive process negative regulation of reproductive process positive regulation of reproductive process negative regulation of signaling receptor activity positive regulation of signaling receptor activity regulation of defecation negative regulation of defecation positive regulation of defecation regulation of mesoderm development negative regulation of mesoderm development positive regulation of mesoderm development regulation of ectoderm development negative regulation of ectoderm development positive regulation of ectoderm development negative regulation of gastrulation positive regulation of gastrulation regulation of steroid hormone secretion negative regulation of steroid hormone secretion positive regulation of steroid hormone secretion regulation of androgen secretion negative regulation of androgen secretion positive regulation of androgen secretion body part movement mouth movement chewing behavior process kinesthetic behavior jaw movement root Viruses Teleostomi Euteleostomi cellular organisms Dipnotetrapodomorpha Bacteria Archaea Eukaryota Tetrapoda Amniota Opisthokonta Metazoa Bilateria Deuterostomia Mammalia Eumetazoa Chordata Vertebrata <vertebrates> Gnathostomata <vertebrates> Sarcopterygii Craniata <chordates> organism quality PATO:0000000 obsolete pato true A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities quality (PATO) PATO:0000072 quality PATO:0000001 quality A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities PATOC:GVG quality PATO:0000002 obsolete value true quality PATO:0000003 obsolete assay true A quality of inhering in a bearer by virtue of the bearer's disposition to move freely. quality PATO:0000004 Should be defined using translocation. mobility A quality of inhering in a bearer by virtue of the bearer's disposition to move freely. PATOC:GVG quality PATO:0000005 obsolete absolute activity true quality PATO:0000006 obsolete process true quality PATO:0000007 obsolete relative activity true A physical quality inhering in a bearer by virtue of the bearer's scalar absolute value of the rate of change of the bearer's position. quality velocity PATO:0000008 speed A physical quality inhering in a bearer by virtue of the bearer's scalar absolute value of the rate of change of the bearer's position. Wikipedia:http://en.wikipedia.org/wiki/Velocity quality PATO:0000009 obsolete absolute speed true quality PATO:0000010 obsolete relative speed true A time quality inhering in a bearer by virtue of how long the bearer has existed. quality PATO:0000011 age A time quality inhering in a bearer by virtue of how long the bearer has existed. WordNet:WordNet quality PATO:0000012 obsolete absolute age true quality PATO:0000013 obsolete relative age true A composite chromatic quality composed of hue, saturation and intensity parts. PATO:0000020 colour relative color quality PATO:0000014 color A composite chromatic quality composed of hue, saturation and intensity parts. PATOC:GVG A chromatic scalar-circular quality inhering in an object that manifests in an observer by virtue of the dominant wavelength of the visible light; may be subject to fiat divisions, typically into 7 or 8 spectra. quality PATO:0000015 color hue A chromatic scalar-circular quality inhering in an object that manifests in an observer by virtue of the dominant wavelength of the visible light; may be subject to fiat divisions, typically into 7 or 8 spectra. PATOC:cjm A scalar optical property that is the intensity, value or amount of perceived light. color intensity color lightness color value quality PATO:0000016 Color brightness refers to the intensity, lightness or value of the light present. Think of this as a dimmer switch. color brightness A scalar optical property that is the intensity, value or amount of perceived light. PATOC:MAH A scalar chromatic property that is the degree of purity of perceived light. quality PATO:0000017 Color saturation refers to the amount of white light or gray paint mixed in with the hue (single wavelength) and is a measure of color purity. color saturation A scalar chromatic property that is the degree of purity of perceived light. PATOC:GVG A luminous flux quality inhering in a bearer by virtue of the bearer's emitting longer wavelength light following the absorption of shorter wavelength radiation; fluorescence is common with aromatic compounds with several rings joined together. quality PATO:0000018 fluorescence A luminous flux quality inhering in a bearer by virtue of the bearer's emitting longer wavelength light following the absorption of shorter wavelength radiation; fluorescence is common with aromatic compounds with several rings joined together. PATOC:GVG A chromatic property that is the relative position of different hues or degrees of saturation. quality PATO:0000019 color pattern A chromatic property that is the relative position of different hues or degrees of saturation. PATOC:GVG true A quality inhering in a bearer by virtue of the bearer's disposition to harmonious coexistence. quality PATO:0000021 Needs redefined or obsoleted. Is this the same as genetic incompatibility? Moved to organismal quality. compatibility A quality inhering in a bearer by virtue of the bearer's disposition to harmonious coexistence. PATOC:GVG quality PATO:0000022 obsolete gametophytic compatability true quality PATO:0000023 obsolete relative compatability true quality PATO:0000024 obsolete sporophytic compatability true A single physical entity inhering in an bearer by virtue of the bearer's quantities or relative ratios of subparts. PATO:0002015 composed of compositionality content structure, composition quality PATO:0000025 For example calcium composition (which may inhere in bone), haemoglobin composition (which may inhere in blood). composition A single physical entity inhering in an bearer by virtue of the bearer's quantities or relative ratios of subparts. PATOC:GVG quality PATO:0000026 obsolete carbohydrate composition true quality PATO:0000027 obsolete electrolyte composition true quality PATO:0000028 obsolete macromolecular composition true quality PATO:0000029 obsolete protein composition true quality PATO:0000030 obsolete enzyme composition true quality PATO:0000031 obsolete metabolite composition true quality PATO:0000032 obsolete secondary product composition true A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance. concentration quality PATO:0000033 concentration of A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance. Wikipedia:http://en.wikipedia.org/wiki/concentration quality PATO:0000034 obsolete protein concentration true quality PATO:0000035 obsolete carbohydrate concentration true quality PATO:0000036 obsolete water content true A physical quality inhering in a bearer by virtue of the bearer's density, firmness, or viscosity. quality firmness PATO:0000037 consistency A physical quality inhering in a bearer by virtue of the bearer's density, firmness, or viscosity. PATOC:GVG quality PATO:0000038 obsolete gel consistency true A physical quality inhering in a bearer by virtue of the bearer's orientation in space. quality PATO:0000039 TODO: consider merging with angular placement. direction A physical quality inhering in a bearer by virtue of the bearer's orientation in space. thesaurus.maths:thesaurus.maths A quality that is the extent of space between two entities. quality PATO:0000040 distance A quality that is the extent of space between two entities. PATOC:GVG quality PATO:0000041 obsolete absolutedistance true quality PATO:0000042 obsolete relative distance true A quality of a physical entity inhering in a bearer by virtue of whether the bearer's molecules are being perceived by a taste and odorant receptors. quality PATO:0000043 flavor A quality of a physical entity inhering in a bearer by virtue of whether the bearer's molecules are being perceived by a taste and odorant receptors. PATOC:GVG A physical quality which inheres in a bearer by virtue of the number of the bearer's repetitive actions in a particular time. quality PATO:0000044 frequency A physical quality which inheres in a bearer by virtue of the number of the bearer's repetitive actions in a particular time. Wikipedia:http://en.wikipedia.org/wiki/frequency quality PATO:0000045 obsolete absolute frequency true quality PATO:0000046 obsolete relative frequency true An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved. quality PATO:0000047 biological sex An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved. MGED:MGED A physical quality inhering in a bearer by virtue of the bearer's resistance to pressure, being broken, or pierced quality impenetrability toughness PATO:0000048 hardness A physical quality inhering in a bearer by virtue of the bearer's resistance to pressure, being broken, or pierced merriam-webster:merriam-webster A quality inhering in a bearer by virtue of the bearer's possessing or displaying a distinctive feature in type or degree or effect or force. quality PATO:0000049 intensity A quality inhering in a bearer by virtue of the bearer's possessing or displaying a distinctive feature in type or degree or effect or force. PATOC:GVG A time quality inhering in a bearer by virtue of the bearer's expected maximum age. quality PATO:0000050 life span A time quality inhering in a bearer by virtue of the bearer's expected maximum age. PATOC:GVG A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. quality PATO:0000051 morphology A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. PATOC:GVG A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc). PATO:0001647 relational shape quality quality PATO:0000052 Shapes are invariant on size transformations. Shapes can be subdivided into 2D and 3D shapes, We can also make a distinction between shapes of complete self-connected objects, and shapes of parts of objects. shape A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc). PATOC:GVG true quality PATO:0000054 obsolete absolute number true quality PATO:0000055 obsolete relative number true An organismal quality inhering in a bearer by virtue of the bearer's disposition to synthesize a particular organic compound required for its growth. quality nutritional quality PATO:0000056 trophic quality An organismal quality inhering in a bearer by virtue of the bearer's disposition to synthesize a particular organic compound required for its growth. Wikipedia:http://en.wikipedia.org/wiki/Trophic_level A quality of a single process inhering in a bearer by virtue of the bearer's occurrence. PATO:0000156 PATO:0000158 temporal incidence quality PATO:0000057 occurrence A quality of a single process inhering in a bearer by virtue of the bearer's occurrence. PATOC:GVG A physical quality inhering in a bearer by virtue of the bearer's molecules being are aerially dispersed and perceived by an odorant receptor. quality PATO:0000058 odor A physical quality inhering in a bearer by virtue of the bearer's molecules being are aerially dispersed and perceived by an odorant receptor. PATOC:GVG A parental quality inhering in a bearer by virtue of exhibiting the characteristic of a parent. parental type quality PATO:0000059 obsolete parental quality true A parental quality inhering in a bearer by virtue of exhibiting the characteristic of a parent. WordNet:WordNet A spatial quality inhering in a bearer by virtue of the bearer's exhibiting repetition of placement of its parts. PATO:0000132 PATO:0001565 distribution quality pattern PATO:0000060 spatial pattern A spatial quality inhering in a bearer by virtue of the bearer's exhibiting repetition of placement of its parts. PATOC:GVG quality PATO:0000061 obsolete relative pattern true A sleep quality defined by the mathematic properties of the relative time frames of the sleep cycle. quality PATO:0000062 sleep pattern A sleep quality defined by the mathematic properties of the relative time frames of the sleep cycle. PATOC:GVG quality PATO:0000063 obsolete percentage true quality PATO:0000064 obsolete absolute percentage true quality PATO:0000065 obsolete relative percentage true A texture quality inhering in a bearer by virtue of the bearer's having hair or bristles. quality PATO:0000066 pilosity A texture quality inhering in a bearer by virtue of the bearer's having hair or bristles. PATOC:GVG quality PATO:0000067 obsolete relative pilosity true quality PATO:0000068 TODO: define this or obsolete it and move children somewhere else. qualitative A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. quality PATO:0000069 deviation (from_normal) A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. PATOC:GVG The number of entities of this type that are part of the whole organism. PATO:0000053 PATO:0000071 PATO:0001169 PATO:0001226 presence or absence in organism quantitative quality count in organism number presence PATO:0000070 This term was originally named "presence". It has been renamed to reduce ambiguity. Consider annotating with the reciprocal relation,PATO:0001555, has_number_of. For example, rather than E=fin ray Q=count in organism C=10, say E=organism Q=has number of E2= fin ray C=10. amount The number of entities of this type that are part of the whole organism. PATOC:GVG true true quality PATO:0000073 obsolete relative_quality true quality PATO:0000074 obsolete shattering true quality PATO:0000075 obsolete threshability true quality PATO:0000076 obsolete regulation true A quality inhering in a bearer by virtue of the whether the bearer's disposition to react to a stimulus or an agent. quality reactivity response responsivity PATO:0000077 response to A quality inhering in a bearer by virtue of the whether the bearer's disposition to react to a stimulus or an agent. PATOC:GVG reactivity GOC:CJM A quality of a single process inhering in a bearer by virtue of the bearer's movement or variation characterized by the regular recurrence or alternation of different quantities or conditions. quality PATO:0000078 rhythm quality A quality of a single process inhering in a bearer by virtue of the bearer's movement or variation characterized by the regular recurrence or alternation of different quantities or conditions. answers.com:answers.com quality PATO:0000079 obsolete absolute rhythym true A physical quality of a process inhering in a bearer by virtue of the size of the bearer's maximum displacement from the 'normal' position, when periodic motion is taking place. quality PATO:0000080 amplitude A physical quality of a process inhering in a bearer by virtue of the size of the bearer's maximum displacement from the 'normal' position, when periodic motion is taking place. thesaurus.maths:thesaurus.maths true A rhythm quality inhering in a bearer by virtue of the repetitiveness of bearer's rhythm. quality PATO:0000082 persistence A rhythm quality inhering in a bearer by virtue of the repetitiveness of bearer's rhythm. reference.com:reference.com A quality that exists by virtue of being a particular point in the time of a cycle. quality PATO:0000083 phase A quality that exists by virtue of being a particular point in the time of a cycle. PATOC:GVG quality PATO:0000084 obsolete relative rhythym true A quality inhering in a bearer by virtue of the bearer's disposition to detect or perceive external stimulation. sensitivity quality PATO:0000085 sensitivity toward A quality inhering in a bearer by virtue of the bearer's disposition to detect or perceive external stimulation. PATOC:GVG quality PATO:0000086 obsolete absolute sensitivity true quality PATO:0000087 obsolete disease sensitivity true quality PATO:0000088 obsolete absolute disease sensitivity true quality PATO:0000089 obsolete relative disease sensitivity true quality PATO:0000090 obsolete relative sensitivity true quality PATO:0000091 obsolete stress sensitivity true quality PATO:0000092 obsolete abiotic stress sensitivity true quality PATO:0000093 obsolete chemical sensitivity true quality PATO:0000094 obsolete drug sensitivity true quality PATO:0000095 obsolete absolute drug sensitivity true quality PATO:0000096 obsolete relative drug sensitivity true quality PATO:0000097 obsolete herbicide sensitivity true quality PATO:0000098 obsolete insecticide sensitivity true quality PATO:0000099 obsolete plant growth hormone sensitivity true quality PATO:0000100 obsolete soil composition sensitivity true quality PATO:0000101 obsolete soil nutrient sensitivity true quality PATO:0000102 obsolete macronutrient sensitivity true quality PATO:0000103 obsolete micronutrient sensitivity true quality PATO:0000104 obsolete osmotic response sensitivity true quality PATO:0000105 obsolete p h sensitivity true quality PATO:0000106 obsolete acid sensitivity true quality PATO:0000107 obsolete alkali sensitivity true quality PATO:0000108 obsolete salt sensitivity true quality PATO:0000109 obsolete water sensitivity true quality PATO:0000110 obsolete drought sensitivity true quality PATO:0000111 obsolete flooding sensitivity true quality PATO:0000112 obsolete humidity sensitivity true quality PATO:0000113 obsolete radiation sensitivity true quality PATO:0000114 obsolete temperature sensitivity true quality PATO:0000115 obsolete absolute temperature sensitivity true quality PATO:0000116 obsolete relative temperature sensitivity true A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude. quality PATO:0000117 size A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude. WordNet:WordNet quality PATO:0000118 obsolete absolute size true A 1-D extent quality inhering in a bearer by virtue of the bearer's vertical dimension of extension. quality PATO:0000119 height A 1-D extent quality inhering in a bearer by virtue of the bearer's vertical dimension of extension. PATOC:GVG quality PATO:0000120 obsolete absolute height true quality PATO:0000121 obsolete relative height true A 1-D extent quality which is equal to the distance between two points. quality PATO:0000122 length A 1-D extent quality which is equal to the distance between two points. PATOC:GVG quality PATO:0000123 obsolete absolute length true quality PATO:0000124 obsolete relative length true A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. quality PATO:0000125 For any biological use of PATO, the concept that should be used is 'mass' and not 'weight'. For example, increased weight of an organism. mass A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. PATOC:GVG quality PATO:0000126 obsolete absolute mass true quality PATO:0000127 obsolete relative mass true A physical quality inhering in a bearer that has mass near a gravitational body. Important usage note: Note that this ontology has a class for a similar concept, mass (PATO:0000125). Mass and weight are not equivalent. For most use cases, the class mass is strongly preferred over weight. quality PATO:0000128 For any biological use of PATO, the concept that should be used is 'mass' and not 'weight'. For example, increased weight of an organism. weight A physical quality inhering in a bearer that has mass near a gravitational body. Important usage note: Note that this ontology has a class for a similar concept, mass (PATO:0000125). Mass and weight are not equivalent. For most use cases, the class mass is strongly preferred over weight. Wikipedia:http://en.wikipedia.org/wiki/Weight https://en.wikipedia.org/wiki/Mass#Weight_vs._mass quality PATO:0000129 obsolete absolute weight true quality PATO:0000130 obsolete relative weight true quality PATO:0000131 obsolete relative size true true A spatial quality inhering in a bearer by virtue of the bearer's placement which is defined by the angle between the bearer and an axis, or the angle between the bearer and another object. PATO:0000137 angular placement quality amount of rotation angle angular magnitude plane angle PATO:0000133 orientation A spatial quality inhering in a bearer by virtue of the bearer's placement which is defined by the angle between the bearer and an axis, or the angle between the bearer and another object. PATOC:JE quality PATO:0000134 obsolete absolute_angle true quality PATO:0000135 obsolete relative_angle true A morphological quality pertaining to the degree to which an object contains an opening, aperture, orifice or vent. quality PATO:0000136 closure A morphological quality pertaining to the degree to which an object contains an opening, aperture, orifice or vent. PATOC:CJM PATOC:GVG true quality PATO:0000138 obsolete absolute orientation true quality PATO:0000139 obsolete relative orientation true A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity. PATO:0001032 PATO:0001631 location placement relational spatial quality quality PATO:0000140 position A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity. PATOC:GVG A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. PATO:0001452 conformation relational structural quality quality PATO:0000141 structure A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form. PATOC:GVG conformation VT:1000738 quality PATO:0000142 obsolete substance true quality PATO:0000143 obsolete addictive substance true quality PATO:0000144 This term was made obsolete because it is not a quality. To update annotations, consider the following term 'quality of a solid; 'PATO:0001546' obsolete solid substance true quality PATO:0000145 This term was made obsolete because it is not a quality. To update annotations, consider the following term 'quality of a liquid; PATO:0001548 ' obsolete liquid substance true A physical quality of the thermal energy of a system. quality PATO:0000146 temperature A physical quality of the thermal energy of a system. PATOC:GVG quality PATO:0000147 obsolete absolute temperature true quality PATO:0000148 obsolete body temperature true quality PATO:0000149 obsolete relative temperature true A morphologic quality inhering in a bearer by virtue of the bearer's relative size, organization and distribution of its surface elements or the representation or invention of the appearance of its surface; visual and tactile surface characteristics. quality PATO:0000150 texture A morphologic quality inhering in a bearer by virtue of the bearer's relative size, organization and distribution of its surface elements or the representation or invention of the appearance of its surface; visual and tactile surface characteristics. PATOC:GVG quality PATO:0000151 obsolete relative texture true A quality inhering in a bearer by virtue of the bearer's sensitivity towards a fixed location or value where a change is observed; upper limit. quality PATO:0000152 threshold A quality inhering in a bearer by virtue of the bearer's sensitivity towards a fixed location or value where a change is observed; upper limit. PATOC:GVG quality PATO:0000153 obsolete absolute threshold true quality PATO:0000154 obsolete pain threshold true quality PATO:0000155 obsolete relative threshold true true quality PATO:0000157 obsolete absolute temporal true true quality PATO:0000159 obsolete absolute incidence true quality PATO:0000160 obsolete relative incidence true A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. quality PATO:0000161 rate A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. PATOC:melissa quality PATO:0000162 obsolete absolute rate true quality PATO:0000163 obsolete relative rate true quality PATO:0000164 obsolete relative temporal true A quality in which events occur in sequence. quality PATO:0000165 time A quality in which events occur in sequence. PATOC:GVG quality PATO:0000166 obsolete absolute time true A limited, often assigned period of activity. quality PATO:0000167 obsolete bouts true A limited, often assigned period of activity. answers.com:answers.com quality PATO:0000168 obsolete relative time true An organismal quality inhering in a bearer or a population by virtue of the bearer's disposition to survive and develop normally or the number of surviving individuals in a given population. quality PATO:0000169 viability An organismal quality inhering in a bearer or a population by virtue of the bearer's disposition to survive and develop normally or the number of surviving individuals in a given population. PATOC:GVG quality PATO:0000170 obsolete yield true quality PATO:0000171 obsolete absolute yield true quality PATO:0000172 obsolete relative yield true quality PATO:0000173 obsolete function true quality PATO:0000174 obsolete autonomic function true quality PATO:0000175 obsolete behavioral function true quality PATO:0000176 obsolete metabolic function true quality PATO:0000177 obsolete physiological function true quality PATO:0000178 obsolete relative function true quality PATO:0000179 obsolete body position true quality PATO:0000180 obsolete body tone true quality PATO:0000181 obsolete piloerection true quality PATO:0000182 obsolete abdominal tone true quality PATO:0000183 obsolete limb tone true quality PATO:0000184 obsolete arousal true A behavioral quality inhering in a bearer by virtue of having physical steadiness. quality PATO:0000185 balance A behavioral quality inhering in a bearer by virtue of having physical steadiness. thefreedictionary:thefreedictionary An organismal quality inhering in a bearer by virtue of the bearer's behavior aggregate of the responses or reactions or movements in a given situation. PATO:0001722 behavioural quality quality PATO:0000186 behavioral quality An organismal quality inhering in a bearer by virtue of the bearer's behavior aggregate of the responses or reactions or movements in a given situation. PATOC:GVG A relational quality of occurrent inhering in a bearer by virtue of the bearer's ability to consume a resource. quality propensity to consume PATO:0000187 Use GO:0007631 obsolete consumption quality true A relational quality of occurrent inhering in a bearer by virtue of the bearer's ability to consume a resource. PATOC:GVG A behavioral quality inhering in a bearer by virtue of the bearer's having or lacking skillful and effective interaction of movement. quality PATO:0000188 coordination A behavioral quality inhering in a bearer by virtue of the bearer's having or lacking skillful and effective interaction of movement. PATOC:GVG A behavioral quality inhering in a bearer by virtue of whether the bearer's disposition to perceive differences between two or more stimuli. quality PATO:0000189 discrimination A behavioral quality inhering in a bearer by virtue of whether the bearer's disposition to perceive differences between two or more stimuli. PATOC:GVG quality PATO:0000190 obsolete gait true quality PATO:0000191 obsolete learning_and memory true quality PATO:0000192 obsolete locomotor_activity true quality PATO:0000193 obsolete mating true quality PATO:0000194 obsolete spontaneous_activity true quality PATO:0000195 obsolete startle response true quality PATO:0000196 obsolete vocalization true quality PATO:0000197 obsolete transfer_arousal true quality PATO:0000198 obsolete absolute consumption true quality PATO:0000199 obsolete relative consumption true quality PATO:0000200 obsolete learning true quality PATO:0000201 obsolete memory true quality PATO:0000202 obsolete long term memory true quality PATO:0000203 obsolete short term memory true quality PATO:0000204 obsolete absolute locomotor_activity true quality PATO:0000205 obsolete relative locomotor_activity true quality PATO:0000206 obsolete enzyme function true quality PATO:0000207 obsolete circulatory function true quality PATO:0000208 obsolete defensive function true quality PATO:0000209 obsolete digestive function true quality PATO:0000210 obsolete excretory function true quality PATO:0000211 obsolete muscle function true quality PATO:0000212 obsolete neural function true quality PATO:0000213 obsolete neurobehavioral function true quality PATO:0000214 obsolete reproductive function true quality PATO:0000215 obsolete respiratory function true quality PATO:0000216 obsolete heart rate true quality PATO:0000217 obsolete immune function true quality PATO:0000218 obsolete repair function true quality PATO:0000219 obsolete healing true quality PATO:0000220 obsolete regeneration true quality PATO:0000221 obsolete urination true quality PATO:0000222 obsolete muscle elevation true quality PATO:0000223 obsolete muscle strength true quality PATO:0000224 obsolete motor function true quality PATO:0000225 obsolete sensory function true quality PATO:0000226 obsolete tactile response true quality PATO:0000227 obsolete motor performance true quality PATO:0000228 obsolete auditory true quality PATO:0000229 obsolete olfactory true quality PATO:0000230 obsolete proprioreception true quality PATO:0000231 obsolete reflex true quality PATO:0000232 obsolete taste true quality PATO:0000233 obsolete touch true quality PATO:0000234 obsolete visual true quality PATO:0000235 obsolete odor_acuity true quality PATO:0000236 obsolete odor type true quality PATO:0000237 obsolete absolute odor_acuity true quality PATO:0000238 obsolete relative odor_acuity true quality PATO:0000239 obsolete blinking reflex true quality PATO:0000240 obsolete contact righting reflex true quality PATO:0000241 obsolete corneal reflex true quality PATO:0000242 obsolete flinch reflex true quality PATO:0000243 obsolete lordosis reflex true quality PATO:0000244 obsolete ocular reflex true quality PATO:0000245 obsolete pinna reflex true quality PATO:0000246 obsolete postural reflex true quality PATO:0000247 obsolete proboscis extension reflex true quality PATO:0000248 obsolete pupillary reflex true quality PATO:0000249 obsolete righting reflex true quality PATO:0000250 obsolete spinal reflex true quality PATO:0000251 obsolete startle reflex true quality PATO:0000252 obsolete suckling reflex true quality PATO:0000253 obsolete swallowing reflex true quality PATO:0000254 obsolete vibrissae reflex true quality PATO:0000255 obsolete taste_acuity true quality PATO:0000256 obsolete taste type true quality PATO:0000257 obsolete absolute taste_acuity true quality PATO:0000258 obsolete relative taste_acuity true quality PATO:0000259 obsolete visual_ability true quality PATO:0000260 obsolete visual_acuity true A quality of a single physical entity which is held by a bearer when the latter exhibits a state of growth, differentiation, or development. quality PATO:0000261 maturity A quality of a single physical entity which is held by a bearer when the latter exhibits a state of growth, differentiation, or development. Merriam-Webster:Merriam-Webster quality PATO:0000262 obsolete visual placing true quality PATO:0000263 obsolete visual threshold true quality PATO:0000264 obsolete absolute visual_ability true quality PATO:0000265 obsolete relative visual_ability true quality PATO:0000266 obsolete absolute visual_acuity true quality PATO:0000267 obsolete relative visual_acuity true quality PATO:0000268 obsolete absolute visual threshold true quality PATO:0000269 obsolete relative visual threshold true quality PATO:0000270 obsolete defecation true quality PATO:0000271 obsolete prepulse inhibition true quality PATO:0000272 obsolete relative neurobehavioral function true A reproductive quality inhering in an organism or population by virtue of the bearer's potential reproductive capacity ad measured by the number of gametes. quality PATO:0000273 fecundity A reproductive quality inhering in an organism or population by virtue of the bearer's potential reproductive capacity ad measured by the number of gametes. Wikipedia:http://en.wikipedia.org/wiki/Fecundity A reproductive quality inhering in a bearer by virtue of the bearer's initiating, sustaining, or supporting reproduction. quality PATO:0000274 fertility A reproductive quality inhering in a bearer by virtue of the bearer's initiating, sustaining, or supporting reproduction. PATOC:GVG quality PATO:0000275 obsolete gestational period true A reproductive quality inhering in the young of an animal by virtue of their number. quality litter size PATO:0000276 brood size A reproductive quality inhering in the young of an animal by virtue of their number. PATOC:GVG A fertility quality inhering in a female by virtue of the bearer's disposition to initiate, sustain, or support reproduction. quality PATO:0000277 female fertility A fertility quality inhering in a female by virtue of the bearer's disposition to initiate, sustain, or support reproduction. PATOC:GVG quality PATO:0000278 obsolete hybrid fertility true A fertility quality of inhering in a male by virtue of the bearer's disposition to initiate, sustain, or support reproduction. quality PATO:0000279 male fertility A fertility quality of inhering in a male by virtue of the bearer's disposition to initiate, sustain, or support reproduction. PATOC:GVG quality PATO:0000280 obsolete backcross fertility true quality PATO:0000281 obsolete cytoplasmic sterility true quality PATO:0000282 obsolete f1 fertility true quality PATO:0000283 obsolete f2 fertility true quality PATO:0000284 obsolete germ line dependent fertility true quality PATO:0000285 obsolete soma dependent fertility true quality PATO:0000286 obsolete cytoplasmic male sterility true quality PATO:0000287 obsolete absolute litter size true quality PATO:0000288 obsolete relative litter size true quality PATO:0000289 obsolete respiratory rate true quality PATO:0000290 obsolete absolute respiratory rate true quality PATO:0000291 obsolete relative respiratory rate true quality PATO:0000292 obsolete mobility value true quality PATO:0000293 obsolete absolute activity value true quality PATO:0000294 obsolete process value true quality PATO:0000295 obsolete relative activity value true quality PATO:0000296 obsolete speed value true A quality of a process which ends earlier than the natural end time or reference process. PATO:0001508 abolished quality incomplete PATO:0000297 TODO: the definition is incorrect. See absent. arrested A quality of a process which ends earlier than the natural end time or reference process. PATOC:LC quality PATO:0000298 obsolete not arrested value true A mobility quality of inhering in a bearer by virtue of the bearer's disposition to move freely. quality PATO:0000299 mobile A mobility quality of inhering in a bearer by virtue of the bearer's disposition to move freely. PATOC:GVG A mobility quality inhering in a bearer by virtue of the bearer's being incapable to move freely. quality fixed PATO:0000300 immobile A mobility quality inhering in a bearer by virtue of the bearer's being incapable to move freely. PATOC:GVG quality PATO:0000301 obsolete absolute speed value true quality PATO:0000302 obsolete relative speed value true A speed which is relatively high. high speed quality fast speed PATO:0000303 increased speed A speed which is relatively high. PATOC:GVG A speed which is relatively low. slow slow speed quality PATO:0000304 decreased speed A speed which is relatively low. PATOC:GVG quality PATO:0000305 obsolete age value true quality PATO:0000306 obsolete absolute age value true quality PATO:0000307 obsolete relative age value true An age which is relatively high. quality PATO:0000308 old An age which is relatively high. PATOC:GVG An age which is relatively low. quality PATO:0000309 young An age which is relatively low. PATOC:GVG quality PATO:0000310 obsolete color value true quality PATO:0000311 obsolete color hue value true quality PATO:0000312 obsolete color intensity value true quality PATO:0000313 obsolete color saturation value true quality PATO:0000314 obsolete flourescence value true quality PATO:0000315 obsolete color pattern value true quality PATO:0000316 obsolete relative color value true A color that lacks any hues as parts. quality PATO:0000317 black A color that lacks any hues as parts. PATOC:GVG A color hue with low wavelength of that portion of the visible spectrum lying between green and indigo, evoked in the human observer by radiant energy with wavelengths of approximately 420 to 490 nanometers. quality PATO:0000318 blue A color hue with low wavelength of that portion of the visible spectrum lying between green and indigo, evoked in the human observer by radiant energy with wavelengths of approximately 420 to 490 nanometers. Dictionary:http://dictionary.reference.com/ A color consisting of green and blue hue. quality PATO:0000319 cyan A color consisting of green and blue hue. PATOC:GVG A color hue with medium-low wavelength of that portion of the visible spectrum lying between yellow and blue, evoked in the human observer by radiant energy with wavelengths of approximately 490 to 570 nanometers. quality PATO:0000320 green A color hue with medium-low wavelength of that portion of the visible spectrum lying between yellow and blue, evoked in the human observer by radiant energy with wavelengths of approximately 490 to 570 nanometers. Dictionary:http://dictionary.reference.com/ A color consisting of red and blue hues. quality PATO:0000321 magenta A color consisting of red and blue hues. Wikipedia:http://en.wikipedia.org/wiki/Magenta A color hue with high wavelength of the long-wave end of the visible spectrum, evoked in the human observer by radiant energy with wavelengths of approximately 630 to 750 nanometers. quality PATO:0000322 red A color hue with high wavelength of the long-wave end of the visible spectrum, evoked in the human observer by radiant energy with wavelengths of approximately 630 to 750 nanometers. Dictionary:http://dictionary.reference.com/ An achromatic color of maximum brightness; the color of objects that reflect nearly all light of all visible wavelengths. quality whitish PATO:0000323 white An achromatic color of maximum brightness; the color of objects that reflect nearly all light of all visible wavelengths. Dictionary:http://dictionary.reference.com/ A color hue with medium wavelength of that portion of the visible spectrum lying between orange and green, evoked in the human observer by radiant energy with wavelengths of approximately 570 to 590 nanometers. quality PATO:0000324 yellow A color hue with medium wavelength of that portion of the visible spectrum lying between orange and green, evoked in the human observer by radiant energy with wavelengths of approximately 570 to 590 nanometers. Dictionary:http://dictionary.reference.com/ quality PATO:0000325 obsolete bright true quality PATO:0000326 obsolete dim true A color brightness which is relatively low. dark quality PATO:0000327 low brightness A color brightness which is relatively low. PATOC:MAH A color saturation which is of low purity. pale quality dull PATO:0000328 low saturation A color saturation which is of low purity. PATOC:MAH A color pattern inhering in a bearer by virtue of bearer's being marked with irregularly shaped spots or blots of a different hue or degree of saturation. blotched quality PATO:0000329 blotchy A color pattern inhering in a bearer by virtue of bearer's being marked with irregularly shaped spots or blots of a different hue or degree of saturation. Dictionary.com:Dictionary.com A spatial pattern inhering in a bearer by virtue of the bearer's magnitude of or the relationships between its repeated parts lack consistency. quality PATO:0000330 irregular spatial pattern A spatial pattern inhering in a bearer by virtue of the bearer's magnitude of or the relationships between its repeated parts lack consistency. PATOC:GVG A color quality inhering in a bearer by virtue of the bearer's being altered or spoiled in color. quality PATO:0000331 discolored A color quality inhering in a bearer by virtue of the bearer's being altered or spoiled in color. Dictionary.com:Dictionary.com true A color pattern inhering in a bearer by virtue of bearer's being marked with a round area of different hue or degree of saturation. quality PATO:0000333 spotted A color pattern inhering in a bearer by virtue of bearer's being marked with a round area of different hue or degree of saturation. PATOC:GVG true quality mottled (sensu Drosophila) PATO:0000335 obsolete variegated true A color quality inhering in a bearer by virtue of the bearer's having color. PATO:0000332 quality pigmented PATO:0000336 colored A color quality inhering in a bearer by virtue of the bearer's having color. PATOC:GVG A color quality inhering in a bearer by virtue of the bearer's lacking color. PATO:0000334 quality unpigmented PATO:0000337 colorless A color quality inhering in a bearer by virtue of the bearer's lacking color. PATOC:GVG quality PATO:0000338 obsolete compatability value true quality PATO:0000339 obsolete gametophytic compatability value true quality PATO:0000340 obsolete relative compatability value true quality PATO:0000341 obsolete sporophytic compatability value true quality PATO:0000342 obsolete gametophyte compatible value true quality PATO:0000343 obsolete gametophyte incompatible value true A compatibility quality inhering in a bearer by virtue of the bearer's being capable of harmonious coexistence. quality PATO:0000344 compatible A compatibility quality inhering in a bearer by virtue of the bearer's being capable of harmonious coexistence. PATOC:GVG A compatibility quality inhering in a bearer by virtue of the bearer's being incapable of harmonious coexistence. quality PATO:0000345 incompatible A compatibility quality inhering in a bearer by virtue of the bearer's being incapable of harmonious coexistence. PATOC:GVG quality PATO:0000346 obsolete sporophyte compatible value true quality PATO:0000347 obsolete sporophyte incompatible value true quality PATO:0000348 obsolete composition value true quality PATO:0000349 obsolete carbohydrate composition value true quality PATO:0000350 obsolete electrolyte composition value true quality PATO:0000351 obsolete macromolecular composition value true quality PATO:0000352 obsolete metabolite composition value true quality PATO:0000353 obsolete secondary product composition value true quality PATO:0000354 obsolete protein composition value true quality PATO:0000355 obsolete enzyme composition value true quality PATO:0000356 obsolete concentration value true quality PATO:0000357 obsolete protein concentration value true quality PATO:0000358 obsolete sugar concentration value true quality PATO:0000359 obsolete water content value true quality PATO:0000360 obsolete consistency value true quality PATO:0000361 obsolete gel consistency value true quality PATO:0000362 obsolete direction value true quality PATO:0000363 obsolete away true quality PATO:0000364 obsolete bi-directional true A directional quality inhering in a bearer by virtue of the bearer's direction from a higher to a lower point. quality PATO:0000365 down A directional quality inhering in a bearer by virtue of the bearer's direction from a higher to a lower point. PATOC:GVG A directional quality inhering in a bearer by virtue of the bearer's direction that is similar to the direction of an object to the north when it faces east. quality PATO:0000366 left A directional quality inhering in a bearer by virtue of the bearer's direction that is similar to the direction of an object to the north when it faces east. PATOC:GVG A directional quality inhering in a bearer by virtue of the bearer's direction that is similar to the direction of an object to the north when it faces west. quality PATO:0000367 right A directional quality inhering in a bearer by virtue of the bearer's direction that is similar to the direction of an object to the north when it faces west. PATOC:GVG quality PATO:0000368 obsolete towards1 true quality PATO:0000369 obsolete unidirectional true A directional quality inhering in a bearer by virtue of the bearer's direction from a lower to a higher point. quality PATO:0000370 up A directional quality inhering in a bearer by virtue of the bearer's direction from a lower to a higher point. PATOC:GVG quality PATO:0000371 obsolete distance value true quality PATO:0000372 obsolete absolute distance value true quality PATO:0000373 obsolete relative distance value true A distance which is greater relative to the normal or average. quality long distance PATO:0000374 increased distance A distance which is greater relative to the normal or average. PATOC:GVG A distance which is lesser relative to the normal or average. quality short distance PATO:0000375 decreased distance A distance which is lesser relative to the normal or average. PATOC:GVG quality PATO:0000376 obsolete flavor value true quality PATO:0000377 obsolete frequency value true quality PATO:0000378 obsolete absolute frequency value true quality PATO:0000379 obsolete relative frequency value true A frequency which is relatively high. high frequency quality frequent PATO:0000380 increased frequency A frequency which is relatively high. PATOC:GVG A frequency which is relatively low. low frequency quality infrequent PATO:0000381 decreased frequency A frequency which is relatively low. PATOC:GVG quality PATO:0000382 obsolete gender value true A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes. quality PATO:0000383 female A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes. MGED:MGED A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes. quality PATO:0000384 male A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes. MGED:MGED quality PATO:0000385 obsolete hardness value true A hardness quality of being rigid and resistant to pressure. quality firm impenetrable tough PATO:0000386 hard A hardness quality of being rigid and resistant to pressure. PATOC:GVG A hardness quality of giving little resistance to pressure. quality PATO:0000387 soft A hardness quality of giving little resistance to pressure. PATOC:GVG quality PATO:0000388 obsolete intensity value true A quality of a process inhering in a bearer by virtue of the bearer's having a sudden onset, sharp rise, and short course. quality PATO:0000389 acute A quality of a process inhering in a bearer by virtue of the bearer's having a sudden onset, sharp rise, and short course. dictionary:reference quality PATO:0000390 obsolete extreme true quality PATO:0000391 obsolete intense true quality PATO:0000392 obsolete limited true quality PATO:0000393 obsolete maximal true An intensity which is less than moderate in type or degree or effect or force. quality PATO:0000394 mild intensity An intensity which is less than moderate in type or degree or effect or force. PATOC:GVG An intensity which is less than extreme in type or degree or effect or force. quality PATO:0000395 moderate intensity An intensity which is less than extreme in type or degree or effect or force. Merriam-Webster:Merriam-Webster An intensity which is extremely bad or unpleasant in type or degree or effect or force. quality PATO:0000396 severe intensity An intensity which is extremely bad or unpleasant in type or degree or effect or force. WordNet:WordNet quality PATO:0000397 obsolete slight true quality PATO:0000398 obsolete vigorous true quality PATO:0000399 obsolete life span value true quality PATO:0000400 obsolete morphology value true quality PATO:0000401 obsolete shape value true A branchiness quality inhering in a bearer by virtue of the bearer's having branches. ramified ramiform quality PATO:0000402 branched A branchiness quality inhering in a bearer by virtue of the bearer's having branches. WordNet:WordNet A concave quality inhering in a bearer by virtue of the bearer's resembling a groove or fissure. quality PATO:0000403 cleft A concave quality inhering in a bearer by virtue of the bearer's resembling a groove or fissure. WordNet:WordNet A shape quality inhering in a bearer by virtue of the bearer's being curled or wound (especially in concentric rings or spirals). PATO:0001363 spiral quality helical helicoid helicoidal helix-shaped PATO:0000404 coiled A shape quality inhering in a bearer by virtue of the bearer's being curled or wound (especially in concentric rings or spirals). WordNet:WordNet A shape quality inhering in a bearer by virtue of the bearer's having parallel chains in undulate fashion on the border. quality PATO:0000405 curled A shape quality inhering in a bearer by virtue of the bearer's having parallel chains in undulate fashion on the border. PATOC:GVG A curvature quality inhering in a bearer by virtue of the bearer's having or being marked by a curve or smoothly rounded bend. bowing quality curled PATO:0000406 curved A curvature quality inhering in a bearer by virtue of the bearer's having or being marked by a curve or smoothly rounded bend. WordNet:WordNet A quality inhering in a bearer by virtue of the bearer's having a horizontal surface without a slope, tilt, or curvature. quality plate-like PATO:0000407 flat A quality inhering in a bearer by virtue of the bearer's having a horizontal surface without a slope, tilt, or curvature. web:http://www.merriam-webster.com/ true A spheroid quality inhering in a bearer by virtue of the bearer's exhibiting an equatorial diameter greater than its polar diameter. oblate spheroid quality PATO:0000409 oblate A spheroid quality inhering in a bearer by virtue of the bearer's exhibiting an equatorial diameter greater than its polar diameter. WordNet:WordNet A shape quality inhering in a bearer by virtue of the bearer's having leaflets or leaflets-like structures on each side of a common axis. quality feather-like of a leaf shape PATO:0000410 pinnate A shape quality inhering in a bearer by virtue of the bearer's having leaflets or leaflets-like structures on each side of a common axis. WordNet:WordNet A shape quality inhering in a bearer by virtue of the bearer's being such that every part of the surface or the circumference is equidistant from the center. quality round rounded PATO:0000411 circular A shape quality inhering in a bearer by virtue of the bearer's being such that every part of the surface or the circumference is equidistant from the center. thefreedictionary.com:thefreedictionary.com true A shape quality inhering in a bearer by virtue of the bearer's having an equal-sided rectangular form. quality PATO:0000413 square A shape quality inhering in a bearer by virtue of the bearer's having an equal-sided rectangular form. answers.com:answers.com A branchiness quality inhering in a bearer by virtue of the bearer's lacking branches. quality PATO:0000414 unbranched A branchiness quality inhering in a bearer by virtue of the bearer's lacking branches. PATOC:GVG A shape quality inhering in a bearer by virtue of the bearer's being not curled or wound (especially in concentric rings or spirals). quality PATO:0000415 uncoiled A shape quality inhering in a bearer by virtue of the bearer's being not curled or wound (especially in concentric rings or spirals). WordNet:WordNet quality PATO:0000416 obsolete count value true quality PATO:0000417 obsolete absolute number value true quality PATO:0000418 obsolete relative number value true true true quality PATO:0000421 obsolete nutritional value true A nutritional quality inhering in a bearer by virtue of the bearer's inability to synthesize a particular organic compound required for its growth. quality PATO:0000422 auxotrophic A nutritional quality inhering in a bearer by virtue of the bearer's inability to synthesize a particular organic compound required for its growth. Wikipedia:http://en.wikipedia.org/wiki/Auxotrophic A nutritional quality inhering in a bearer by virtue of the bearer's ability to synthesize a particular organic compound required for its growth. quality PATO:0000423 prototrophic A nutritional quality inhering in a bearer by virtue of the bearer's ability to synthesize a particular organic compound required for its growth. Wikipedia:http://en.wikipedia.org/wiki/Prototrophic quality PATO:0000424 obsolete occurence value true quality PATO:0000425 obsolete continual true true A quality of a single process inhering in a bearer by virtue of the bearer's occurring or appearing again or repeatedly. quality PATO:0000427 recurrent A quality of a single process inhering in a bearer by virtue of the bearer's occurring or appearing again or repeatedly. thefreedictionary.com:thefreedictionary.com A quality of a single process inhering in a bearer by virtue of the bearer's once or in or a few unpredictable instances. quality PATO:0000428 sporadic A quality of a single process inhering in a bearer by virtue of the bearer's once or in or a few unpredictable instances. PATO:MAH WordNet:WordNet true quality PATO:0000430 obsolete unique true quality PATO:0000431 obsolete odor value true quality PATO:0000432 obsolete parental type value true A parental quality inhering in a bearer by virtue of exhibiting the characteristic of a father. quality PATO:0000433 obsolete paternal true A parental quality inhering in a bearer by virtue of exhibiting the characteristic of a father. WordNet:WordNet A parental quality inhering in a bearer by virtue of exhibiting the characteristic of a mother. quality PATO:0000434 obsolete maternal true A parental quality inhering in a bearer by virtue of exhibiting the characteristic of a mother. WordNet:WordNet quality PATO:0000435 obsolete pattern value true quality PATO:0000436 obsolete concrete true quality PATO:0000437 obsolete sleep pattern value true A variability quality inhering in a bearer by virtue of the bearer's lacking or not exhibiting variation. uniform quality constant PATO:0000438 invariant A variability quality inhering in a bearer by virtue of the bearer's lacking or not exhibiting variation. Dictionary:http://dictionary.reference.com/ quality PATO:0000439 obsolete perseverative true A pattern quality inhering in a bearer by virtue of the bearer's having a repeatable or predictable placement. quality PATO:0000440 regular spatial pattern A pattern quality inhering in a bearer by virtue of the bearer's having a repeatable or predictable placement. PATOC:GVG A quality of a single process inhering in a bearer by virtue of the bearer's marked by tedious repetition. quality PATO:0000441 repetitive A quality of a single process inhering in a bearer by virtue of the bearer's marked by tedious repetition. thefreedictionary.com:thefreedictionary.com A sleep pattern quality inhering in a bearer by virtue of the bearer's inability to sleep. quality PATO:0000442 Consider NBO:0000422. obsolete insomnia true A sleep pattern quality inhering in a bearer by virtue of the bearer's inability to sleep. WordNet:WordNet A sleep pattern quality inhering in a bearer by virtue of the bearer's disrupted sleep during normal sleeping period; often accompanied by cataplexy, sleep paralysis. quality PATO:0000443 Consider NBO:0000423 obsolete narcolepsy true quality PATO:0000444 obsolete percentage value true quality PATO:0000445 obsolete relative percentage value true quality PATO:0000446 obsolete absolute percentage value true quality PATO:0000447 obsolete decreased percentage true quality PATO:0000448 obsolete high percentage true quality PATO:0000449 obsolete increased percentage true quality PATO:0000450 obsolete low percentage true quality PATO:0000451 obsolete pilosity value true quality PATO:0000452 obsolete relative pilosity value true A pilosity quality inhering in a bearer by virtue of the bearer's lack of hairs or bristles. quality hairless PATO:0000453 glabrous A pilosity quality inhering in a bearer by virtue of the bearer's lack of hairs or bristles. PATOC:CJM PATOC:GVG A pilosity quality inhering in a bearer by virtue of the bearer's being covered with hair or hairlike projections. quality PATO:0000454 hairy A pilosity quality inhering in a bearer by virtue of the bearer's being covered with hair or hairlike projections. PATOC:GVG A maturity quality inhering in a bearer by virtue of the bearer's having arrived at the onset of puberty (the age at which sex glands become functional) but not yet fully mature. quality PATO:0000455 pubescent A maturity quality inhering in a bearer by virtue of the bearer's having arrived at the onset of puberty (the age at which sex glands become functional) but not yet fully mature. WordNet:WordNet quality PATO:0000456 obsolete abstract true quality PATO:0000457 obsolete deviation(from_normal) value true quality PATO:0000458 obsolete presence value true quality PATO:0000459 obsolete relative quantity value true A quality inhering in a bearer by virtue of the bearer's deviation from normal or average. quality aberrant atypia atypical defective PATO:0000460 abnormal A quality inhering in a bearer by virtue of the bearer's deviation from normal or average. PATOC:GVG A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average. quality average PATO:0000461 normal A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average. PATOC:GVG A quality denoting the lack of an entity. PATO:0001996 absence absent from organism quality PATO:0000462 See documentation here: http://code.google.com/p/phenotype-ontologies/wiki/ModelingOfAbsence absent A quality denoting the lack of an entity. thefreedictionary.:thefreedictionary. A quality inhering in a bearer by virtue of being clearly visible. quality distinct PATO:0000463 conspicuous A quality inhering in a bearer by virtue of being clearly visible. thefreedictionary:thefreedictionary A quality inhering in a bearer by virtue of not being clearly visible. quality faint PATO:0000464 inconspicuous A quality inhering in a bearer by virtue of not being clearly visible. thefreedictionary:thefreedictionary quality PATO:0000465 obsolete marked true quality PATO:0000466 obsolete none true A quality inhering in a bearer by virtue of the bearer's existence. quality present in organism PATO:0000467 present A quality inhering in a bearer by virtue of the bearer's existence. PATOC:GVG true quality PATO:0000469 obsolete high true An amount which is relatively high. PATO:0000420 PATO:0000650 increased number present in greater numbers in organism supernumerary quality accessory increased PATO:0000470 increased amount An amount which is relatively high. PATOC:GVG quality PATO:0000471 obsolete low true quality PATO:0000472 obsolete quality value true quality PATO:0000473 obsolete relative_quality value true quality PATO:0000474 obsolete shattering value true quality PATO:0000475 obsolete threshability value true quality PATO:0000476 obsolete bad value true quality PATO:0000477 obsolete good value true quality PATO:0000478 obsolete poor value true quality PATO:0000479 obsolete regulation value true quality PATO:0000480 obsolete positive regulation true quality PATO:0000481 obsolete negative regulation true quality PATO:0000482 obsolete response value true quality PATO:0000483 obsolete tactile hyperresponsive true quality PATO:0000484 obsolete tactile hyporesponsive true quality PATO:0000485 obsolete mild response true quality PATO:0000486 obsolete moderate response true A response quality inhering in a bearer by virtue of the bearer's disposition to react to a stimulus or an agent. responsive quality PATO:0000487 responsive to A response quality inhering in a bearer by virtue of the bearer's disposition to react to a stimulus or an agent. PATOC:GVG A response quality inhering in a bearer by virtue of the bearer's lack of reaction to a stimulus or an agent. unresponsive quality PATO:0000488 unresponsive to A response quality inhering in a bearer by virtue of the bearer's lack of reaction to a stimulus or an agent. PATOC:GVG quality PATO:0000489 obsolete vigorous response true quality PATO:0000490 obsolete rhythym value true quality PATO:0000491 obsolete sensitivity value true quality PATO:0000492 obsolete absolute rhythym value true quality PATO:0000493 obsolete amplitude value true quality PATO:0000494 obsolete period value true quality PATO:0000495 obsolete persistence value true quality PATO:0000496 obsolete phase value true quality PATO:0000497 obsolete relative rhythym value true A duration quality of a process which is relatively high. PATO:0000715 high time increased period increased time quality chronic prolonged period slow time PATO:0000498 increased duration A duration quality of a process which is relatively high. PATOC:GVG A duration quality of a process which is relatively low. PATO:0000716 decreased period decreased time low period shortened period quality fast time PATO:0000499 decreased duration A duration quality of a process which is relatively low. PATOC:GVG A phase which occurs earlier than the natural start time. quality PATO:0000500 advanced phase A phase which occurs earlier than the natural start time. PATOC:GVG A phase which occurs during dark cycle. quality PATO:0000501 dark phase A phase which occurs during dark cycle. PATOC:GVG A quality of a process which starts later than the natural start time or the reference process. quality late PATO:0000502 delayed A quality of a process which starts later than the natural start time or the reference process. PATOC:LC A phase which occurs during the light cycle. quality PATO:0000503 light phase A phase which occurs during the light cycle. PATOC:GVG A rhythm quality inhering in a bearer by virtue of the bearer's lacking rhythm. quality PATO:0000504 arrhythmic A rhythm quality inhering in a bearer by virtue of the bearer's lacking rhythm. PATOC:GVG A rhythm quality inhering in a bearer by virtue of the bearer's having rhythm. quality PATO:0000505 rhythmic A rhythm quality inhering in a bearer by virtue of the bearer's having rhythm. PATOC:GVG quality PATO:0000506 obsolete absolute sensitivity value true quality PATO:0000507 obsolete disease sensitivity value true quality PATO:0000508 obsolete relative sensitivity value true quality PATO:0000509 obsolete stress sensitivity value true quality PATO:0000510 obsolete temperature sensitivity value true quality PATO:0000511 obsolete absolute disease sensitivity value true quality PATO:0000512 obsolete relative disease sensitivity value true A quality inhering in a bearer by virtue of the bearer's lacking sensitivity toward an external stimulus. insensitive quality resistant PATO:0000513 insensitive toward A quality inhering in a bearer by virtue of the bearer's lacking sensitivity toward an external stimulus. PATOC:GVG quality PATO:0000514 obsolete intolerant value true A resistance quality inhering in a bearer by virtue of its disposition to endure or being insensitive to a stimulus. tolerant quality PATO:0000515 tolerant to A resistance quality inhering in a bearer by virtue of its disposition to endure or being insensitive to a stimulus. PATOC:GVG A quality inhering in a bearer by virtue of the bearer's having sensitivity toward an external stimulus. sensitive quality PATO:0000516 sensitive toward A quality inhering in a bearer by virtue of the bearer's having sensitivity toward an external stimulus. PATOC:GVG quality PATO:0000517 obsolete abiotic stress sensitivity value true quality PATO:0000518 obsolete chemical sensitivity value true quality PATO:0000519 obsolete humidity sensitivity value true quality PATO:0000520 obsolete radiation sensitivity value true quality PATO:0000521 obsolete drug sensitivity value true quality PATO:0000522 obsolete herbicide sensitivity value true quality PATO:0000523 obsolete insecticide sensitivity value true quality PATO:0000524 obsolete plant growth hormone sensitivity value true quality PATO:0000525 obsolete soil composition sensitivity value true quality PATO:0000526 obsolete absolute drug sensitivity value true quality PATO:0000527 obsolete relative drug sensitivity value true quality PATO:0000528 obsolete drug insensitive true quality PATO:0000529 obsolete drug sensitive true quality PATO:0000530 obsolete soil nutrient sensitivity value true quality PATO:0000531 obsolete macronutrient sensitivity value true quality PATO:0000532 obsolete micronutrient sensitivity value true quality PATO:0000533 obsolete osmotic response sensitivity true quality PATO:0000534 obsolete p h sensitivity value true quality PATO:0000535 obsolete salt sensitivity value true quality PATO:0000536 obsolete water sensitivity value true quality PATO:0000537 obsolete acid sensitivity value true quality PATO:0000538 obsolete alkali sensitivity value true quality PATO:0000539 obsolete drought sensitivity value true quality PATO:0000540 obsolete flooding sensitivity value true quality PATO:0000541 obsolete photosensitivity value true quality PATO:0000542 obsolete absolute photosensitivity value true quality PATO:0000543 obsolete light intensivity sensitivity value true quality PATO:0000544 obsolete light_quality sensitivity value true quality PATO:0000545 obsolete relative photosensitivity value true A photosensitivity quality inhering in a bearer by virtue of the bearer's lacking photosensitivity. quality photoresistant PATO:0000546 photoinsensitive A photosensitivity quality inhering in a bearer by virtue of the bearer's lacking photosensitivity. PATOC:GVG A photosensitivity quality inhering in a bearer by virtue of the bearer's exhibiting photosensitivity. quality PATO:0000547 photosensitive A photosensitivity quality inhering in a bearer by virtue of the bearer's exhibiting photosensitivity. PATOC:GVG quality PATO:0000548 obsolete blue light sensitivity value true quality PATO:0000549 obsolete far red light sensitivity value true quality PATO:0000550 obsolete red light sensitivity value true quality PATO:0000551 obsolete u v light sensitivity value true quality PATO:0000552 obsolete absolute temperature sensitivity value true quality PATO:0000553 obsolete relative temperature sensitivity value true quality PATO:0000554 obsolete cold sensitive true quality PATO:0000555 obsolete heat sensitive true quality thermoresistant PATO:0000556 obsolete thermoinsensitive true quality PATO:0000557 obsolete thermosensitive true quality PATO:0000558 obsolete size value true quality PATO:0000559 obsolete absolute size value true quality PATO:0000560 obsolete height value true quality PATO:0000561 obsolete length value true quality PATO:0000562 obsolete mass value true quality PATO:0000563 obsolete relative size value true quality PATO:0000564 obsolete thickness value true quality PATO:0000565 obsolete volume value true quality :breadth PATO:0000566 obsolete width value true quality PATO:0000567 obsolete absolute height value true quality PATO:0000568 obsolete relative height value true A height which is relatively low. quality short PATO:0000569 decreased height A height which is relatively low. PATOC:GVG A height which is relatively high. quality tall PATO:0000570 increased height A height which is relatively high. PATOC:GVG quality PATO:0000571 obsolete absolute length value true quality PATO:0000572 obsolete relative length value true A length quality which is relatively large. long quality PATO:0000573 increased length A length quality which is relatively large. PATOC:GVG A length quality which is relatively small. short quality shortened stubby PATO:0000574 decreased length A length quality which is relatively small. PATOC:GVG quality PATO:0000575 obsolete absolute mass value true quality PATO:0000576 obsolete relative mass value true quality PATO:0000577 obsolete weight value true true true quality PATO:0000580 obsolete absolute weight value true quality PATO:0000581 obsolete relative weight value true A weight which is relatively high. heavy high weight quality PATO:0000582 increased weight A weight which is relatively high. PATOC:GVG A weight which is relatively low. light weight low weight quality PATO:0000583 decreased weight A weight which is relatively low. PATOC:GVG An increased size quality inhering in a bearer by virtue of the bearer's exhibiting enlargement of a cell or constituent group of cells (for example, organ). hypertrophy quality PATO:0000584 hypertrophic An increased size quality inhering in a bearer by virtue of the bearer's exhibiting enlargement of a cell or constituent group of cells (for example, organ). PATOC:MAH A decreased size quality inhering in a bearer by virtue of the bearer's exhibiting reduced size of a cell or constituent group of cells (for example, organ). PATO:0000412 shrunken quality PATO:0000585 hypotrophic A decreased size quality inhering in a bearer by virtue of the bearer's exhibiting reduced size of a cell or constituent group of cells (for example, organ). PATOC:MAH A size quality which is relatively high. PATO:0001202 quality big enlarged expanded great large PATO:0000586 increased size A size quality which is relatively high. PATOC:GVG A size quality which is relatively low. hypoplasia underdeveloped quality reduced small tiny PATO:0000587 decreased size A size quality which is relatively low. PATOC:GVG A quality inhering in a bearer by virtue of the bearer's being a remnant structure from earlier development or evolution. quality PATO:0000588 May be part of an animal (such as an organ or bone) that is no longer used by the species and has therefore become smaller or less developed. vestigial A quality inhering in a bearer by virtue of the bearer's being a remnant structure from earlier development or evolution. PATOC:MAH quality PATO:0000589 obsolete absolute thickness value true quality PATO:0000590 obsolete relative thickness value true A thickness which is relatively high. high thickness stout thickened quality thick PATO:0000591 increased thickness A thickness which is relatively high. PATOC:GVG A thickness which is relatively low. low thickness quality slender thin PATO:0000592 decreased thickness A thickness which is relatively low. PATOC:GVG quality PATO:0000593 obsolete absolute volume value true quality PATO:0000594 obsolete relative volume value true A volume which is relatively high. high volume quality large volume PATO:0000595 increased volume A volume which is relatively high. PATOC:GVG A volume which is relatively low. low volume quality small volume PATO:0000596 decreased volume A volume which is relatively low. PATOC:GVG quality PATO:0000597 obsolete absolute width value true quality PATO:0000598 obsolete relative width value true A width which is relatively small. quality narrow PATO:0000599 decreased width A width which is relatively small. PATOC:GVG A width which is relatively large. quality broad wide wide/broad PATO:0000600 increased width A width which is relatively large. PATOC:GVG quality PATO:0000601 obsolete spatial value true quality PATO:0000602 obsolete angle value true quality PATO:0000603 obsolete closure value true quality PATO:0000604 obsolete orientation value true quality location position PATO:0000605 obsolete placement value true quality PATO:0000606 obsolete absolute angle value true quality PATO:0000607 obsolete relative angle value true A morphological quality inhering in a bearer by virtue of the bearer's affording blocked passage or view. quality blocked PATO:0000608 closed A morphological quality inhering in a bearer by virtue of the bearer's affording blocked passage or view. answers.com:answers.com A morphological quality inhering in a bearer by virtue of the bearer's affording not completed blocked passage or view. quality PATO:0000609 closure incomplete A morphological quality inhering in a bearer by virtue of the bearer's affording not completed blocked passage or view. PATOC:GVG A morphological quality inhering in a bearer by virtue of the bearer's affording unobstructed passage or view. quality PATO:0000610 open A morphological quality inhering in a bearer by virtue of the bearer's affording unobstructed passage or view. answers.com:answers.com quality PATO:0000611 obsolete absolute orientation value true quality PATO:0000612 obsolete relative orientation value true A spatial pattern inhering in a bearer by virtue of the bearer's lacking orientation. quality PATO:0000613 disoriented A spatial pattern inhering in a bearer by virtue of the bearer's lacking orientation. PATOC:GVG A pattern where all the repeated elements are oriented in the same direction. quality PATO:0000614 oriented A pattern where all the repeated elements are oriented in the same direction. PATOC:MAH An anterioralized quality inhering in a bearer by virtue of the bearer's gross morphology containing only what are normally anterior structures. quality anterioralized PATO:0000615 wholly anterioralized An anterioralized quality inhering in a bearer by virtue of the bearer's gross morphology containing only what are normally anterior structures. PATOC:GVG A symmetry quality inhering in a bearer by virtue of the bearer's lacking symmetry. asymmetric asymmetry quality PATO:0000616 asymmetrical A symmetry quality inhering in a bearer by virtue of the bearer's lacking symmetry. PATOC:GVG A shape quality inhering in a bearer by virtue of the bearer's having one or more angle(s) in its length. angled flexed quality PATO:0000617 bent A shape quality inhering in a bearer by virtue of the bearer's having one or more angle(s) in its length. PATOC:MAH A positional quality inhering in a bearer by virtue of the bearer's having two sides; two-sided. quality PATO:0000618 bilateral A positional quality inhering in a bearer by virtue of the bearer's having two sides; two-sided. thefreedictionary.com:thefreedictionary.com A positional quality inhering in a bearer by virtue of the bearer's being overfilled. quality PATO:0000619 crowded A positional quality inhering in a bearer by virtue of the bearer's being overfilled. WordNet:WordNet A dorsalized quality inhering in a bearer by virtue of the bearer's gross morphology containing only what are normally dorsal structures. quality dorsalized PATO:0000620 wholly dorsalized A dorsalized quality inhering in a bearer by virtue of the bearer's gross morphology containing only what are normally dorsal structures. PATOC:melissa true A positional quality inhering in a bearer by virtue of the bearer's being upright in position or posture. upright quality PATO:0000622 erect A positional quality inhering in a bearer by virtue of the bearer's being upright in position or posture. WordNet:WordNet A quality inhering in a bearer by virtue of the bearer's protruding or projecting from the body. quality prolapse prolapsed PATO:0000623 exserted A quality inhering in a bearer by virtue of the bearer's protruding or projecting from the body. sdvc:sdvc A spatial quality inhering in a bearer by virtue of the bearer's becoming joined together with an additional entity. inserted quality introduced into PATO:0000624 inserted into A spatial quality inhering in a bearer by virtue of the bearer's becoming joined together with an additional entity. PATOC:nw An oriented quality inhering in a bearer by virtue of the bearer's being reversed in position, order, or condition. quality backward reversed PATO:0000625 inverted An oriented quality inhering in a bearer by virtue of the bearer's being reversed in position, order, or condition. PATOC:GVG A positional quality inhering in a bearer by virtue of the bearer's being moved or displaced to one side so as to make lateral. quality PATO:0000626 lateralized A positional quality inhering in a bearer by virtue of the bearer's being moved or displaced to one side so as to make lateral. thefreedictionary.com:thefreedictionary.com A spatial pattern quality inhering in a bearer by virtue of the bearer's being confined or restricted to a particular location. focal localised quality PATO:0000627 localized A spatial pattern quality inhering in a bearer by virtue of the bearer's being confined or restricted to a particular location. WordNet:WordNet A positional quality inhering in a bearer by virtue the bearer's being changed in abnormal position. PATO:0000621 ectopic mislocalized quality PATO:0000628 mislocalised A positional quality inhering in a bearer by virtue the bearer's being changed in abnormal position. PATOC:GVG A positional quality inhering in a bearer by virtue of the bearer's having mistakenly taken course, way, or passage; ill-routed. quality PATO:0000629 misrouted A positional quality inhering in a bearer by virtue of the bearer's having mistakenly taken course, way, or passage; ill-routed. NDI:NDI A posterioralized quality inhering in a bearer by virtue of the bearer's gross morphology containing only what are normally posterior structures. quality posterioralized PATO:0000630 wholly posterioralized A posterioralized quality inhering in a bearer by virtue of the bearer's gross morphology containing only what are normally posterior structures. PATOC:GVG A positional quality inhering in a bearer by virtue of the bearer's being stretched out and lying at full length along the ground. quality PATO:0000631 prostrate A positional quality inhering in a bearer by virtue of the bearer's being stretched out and lying at full length along the ground. thefreedictionary.com:thefreedictionary.com A symmetry quality inhering in a bearer by virtue of the bearer's being capable of division by a longitudinal plane into similar halves. symmetric quality PATO:0000632 similar pattern in both halves symmetrical A symmetry quality inhering in a bearer by virtue of the bearer's being capable of division by a longitudinal plane into similar halves. PATOC:GVG A spatial pattern inhering in a bearer by virtue of the bearer's being not overfilled. quality PATO:0000633 uncrowded A spatial pattern inhering in a bearer by virtue of the bearer's being not overfilled. PATOC:GVG A spatial pattern inhering in a bearer by virtue of the bearer's involvement of only one part or side. quality PATO:0000634 unilateral A spatial pattern inhering in a bearer by virtue of the bearer's involvement of only one part or side. WordNet:WordNet A spatial pattern inhering in a bearer by virtue of the bearer's not being confined or restricted to a particular location. quality PATO:0000635 unlocalised A spatial pattern inhering in a bearer by virtue of the bearer's not being confined or restricted to a particular location. WordNet:WordNet A ventralized quality inhering in a bearer by virtue of the bearer's gross morphology containing only what are normally ventral structures. quality ventralized PATO:0000636 wholly ventralized A ventralized quality inhering in a bearer by virtue of the bearer's gross morphology containing only what are normally ventral structures. PATOC:GVG quality PATO:0000637 obsolete structure value true A structural quality inhering in a bearer by virtue of the bearer's consisting of blebbing of the nucleus and DNA fragmentation due to the cell undergoing a specific form of programmed cell death termed apoptosis. GO:0006915 quality PATO:0000638 apoptotic A structural quality inhering in a bearer by virtue of the bearer's consisting of blebbing of the nucleus and DNA fragmentation due to the cell undergoing a specific form of programmed cell death termed apoptosis. PATOC:GVG A structural quality inhering in a bearer whose structure deteriorates or is lost over time due to an active pathological process. degeneration quality PATO:0000639 degenerate A structural quality inhering in a bearer whose structure deteriorates or is lost over time due to an active pathological process. PATOC:PortlandMeetingFeb2015 PATOC:mb A structural quality inhering in a bearer by virtue of the bearer's exhibiting an alteration in size, shape or organization of its constituent cells. dysplasia quality PATO:0000640 dysplastic A structural quality inhering in a bearer by virtue of the bearer's exhibiting an alteration in size, shape or organization of its constituent cells. PATOC:MAH quality PATO:0000641 obsolete deposition defective true A structural quality inhering in a bearer by virtue of the bearer's being merged with another entity. fused fused to quality coalesced joined with merged with PATO:0000642 fused with A structural quality inhering in a bearer by virtue of the bearer's being merged with another entity. PATOC:GVG A quality inhering in a bearer by virtue of the bearer's bodily structure that has protruded through an abnormal opening in the wall that contains it. quality PATO:0000643 herniated A quality inhering in a bearer by virtue of the bearer's bodily structure that has protruded through an abnormal opening in the wall that contains it. spinalstenosis:spinalstenosis A increased size quality inhering in an organ or tissue by virtue of the bearer's exhibiting increased number of cells. PATO:0000943 hyperplasia quality overdeveloped PATO:0000644 hyperplastic A increased size quality inhering in an organ or tissue by virtue of the bearer's exhibiting increased number of cells. Wikipedia:http://en.wikipedia.org/wiki/Hyperplastic A decreased size quality inhering in a bearer by virtue of the bearer's exhibiting reduced number of cells within an organ or tissue. PATO:0000942 hypoplasia quality underdeveloped PATO:0000645 hypoplastic A decreased size quality inhering in a bearer by virtue of the bearer's exhibiting reduced number of cells within an organ or tissue. PATOC:GVG A morphological quality inhering in a bearer by virtue of the bearer's being distorted during formation. malformation quality PATO:0000646 malformed A morphological quality inhering in a bearer by virtue of the bearer's being distorted during formation. PATOC:MAH A structural quality inhering in a bearer by virtue of the bearer's undergoing unprogrammed cell death. quality PATO:0000647 necrotic A structural quality inhering in a bearer by virtue of the bearer's undergoing unprogrammed cell death. Wikipedia:http://en.wikipedia.org/wiki/Necrotic A morphological quality inhering in a bearer by virtue of the bearer's being blocked or filled with obstacles or an obstacle. quality PATO:0000648 obstructed A morphological quality inhering in a bearer by virtue of the bearer's being blocked or filled with obstacles or an obstacle. thefreedictionary.com:thefreedictionary.com true true A structural quality inhering in a bearer by virtue of the bearer's being no longer merged with another entity. unfused quality PATO:0000651 unfused from A structural quality inhering in a bearer by virtue of the bearer's being no longer merged with another entity. PATOC:nw quality PATO:0000652 obsolete substance value true quality PATO:0000653 obsolete addictive substance value true quality PATO:0000654 obsolete alcochol value true quality PATO:0000655 obsolete amphetamine value true quality PATO:0000656 obsolete time_quantity true quality PATO:0000657 obsolete length_quantity true quality PATO:0000658 obsolete metamphetamine value true quality PATO:0000659 obsolete temparature_quantity true quality PATO:0000660 obsolete angle_quantity true quality PATO:0000661 obsolete solid substance value true quality PATO:0000662 obsolete volume_quantity true quality PATO:0000663 obsolete occurrent true quality PATO:0000664 obsolete substance_quantity true A color brightness which is relatively high. light quality PATO:0000665 high brightness A color brightness which is relatively high. PATOC:MAH quality PATO:0000666 obsolete energy_quantity true quality PATO:0000667 obsolete liquid substance value true quality PATO:0000668 obsolete mass_quantity true quality PATO:0000669 obsolete concentration_unit true quality PATO:0000670 obsolete saccharin versus water value true quality PATO:0000671 obsolete water value true quality PATO:0000672 obsolete unit true quality PATO:0000673 obsolete temperature value true quality PATO:0000674 obsolete absolute temperature value true quality PATO:0000675 obsolete body temperature value true quality PATO:0000676 obsolete relative temperature value true true true quality PATO:0000679 obsolete temporal value true quality PATO:0000680 obsolete absolute temporal value true quality PATO:0000681 obsolete incidence value true quality PATO:0000682 obsolete rate value true quality PATO:0000683 obsolete relative temporal value true quality PATO:0000684 obsolete absolute incidence value true quality PATO:0000685 obsolete relative incidence value true quality PATO:0000686 obsolete absolute rate value true quality PATO:0000687 obsolete relative rate value true A quality of a single process inhering in a bearer by virtue of the bearer's not occurring or existing at the same time or having the same period or phase. quality PATO:0000688 asynchronous A quality of a single process inhering in a bearer by virtue of the bearer's not occurring or existing at the same time or having the same period or phase. WordNet:WordNet A quality of a single process inhering in a bearer by virtue of the bearer's being uninterrupted in time, sequence, substance, or extent. PATO:0000429 uninterrupted quality PATO:0000689 continuous A quality of a single process inhering in a bearer by virtue of the bearer's being uninterrupted in time, sequence, substance, or extent. thefreedictionary.com:thefreedictionary.com A quality of a single process inhering in a bearer by virtue of the bearer's being marked by breaks or interruptions. PATO:0000426 interrupted quality intermittent PATO:0000690 discontinuous A quality of a single process inhering in a bearer by virtue of the bearer's being marked by breaks or interruptions. thefreedictionary.com:thefreedictionary.com true A quality of a single process inhering in a bearer by virtue of the bearer's origin or development at an unusual time or out of the regular sequence. quality PATO:0000692 heterochronic A quality of a single process inhering in a bearer by virtue of the bearer's origin or development at an unusual time or out of the regular sequence. answers.com:answers.com quality PATO:0000693 obsolete late true A quality of a process which starts earlier than the natural start time or the reference process. PATO:0000691 PATO:0002086 advanced quality early precocious PATO:0000694 premature A quality of a process which starts earlier than the natural start time or the reference process. PATO:LC A quality of a single process inhering in a bearer by virtue of the bearer's occurring or existing at the same time or having the same period or phase. quality PATO:0000695 synchronous A quality of a single process inhering in a bearer by virtue of the bearer's occurring or existing at the same time or having the same period or phase. PATOC:GVG quality PATO:0000696 obsolete texture value true quality PATO:0000697 obsolete relative texture value true quality PATO:0000698 obsolete floury true quality PATO:0000699 obsolete glutinous true A texture quality inhering in a bearer by virtue of the bearer's irregular surface. PATO:0001616 coarse quality PATO:0000700 rough A texture quality inhering in a bearer by virtue of the bearer's irregular surface. PATOC:GVG A texture quality inhering in a bearer by virtue of the bearer's processing a surface free of roughness or irregularities. quality PATO:0000701 smooth A texture quality inhering in a bearer by virtue of the bearer's processing a surface free of roughness or irregularities. PATOC:GVG quality PATO:0000702 obsolete threshold value true quality PATO:0000703 obsolete absolute threshold value true quality PATO:0000704 obsolete pain threshold value true quality PATO:0000705 obsolete relative threshold value true A threshold which is relatively high. PATO:0000709 high threshold quality PATO:0000706 increased threshold A threshold which is relatively high. PATOC:GVG true A threshold which is relatively low. PATO:0000707 low threshold quality PATO:0000708 decreased threshold A threshold which is relatively low. PATOC:GVG true quality PATO:0000710 obsolete time value true quality PATO:0000711 obsolete absolute time value true quality PATO:0000712 obsolete bouts value true quality PATO:0000713 obsolete relative time value true quality PATO:0000714 obsolete latency value true true true quality PATO:0000717 obsolete viability value true A viability quality inhering in a population by virtue of the bearer's long term survival inability. quality PATO:0000718 lethal (sensu genetics) A viability quality inhering in a population by virtue of the bearer's long term survival inability. PATOC:GVG A viability quality inhering in a bearer or a population by virtue of the bearer's ability to survive or the long term survival ability of a given population. quality PATO:0000719 viable A viability quality inhering in a bearer or a population by virtue of the bearer's ability to survive or the long term survival ability of a given population. PATOC:GVG quality PATO:0000720 obsolete yield value true quality PATO:0000721 obsolete absolute yield value true quality PATO:0000722 obsolete relative yield value true quality PATO:0000723 obsolete high yield true quality PATO:0000724 obsolete low yield true quality PATO:0000725 obsolete function value true quality PATO:0000726 obsolete autonomic function value true quality PATO:0000727 obsolete behavioral function value true quality PATO:0000728 obsolete metabolic function value true quality PATO:0000729 obsolete physiological function value true quality PATO:0000730 obsolete relative function value true quality PATO:0000731 obsolete body position value true quality PATO:0000732 obsolete body tone value true quality PATO:0000733 obsolete piloerection value true quality PATO:0000734 obsolete abdominal tone value true quality PATO:0000735 obsolete limb tone value true quality PATO:0000736 obsolete dysfunctional value true quality PATO:0000737 obsolete functional value true quality PATO:0000738 obsolete enzyme function value true quality PATO:0000739 obsolete absolute enzyme function value true quality PATO:0000740 obsolete relative enzyme function value true quality PATO:0000741 obsolete high enzyme function value true quality PATO:0000742 obsolete low enzyme function value true quality PATO:0000743 obsolete arousal value true quality PATO:0000744 obsolete balance value true quality PATO:0000745 obsolete behavioral quality value true quality PATO:0000746 obsolete consumption value true quality PATO:0000747 obsolete coordination value true quality PATO:0000748 obsolete discrimination value true quality PATO:0000749 obsolete gait value true quality PATO:0000750 obsolete learning and memory value true quality PATO:0000751 obsolete locomotor activity value true quality PATO:0000752 obsolete mating value true quality PATO:0000753 obsolete spontaneous activity value true quality PATO:0000754 obsolete startle response true quality PATO:0000755 obsolete vocalization value true quality PATO:0000756 obsolete transfer arousal value true A balance quality inhering in a bearer by virtue of the bearer's having balance. quality PATO:0000757 balanced A balance quality inhering in a bearer by virtue of the bearer's having balance. PATOC:GVG A balance quality inhering in a bearer by virtue of the bearer's lacking balance. quality PATO:0000758 unbalanced A balance quality inhering in a bearer by virtue of the bearer's lacking balance. PATOC:GVG A behavioral quality inhering in a bearer by virtue of the bearer's exhibiting paralytic behaviour when subjected to mechanical shock. quality PATO:0000759 bang sensitive A behavioral quality inhering in a bearer by virtue of the bearer's exhibiting paralytic behaviour when subjected to mechanical shock. PATOC:flybase A behavioral quality of a process inhering in a bearer by virtue of the bearer's exhibiting increased activity. hyperactive quality PATO:0000760 increased behavioural activity A behavioral quality of a process inhering in a bearer by virtue of the bearer's exhibiting increased activity. PATOC:GVG A behavioral quality of a process inhering in a bearer by virtue of the bearer's exhibiting reduced activity. hypoactive quality PATO:0000761 decreased behavioural activity A behavioral quality of a process inhering in a bearer by virtue of the bearer's exhibiting reduced activity. PATOC:GVG Diminished, damaged, or weakened. PATO:0001624 quality PATO:0000762 obsolete impaired true Diminished, damaged, or weakened. answers.com:answers.com A behavioral quality inhering in a bearer by virtue of the bearer's being affected by loss of the ability to move a body part. palsy quality PATO:0000763 paralysed A behavioral quality inhering in a bearer by virtue of the bearer's being affected by loss of the ability to move a body part. PATOC:GVG A behavioral quality inhering in a bearer by virtue of the bearer's receiving or being subjected to an action without responding or initiating an action in return. quality PATO:0000764 passive A behavioral quality inhering in a bearer by virtue of the bearer's receiving or being subjected to an action without responding or initiating an action in return. www.answers.com:www.answers.com quality PATO:0000765 obsolete absolute consumption value true quality PATO:0000766 obsolete relative consumption value true A consumption which is relatively high. high consumption quality increased propensity to consume PATO:0000767 Use GO:0007631 obsolete increased consumption true A consumption which is relatively high. PATOC:GVG A consumption which is relatively low. low consumption quality decreased propensity to consume PATO:0000768 Use GO:0007631 obsolete decreased consumption true A consumption which is relatively low. PATOC:GVG A coordination quality of inhering in a bearer by virtue of the bearer's having skillful and effective interaction of movement. quality PATO:0000769 coordinated A coordination quality of inhering in a bearer by virtue of the bearer's having skillful and effective interaction of movement. PATOC:GVG A coordination quality of inhering in a bearer by virtue of the bearer's lacking skillful and effective interaction of movement. quality PATO:0000770 uncoordinated A coordination quality of inhering in a bearer by virtue of the bearer's lacking skillful and effective interaction of movement. PATOC:GVG A preference quality in a bearer by virtue of the bearer's disliking a perceived stimulus. quality PATO:0000771 aversion A preference quality in a bearer by virtue of the bearer's disliking a perceived stimulus. PATOC:GVG A preference quality in a bearer by virtue of the bearer's having no preference to a perceived stimulus. quality PATO:0000772 indifference A preference quality in a bearer by virtue of the bearer's having no preference to a perceived stimulus. PATOC:GVG A discrimination quality in a bearer by virtue of the bearer's liking a perceived stimulus. quality PATO:0000773 preference A discrimination quality in a bearer by virtue of the bearer's liking a perceived stimulus. PATOC:GVG quality PATO:0000774 obsolete bizarre gate true quality PATO:0000775 obsolete learning value true quality PATO:0000776 obsolete memory value true quality PATO:0000777 obsolete long term memory value true quality PATO:0000778 obsolete short term memory value true quality PATO:0000779 obsolete absolute locomotor activity value true quality PATO:0000780 obsolete relative locomotor activity value true quality PATO:0000781 obsolete circulatory function value true quality PATO:0000782 obsolete defensive function value true quality PATO:0000783 obsolete digestive function value true quality PATO:0000784 obsolete excretory function value true quality PATO:0000785 obsolete muscle function value true quality PATO:0000786 obsolete neural function value true quality PATO:0000787 obsolete neurobehavioral function value true quality PATO:0000788 obsolete reproductive function value true quality PATO:0000789 obsolete respiratory function value true quality PATO:0000790 obsolete heart rate value true quality PATO:0000791 obsolete immune function value true quality PATO:0000792 obsolete repair function value true quality PATO:0000793 obsolete immubocompetent value true quality PATO:0000794 obsolete immunodeficient value true quality PATO:0000795 obsolete healing value true quality PATO:0000796 obsolete regeneration value true quality PATO:0000797 obsolete urination value true quality PATO:0000798 obsolete defecation value true quality PATO:0000799 obsolete muscle elevation value true quality PATO:0000800 obsolete muscle strength value true quality PATO:0000801 obsolete motor function value true quality PATO:0000802 obsolete sensory function value true quality PATO:0000803 obsolete tactile response value true quality PATO:0000804 obsolete motor performance value true quality PATO:0000805 obsolete auditory value true quality PATO:0000806 obsolete olfactory value true quality PATO:0000807 obsolete proprioreception value true quality PATO:0000808 obsolete reflex value true quality PATO:0000809 obsolete taste value true quality PATO:0000810 obsolete touch value true quality PATO:0000811 obsolete visual value true quality PATO:0000812 obsolete odor acuity value true quality PATO:0000813 obsolete odor type value true quality PATO:0000814 obsolete taste acuity value true quality PATO:0000815 obsolete absolute odor acuity value true quality PATO:0000816 obsolete relative odor acuity value true quality PATO:0000817 obsolete anosmia true quality PATO:0000818 obsolete concentration_quantity true quality PATO:0000819 obsolete quantity true quality PATO:0000820 obsolete absolute taste acuity value true quality PATO:0000821 obsolete relative taste acuity value true quality PATO:0000822 obsolete taste type value true quality PATO:0000823 obsolete quinine taste true quality PATO:0000824 obsolete water taste true quality PATO:0000825 obsolete visual ability value true quality PATO:0000826 obsolete visual acuity value true quality PATO:0000827 obsolete visual threshold value true quality PATO:0000828 obsolete visual placing value true quality PATO:0000829 obsolete absolute visual ability value true quality PATO:0000830 obsolete relative visual ability value true quality PATO:0000831 obsolete absolute visual acuity value true quality PATO:0000832 obsolete relative visual acuity value true quality PATO:0000833 obsolete absolute visual threshold value true quality PATO:0000834 obsolete relative visual threshold value true quality PATO:0000835 obsolete auditory acuity value true quality PATO:0000836 obsolete auditory ability value true quality PATO:0000837 obsolete auditory threshold value true quality PATO:0000838 obsolete absolute auditory ability value true quality PATO:0000839 obsolete relative auditory ability value true quality PATO:0000840 obsolete absolute auditory acuity value true quality PATO:0000841 obsolete relative auditory acuity value true quality PATO:0000842 obsolete absolute auditory threshold value true quality PATO:0000843 obsolete relative auditory threshold value true quality PATO:0000844 obsolete auditory acuity true quality PATO:0000845 obsolete auditory ability true quality PATO:0000846 obsolete auditory threshold true quality PATO:0000847 obsolete absolute auditory acuity true quality PATO:0000848 obsolete relative auditory acuity true quality PATO:0000849 obsolete absolute auditory ability true quality PATO:0000850 obsolete relative auditory ability true quality PATO:0000851 obsolete absolute auditory threshold true quality PATO:0000852 obsolete relative auditory threshold true quality PATO:0000853 obsolete blinking reflex value true quality PATO:0000854 obsolete contact righting reflex value true quality PATO:0000855 obsolete corneal reflex value true quality PATO:0000856 obsolete flinch reflex value true quality PATO:0000857 obsolete lordosis reflex value true quality PATO:0000858 obsolete ocular reflex value true quality PATO:0000859 obsolete pinna reflex value true quality PATO:0000860 obsolete postural reflex value true quality PATO:0000861 obsolete proboscis extension reflex value true quality PATO:0000862 obsolete pupillary reflex value true quality PATO:0000863 obsolete righting reflex value true quality PATO:0000864 obsolete spinal reflex value true quality PATO:0000865 obsolete startle reflex value true quality PATO:0000866 obsolete suckling reflex value true quality PATO:0000867 obsolete swallowing reflex value true quality PATO:0000868 obsolete vibrissae reflex value true quality PATO:0000869 obsolete prepulse inhibition value true quality PATO:0000870 obsolete relative neurobehavioral function value true quality PATO:0000871 obsolete aggressive true quality PATO:0000872 obsolete anxious true quality PATO:0000873 obsolete cataleptic true quality PATO:0000874 obsolete fearful true quality PATO:0000875 obsolete irritable true quality PATO:0000876 obsolete respiratory rate value true quality PATO:0000877 obsolete absolute respiratory rate value true quality PATO:0000878 obsolete relative respiratory rate value true quality PATO:0000879 obsolete fecundity value true quality PATO:0000880 obsolete fertility value true quality PATO:0000881 obsolete gestational period value true quality PATO:0000882 obsolete litter size value true quality PATO:0000883 obsolete female fertility value true quality PATO:0000884 obsolete hybrid fertility value true quality PATO:0000885 obsolete male fertility value true quality PATO:0000886 obsolete absolute litter size value true quality PATO:0000887 obsolete relative litter size value true A female fertility quality inhering in a female by virtue of the bearer's disposition to initiate, sustain, or support reproduction. quality PATO:0000888 female fertile A female fertility quality inhering in a female by virtue of the bearer's disposition to initiate, sustain, or support reproduction. PATOC:GVG quality PATO:0000889 obsolete cytoplasmic male sterility value true A male fertility quality inhering in a male by virtue of the bearer's being incapable of initiating, sustaining, or supporting reproduction. quality male infertile PATO:0000890 male sterile A male fertility quality inhering in a male by virtue of the bearer's being incapable of initiating, sustaining, or supporting reproduction. PATOC:GVG A male fertility quality inhering in a male by virtue of the bearer's being capable of initiating, sustaining, or supporting reproduction. quality PATO:0000891 male fertile A male fertility quality inhering in a male by virtue of the bearer's being capable of initiating, sustaining, or supporting reproduction. PATOC:GVG A female fertility quality inhering in a female by virtue of the bearer's being incapable of initiating, sustaining, or supporting reproduction. quality female infertile PATO:0000892 female sterile A female fertility quality inhering in a female by virtue of the bearer's being incapable of initiating, sustaining, or supporting reproduction. PATOC:GVG quality PATO:0000893 obsolete backcross fertility value true quality PATO:0000894 obsolete cytoplasmic sterility value true quality PATO:0000895 obsolete f1 fertility value true quality PATO:0000896 obsolete f2 fertility value true quality PATO:0000897 obsolete germ line dependent fertility value true quality PATO:0000898 obsolete intercross fertility value true quality PATO:0000899 obsolete soma dependent fertility value true quality PATO:0000900 obsolete backcross fertile true quality backcross infertile PATO:0000901 obsolete backcross sterile true quality PATO:0000902 obsolete chinsurah boro type value true quality PATO:0000903 obsolete cms-hl type value true quality PATO:0000904 obsolete wild abortive value true quality PATO:0000905 obsolete f1 fertile true quality F1 infertile PATO:0000906 obsolete f1 sterile true quality PATO:0000907 obsolete f2 fertile true quality F2 infertile PATO:0000908 obsolete f2 sterile true quality PATO:0000909 obsolete intercross fertile true quality intercross infertile PATO:0000910 obsolete intercross sterile true A rate which is relatively low. slow rate quality PATO:0000911 decreased rate A rate which is relatively low. PATO:GVG A rate which is relatively high. fast rate high rate quality PATO:0000912 increased rate A rate which is relatively high. PATO:GVG quality PATO:0000913 obsolete qualitative value true quality PATO:0000914 obsolete continuant true A 1-D extent quality which is equal to the dimension through an object as opposed to its length or width. quality PATO:0000915 thickness A 1-D extent quality which is equal to the dimension through an object as opposed to its length or width. WordNet:WordNet quality PATO:0000916 obsolete absolute thickness true quality PATO:0000917 obsolete relative thickness true A 3-D extent quality inhering in a bearer by virtue of the bearer's amount of 3-dimensional space it occupies. quality PATO:0000918 volume A 3-D extent quality inhering in a bearer by virtue of the bearer's amount of 3-dimensional space it occupies. PATOC:GVG quality PATO:0000919 obsolete absolute volume true quality PATO:0000920 obsolete relative volume true A 1-D extent quality which is equal to the distance from one side of an object to another side which is opposite. quality breadth PATO:0000921 width A 1-D extent quality which is equal to the distance from one side of an object to another side which is opposite. PATOC:GVG quality PATO:0000922 obsolete absolute width true quality PATO:0000923 obsolete relative width true quality PATO:0000924 obsolete relative enzyme function true quality PATO:0000925 obsolete absolute enzyme function true quality PATO:0000926 obsolete intercross fertility true A quality inhering in a bearer by virtue of the bearer's disposition to being sensitivity to the action of radiant energy. quality PATO:0000927 photosensitivity A quality inhering in a bearer by virtue of the bearer's disposition to being sensitivity to the action of radiant energy. WordNet:WordNet quality PATO:0000928 obsolete absolute photosensitivity true quality PATO:0000929 obsolete light intensivity sensitivity true quality PATO:0000930 obsolete light_quality sensitivity true quality PATO:0000931 obsolete blue light sensitivity true quality PATO:0000932 obsolete far red light sensitivity true quality PATO:0000933 obsolete red light sensitivity true quality PATO:0000934 obsolete u v light sensitivity true quality PATO:0000935 obsolete relative photosensitivity true A shape quality inhering in a bearer by virtue of the bearer's terminating abruptly by having or as if having an end or point cut off. truncate quality PATO:0000936 truncated A shape quality inhering in a bearer by virtue of the bearer's terminating abruptly by having or as if having an end or point cut off. thefreedictionary.com:thefreedictionary.com A structural quality inhering in a bearer by virtue of the bearer's lacking organisation. quality PATO:0000937 disorganized A structural quality inhering in a bearer by virtue of the bearer's lacking organisation. PATOC:GVG A structural quality inhering in a bearer by virtue of the bearer's exhibiting organisation. quality PATO:0000938 organized A structural quality inhering in a bearer by virtue of the bearer's exhibiting organisation. PATOC:GVG quality PATO:0000939 obsolete regular shape true quality PATO:0000940 obsolete irregular shape true A structural quality inhering in a cytoplasm that contains fluid filled cavities. quality PATO:0000941 vacuolated A structural quality inhering in a cytoplasm that contains fluid filled cavities. PATOC:mh true true A shape quality inhering in a bearer by virtue of the bearer's having a sharp or tapered end or point. apiculate quality PATO:0000944 sharpness A shape quality inhering in a bearer by virtue of the bearer's having a sharp or tapered end or point. PATOC:GVG A shape quality inhering in a bearer by virtue of the bearer's exhibiting a downward bending of its leaves or other plant parts. quality PATO:0000945 epinastic A shape quality inhering in a bearer by virtue of the bearer's exhibiting a downward bending of its leaves or other plant parts. PATOC:GVG A shape quality inhering in a bearer by virtue of the bearer's having a somewhat elongated form with approximately parallel sides. quality PATO:0000946 oblong A shape quality inhering in a bearer by virtue of the bearer's having a somewhat elongated form with approximately parallel sides. PATOC:GVG A spheroid quality inhering in a bearer by virtue of the bearer's being oval with two axes of symmetry, as produced by a conical section. ellipse-shaped ellipsoid elliptical quality oval ovoid PATO:0000947 elliptic A spheroid quality inhering in a bearer by virtue of the bearer's being oval with two axes of symmetry, as produced by a conical section. PATOC:GVG A concave 3-D shape quality inhering in a bearer by virtue of the bearer's having a sinus or rounded lobe at the base. cordate cordiform quality PATO:0000948 Having the shape of heart. heart shaped A concave 3-D shape quality inhering in a bearer by virtue of the bearer's having a sinus or rounded lobe at the base. PATOC:GVG A shape quality inhering in a bearer by virtue of the bearer's being abnormally flattened or coalesced. quality PATO:0000949 fasciated A shape quality inhering in a bearer by virtue of the bearer's being abnormally flattened or coalesced. PATOC:GVG A color between white and black colors. quality plumbeous PATO:0000950 grey A color between white and black colors. http://en.wikipedia.org/wiki/Grey A color that falls about midway between red and blue in hue. quality PATO:0000951 purple A color that falls about midway between red and blue in hue. Dictionary:http://dictionary.reference.com/ A color consisting of dark orange, red, of very low intensity. quality PATO:0000952 brown A color consisting of dark orange, red, of very low intensity. Wikipedia:http://en.wikipedia.org/wiki/Brown A color hue with high-medium wavelength that of that portion of the visible spectrum lying between red and yellow, evoked in the human observer by radiant energy with wavelengths of approximately 585 to 620 nanometers. quality PATO:0000953 orange A color hue with high-medium wavelength that of that portion of the visible spectrum lying between red and yellow, evoked in the human observer by radiant energy with wavelengths of approximately 585 to 620 nanometers. Wikipedia:http://en.wikipedia.org/wiki/Orange Red color having medium to high brightness and low to moderate saturation. quality PATO:0000954 pink Red color having medium to high brightness and low to moderate saturation. PATOC:MAH A fertility quality inhering in a bearer by virtue of the bearer's being capable of initiating, sustaining, or supporting reproduction. quality PATO:0000955 fertile A fertility quality inhering in a bearer by virtue of the bearer's being capable of initiating, sustaining, or supporting reproduction. PATOC:GVG A fertility quality inhering in a bearer by virtue of the bearer's being incapable of initiating, sustaining, or supporting reproduction. quality PATO:0000956 sterile A fertility quality inhering in a bearer by virtue of the bearer's being incapable of initiating, sustaining, or supporting reproduction. PATOC:GVG An optical quality which obtains by virtue of the ability of the bearer to absorb visible light. quality PATO:0000957 opacity An optical quality which obtains by virtue of the ability of the bearer to absorb visible light. PATOC:GVG quality PATO:0000958 obsolete opacity value true quality PATO:0000959 obsolete relative opacity true quality PATO:0000960 obsolete absolute opacity true quality PATO:0000961 obsolete relative opacity value true quality PATO:0000962 obsolete absolute opacity value true A optical quality inhering in a bearer by virtue of the bearer's not being clear; not transmitting or reflecting light or radiant energy. non-transparent quality clouding cloudy PATO:0000963 opaque A optical quality inhering in a bearer by virtue of the bearer's not being clear; not transmitting or reflecting light or radiant energy. PATOC:GVG A optical quality inhering in a bearer by virtue of the bearer's lacking opacity. clear hyaline quality PATO:0000964 transparent A optical quality inhering in a bearer by virtue of the bearer's lacking opacity. PATOC:GVG A pattern quality of inhering in a bearer by virtue of the correspondence in size, shape, and relative position of the bearer's parts on opposite sides of a dividing line or median plane or about a center or axis. quality PATO:0000965 symmetry A pattern quality of inhering in a bearer by virtue of the correspondence in size, shape, and relative position of the bearer's parts on opposite sides of a dividing line or median plane or about a center or axis. PATOC:GVG quality PATO:0000966 obsolete symmetry value true A shape quality inhering in a bearer by virtue of the bearer's having a sinuate margin and rippled surface. PATO:0001610 PATO:0001939 undulated undulating waved wavy quality rippled sinuate PATO:0000967 undulate A shape quality inhering in a bearer by virtue of the bearer's having a sinuate margin and rippled surface. PATOC:GVG quality PATO:0000968 obsolete albino value true A size quality inhering in a bearer by virtue of the bearer's being abnormally small. dwarfed quality PATO:0000969 dwarf-like A size quality inhering in a bearer by virtue of the bearer's being abnormally small. Answers.com:Answers.com A structural quality inhering in a bearer by virtue of the bearer's disposition to being permeated or pervaded by a gas or liquid (as by osmosis or diffusion). quality PATO:0000970 permeability A structural quality inhering in a bearer by virtue of the bearer's disposition to being permeated or pervaded by a gas or liquid (as by osmosis or diffusion). Biology-online:Biology-online quality PATO:0000971 obsolete absolute permeability true quality PATO:0000972 obsolete relative permeability true A structure quality inhering in a bearer by virtue of the bearer's disposition to admit the passage of gas or liquid through pores or interstices. quality PATO:0000973 porosity A structure quality inhering in a bearer by virtue of the bearer's disposition to admit the passage of gas or liquid through pores or interstices. PATOC:GVG quality PATO:0000974 obsolete relative porosity true quality PATO:0000975 obsolete absolute porosity true quality PATO:0000976 obsolete permeability value true quality PATO:0000977 obsolete absolute permeability value true quality PATO:0000978 obsolete relative permeability value true quality PATO:0000979 obsolete porosity value true quality PATO:0000980 obsolete absolute porosity value true quality PATO:0000981 obsolete relative porosity value true A permeability quality inhering in a bearer by virtue of the bearer's being capable to be permeated or pervaded by a gas or liquid (as by osmosis or diffusion). quality porous PATO:0000982 permeable A permeability quality inhering in a bearer by virtue of the bearer's being capable to be permeated or pervaded by a gas or liquid (as by osmosis or diffusion). Biology-online:Biology-online A permeability quality inhering in a bearer by virtue of the bearer's being incapable of being permeated or pervaded by a gas or liquid (as by osmosis or diffusion). quality PATO:0000983 impermeable A permeability quality inhering in a bearer by virtue of the bearer's being incapable of being permeated or pervaded by a gas or liquid (as by osmosis or diffusion). Biology-online:Biology-online A porosity quality inhering in a bearer by virtue of the bearer's being capable of admitting the passage of gas or liquid through pores or interstices. quality PATO:0000984 porous A porosity quality inhering in a bearer by virtue of the bearer's being capable of admitting the passage of gas or liquid through pores or interstices. PATOC:GVG A porosity quality inhering in a bearer by virtue of the bearer's being incapable of admitting the passage of gas or liquid through pores or interstices. quality PATO:0000985 non-porous A porosity quality inhering in a bearer by virtue of the bearer's being incapable of admitting the passage of gas or liquid through pores or interstices. PATOC:GVG quality PATO:0000986 obsolete absolute consistency true quality PATO:0000987 obsolete relative consistency true quality PATO:0000988 obsolete relative consistency value true quality PATO:0000989 obsolete absolute consistency value true quality PATO:0000990 obsolete consistent true quality PATO:0000991 obsolete inconsistent true A physical quality of a liquid inhering in a bearer by virtue of the bearer's disposition to internal resistance to flow. quality PATO:0000992 viscosity A physical quality of a liquid inhering in a bearer by virtue of the bearer's disposition to internal resistance to flow. PATOC:GVG quality PATO:0000993 obsolete relative viscosity true quality PATO:0000994 obsolete absolute viscosity true quality PATO:0000995 obsolete viscosity value true quality PATO:0000996 obsolete absolute viscosity value true quality PATO:0000997 obsolete relative viscosity value true A viscosity quality inhering in a bearer by virtue of the bearer's having viscosity. quality PATO:0000998 viscous A viscosity quality inhering in a bearer by virtue of the bearer's having viscosity. PATOC:GVG A quality of a single process inhering in a bearer by virtue of the bearer's successive change from one thing or state to another and back again. quality PATO:0000999 alternation A quality of a single process inhering in a bearer by virtue of the bearer's successive change from one thing or state to another and back again. WordNet:WordNet quality PATO:0001000 obsolete relative alternation true quality PATO:0001001 obsolete absolute alternation true quality PATO:0001002 obsolete alternation value true quality PATO:0001003 obsolete relative alternation value true quality PATO:0001004 obsolete absolute alternation value true A time quality inhering in a bearer by virtue of the time it elapses for the bearer to respond to a stimulus. quality PATO:0001005 This class is a candidate for obsoletion. The definition is not clear, and the placement under "delayed" is not consistent with the definition. latency A time quality inhering in a bearer by virtue of the time it elapses for the bearer to respond to a stimulus. PATOC:GVG quality PATO:0001006 obsolete absolute latency true quality PATO:0001007 obsolete relative latency true quality PATO:0001008 obsolete absolute latency value true quality PATO:0001009 obsolete relative latency value true quality PATO:0001010 obsolete relative intensity true quality PATO:0001011 obsolete absolute intensity true quality PATO:0001012 obsolete relative intensity value true quality PATO:0001013 obsolete absolute intensity value true quality PATO:0001014 obsolete absolute occurence true quality PATO:0001015 obsolete relative occurence true quality PATO:0001016 obsolete absolute occurence value true quality PATO:0001017 obsolete relative occurence value true A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. PATO:0002079 Wikipedia:Physical_property relational physical quality quality PATO:0001018 physical quality A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. PATOC:GVG A physical quality which inheres in a bearer by virtue of some influence is exerted by the bearer's mass per unit size. quality density PATO:0001019 mass density A physical quality which inheres in a bearer by virtue of some influence is exerted by the bearer's mass per unit size. WordNet:WordNet A structural quality inhering in a bearer by virtue of whether the bearer has been harmed or injured or spoiled. quality PATO:0001020 damage A structural quality inhering in a bearer by virtue of whether the bearer has been harmed or injured or spoiled. WordNet:WordNet A physical quality inhering in a bearer by virtue of the bearer's capacity to do work. quality PATO:0001021 energy A physical quality inhering in a bearer by virtue of the bearer's capacity to do work. Wikipedia:http://en.wikipedia.org/wiki/Energy A physical quality inhering in a bearer by virtue of the amount of momentum caused a certain force will produce over time. quality PATO:0001022 impulse A physical quality inhering in a bearer by virtue of the amount of momentum caused a certain force will produce over time. url:http://www.wikipremed.com/home_resources/010104_momentum_concepts.pdf A physical quality inhering in a bearer by virtue of the bearer's velocity multiplied by its mass. quality PATO:0001023 momentum A physical quality inhering in a bearer by virtue of the bearer's velocity multiplied by its mass. PATOC:GVG A physical quality inhering in a bearer by virtue of the bearer's rate of doing work. quality PATO:0001024 power A physical quality inhering in a bearer by virtue of the bearer's rate of doing work. Wikipedia:http://en.wikipedia.org/wiki/Power A physical quality that inheres in a bearer by virtue of the bearer's amount of force per unit area it exerts. quality PATO:0001025 pressure A physical quality that inheres in a bearer by virtue of the bearer's amount of force per unit area it exerts. PATOC:GVG A physical quality which is equal to the energy transferred by a force to a moving object. W quality PATO:0001026 work A physical quality which is equal to the energy transferred by a force to a moving object. Wikipedia:http://en.wikipedia.org/wiki/Work quality PATO:0001027 obsolete physical quantity true A physical quality inhering in a bearer by virtue of the rate of change of the bearer's velocity in either speed or direction. quality PATO:0001028 acceleration A physical quality inhering in a bearer by virtue of the rate of change of the bearer's velocity in either speed or direction. Wikipedia:http://en.wikipedia.org/wiki/Acceleration A physical quality inhering in a bearer by virtue of ratio of the bearer's output to the bearer's input. quality PATO:0001029 efficiency A physical quality inhering in a bearer by virtue of ratio of the bearer's output to the bearer's input. WordNet:WordNet A physical quality that exists by virtue of the rate of flow of the bearer across a given surface. quality PATO:0001030 flux A physical quality that exists by virtue of the rate of flow of the bearer across a given surface. WordNet:WordNet A physical quality inhering in a bearer by virtue of the bearer's disposition to recover its size and shape after deformation in any way. quality PATO:0001031 elasticity A physical quality inhering in a bearer by virtue of the bearer's disposition to recover its size and shape after deformation in any way. merriam-webster:merriam-webster true quality PATO:0001033 obsolete stiffness true A physical quality inhering in a bearer by virtue of the relative change in the bearer's length or the bearer's volume when being stretched or squashed. quality PATO:0001034 strain A physical quality inhering in a bearer by virtue of the relative change in the bearer's length or the bearer's volume when being stretched or squashed. PATOC:GVG A physical quality inhering in a bearer by virtue of the bearer's rate of change of momentum. force amplitude quality PATO:0001035 force A physical quality inhering in a bearer by virtue of the bearer's rate of change of momentum. thesaurus.maths:thesaurus.maths quality PATO:0001036 obsolete relative life span true quality PATO:0001037 obsolete absolute life span true quality PATO:0001038 obsolete ratio true quality PATO:0001039 obsolete absolute ratio true quality PATO:0001040 obsolete relative ratio true quality PATO:0001041 obsolete relative amplitude true quality PATO:0001042 obsolete absolute amplitude true A quality inhering in an entity by virtue of the bearer's propensity to resist an external stimulus. susceptibility quality PATO:0001043 susceptibility toward A quality inhering in an entity by virtue of the bearer's propensity to resist an external stimulus. PATOC:GVG quality PATO:0001044 obsolete absolute power true quality PATO:0001045 obsolete relative power true A quality inhering in a bearer by virtue of the bearer's disposition to resist to a stimulus. resistance quality PATO:0001046 resistance to A quality inhering in a bearer by virtue of the bearer's disposition to resist to a stimulus. PATOC:GVG quality PATO:0001047 obsolete absolute resistance true quality PATO:0001048 obsolete relative resistance true quality PATO:0001049 obsolete absolute susceptibility true quality PATO:0001050 obsolete relative susceptibility true An angle which is less than 90 degrees. quality PATO:0001051 acute angle to An angle which is less than 90 degrees. thesaurus.maths:thesaurus.maths An angle which is between 90 degrees and 180 degrees to another entity. quality PATO:0001052 obtuse angle to An angle which is between 90 degrees and 180 degrees to another entity. thesaurus.maths:thesaurus.maths An angle which is less than 180 degrees to another entity. quality PATO:0001053 convex angle to An angle which is less than 180 degrees to another entity. maths.org:maths.org A convex angle that is inside two adjacent sides of a polygon. quality PATO:0001054 internal angle A convex angle that is inside two adjacent sides of a polygon. PATOC:GVG An angular placement quality inhering in a bearer by virtue of the bearer's placement at an angle that is greater than 180 degrees but less than 360 degrees to another entity. quality PATO:0001055 reflex angle to An angular placement quality inhering in a bearer by virtue of the bearer's placement at an angle that is greater than 180 degrees but less than 360 degrees to another entity. thesaurus.maths:thesaurus.maths quality PATO:0001056 obsolete number true quality PATO:0001057 obsolete relative acceleration true quality PATO:0001058 obsolete absolute acceleration true quality PATO:0001059 obsolete relative efficiency true quality PATO:0001060 obsolete absolute efficiency true quality PATO:0001061 obsolete relative elasticity true quality PATO:0001062 obsolete absolute elasticity true quality PATO:0001063 obsolete relative flux true quality PATO:0001064 obsolete absolute flux true quality PATO:0001065 obsolete relative stiffness true quality PATO:0001066 obsolete absolute stiffness true quality PATO:0001067 obsolete absolute strain true quality PATO:0001068 obsolete relative strain true quality PATO:0001069 obsolete relative density true quality PATO:0001070 obsolete absolute density true quality PATO:0001071 obsolete relative energy true quality PATO:0001072 obsolete absolute energy true quality PATO:0001073 obsolete relative impulse true quality PATO:0001074 obsolete absolute impulse true quality PATO:0001075 obsolete absolute momentum true quality PATO:0001076 obsolete relative momentum true quality PATO:0001077 obsolete absolute pressure true quality PATO:0001078 obsolete relative pressure true quality PATO:0001079 obsolete absolute work true quality PATO:0001080 obsolete relative work true quality PATO:0001081 obsolete physical measure value true quality PATO:0001082 obsolete damage value true quality PATO:0001083 obsolete acceleration value true quality PATO:0001084 obsolete relative acceleration value true quality PATO:0001085 obsolete absolute acceleration value true quality PATO:0001086 obsolete efficiency value true quality PATO:0001087 obsolete relative efficiency value true quality PATO:0001088 obsolete absolute efficiency value true quality PATO:0001089 obsolete elasticity value true quality PATO:0001090 obsolete absolute elasticity value true quality PATO:0001091 obsolete relative elasticity value true quality PATO:0001092 obsolete flux value true quality PATO:0001093 obsolete relative flux value true quality PATO:0001094 obsolete absolute flux value true quality PATO:0001095 obsolete force value true quality PATO:0001096 obsolete absolute force value true quality PATO:0001097 obsolete relative force value true quality PATO:0001098 obsolete absolute force true quality PATO:0001099 obsolete relative force true quality PATO:0001100 obsolete position value true quality PATO:0001101 obsolete stiffness value true quality PATO:0001102 obsolete absolute stiffness value true quality PATO:0001103 obsolete relative stiffness value true quality PATO:0001104 obsolete strain value true quality PATO:0001105 obsolete absolute strain value true quality PATO:0001106 obsolete relative strain value true quality PATO:0001107 obsolete density value true quality PATO:0001108 obsolete relative amplitude value true quality PATO:0001109 obsolete absolute amplitude value true quality PATO:0001110 obsolete absolute density value true quality PATO:0001111 obsolete relative density value true quality PATO:0001112 obsolete energy value true quality PATO:0001113 obsolete absolute energy value true quality PATO:0001114 obsolete relative energy value true quality PATO:0001115 obsolete impulse value true quality PATO:0001116 obsolete relative impulse value true quality PATO:0001117 obsolete absolute impulse value true quality PATO:0001118 obsolete momentum value true quality PATO:0001119 obsolete absolute momentum value true quality PATO:0001120 obsolete relative momentum value true quality PATO:0001121 obsolete power value true quality PATO:0001122 obsolete absolute power value true quality PATO:0001123 obsolete relative power value true quality PATO:0001124 obsolete pressure value true quality PATO:0001125 obsolete absolute pressure value true quality PATO:0001126 obsolete relative pressure value true quality PATO:0001127 obsolete work value true quality PATO:0001128 obsolete absolute work value true quality PATO:0001129 obsolete relative work value true quality PATO:0001130 obsolete ratio value true quality PATO:0001131 obsolete absolute ratio value true quality PATO:0001132 obsolete relative ratio value true quality PATO:0001133 obsolete immunoglobulin concentration true quality PATO:0001134 obsolete ig a concentration true quality PATO:0001135 obsolete ig d concentration true quality PATO:0001136 obsolete ig e concentration true quality PATO:0001137 obsolete ig g concentration true quality PATO:0001138 obsolete ig m concentration true quality PATO:0001139 obsolete urine glucose composition true quality PATO:0001140 obsolete immunoglobulin concentration value true quality PATO:0001141 obsolete ig a concentration value true quality PATO:0001142 obsolete ig d concentration value true quality PATO:0001143 obsolete ig e concentration value true quality PATO:0001144 obsolete ig g concentration value true quality PATO:0001145 obsolete ig m concentration value true quality PATO:0001146 obsolete resistance value true quality PATO:0001147 obsolete absolute resistance value true quality PATO:0001148 obsolete relative resistance value true quality PATO:0001149 obsolete susceptibility value true quality PATO:0001150 obsolete absolute susceptibility value true quality PATO:0001151 obsolete relative susceptibility value true A quality inhering in a bearer by virtue of the bearer's having susceptibilty toward an external stimulus. susceptible quality PATO:0001152 susceptible toward A quality inhering in a bearer by virtue of the bearer's having susceptibilty toward an external stimulus. PATOC:GVG A quality inhering in a bearer by virtue of the bearer's lacking susceptibilty toward an external stimulus. insusceptible quality PATO:0001153 insusceptible toward A quality inhering in a bearer by virtue of the bearer's lacking susceptibilty toward an external stimulus. PATO:GVG A quality inhering in a bearer by virtue of the bearer's length being notably higher than its width. quality PATO:0001154 elongated A quality inhering in a bearer by virtue of the bearer's length being notably higher than its width. WordNet:WordNet quality PATO:0001155 obsolete absolute concentration true quality PATO:0001156 obsolete relative concentration true quality PATO:0001157 obsolete absolute concentration value true quality PATO:0001158 obsolete relative concentration value true A concentration quality inhering in a bearer by virtue of the bearer's exhibiting concentration. quality PATO:0001159 concentrated A concentration quality inhering in a bearer by virtue of the bearer's exhibiting concentration. PATOC:GVG quality PATO:0001160 obsolete unconcentrated true A concentration which relatively low. quality PATO:0001161 diluted A concentration which relatively low. PATOC:GVG A concentration which is higher relative to the normal or average. high concentration quality PATO:0001162 increased concentration A concentration which is higher relative to the normal or average. PATOC:GVG A concentration which is lower relative to the normal or average. low concentration quality PATO:0001163 decreased concentration A concentration which is lower relative to the normal or average. PATOC:GVG A physical quality which inheres in a bearer by virtue of the bearer's exhibiting density. quality PATO:0001164 dense A physical quality which inheres in a bearer by virtue of the bearer's exhibiting density. PATOC:GVG quality PATO:0001165 obsolete urine enzyme composition value true quality PATO:0001166 obsolete urine enzyme composition true A structural quality inhering in a bearer by virtue of the bearer being harmed or injured or spoiled, such that its functionality is impaired. quality PATO:0001167 damaged A structural quality inhering in a bearer by virtue of the bearer being harmed or injured or spoiled, such that its functionality is impaired. WordNet:WordNet A structural quality inhering in a bearer by virtue of not being harmed or injured or spoiled. quality PATO:0001168 undamaged A structural quality inhering in a bearer by virtue of not being harmed or injured or spoiled. WordNet:WordNet true quality PATO:0001170 obsolete numerical value true An elasticity quality inhering in a bearer by virtue of the bearer's ability to recover its size and shape after deformation in any way. quality PATO:0001171 elastic An elasticity quality inhering in a bearer by virtue of the bearer's ability to recover its size and shape after deformation in any way. merriam-webster:merriam-webster An elasticity quality inhering in a bearer by virtue of the bearer's inability to recover its size and shape after deformation in any way. quality PATO:0001172 inelastic An elasticity quality inhering in a bearer by virtue of the bearer's inability to recover its size and shape after deformation in any way. merriam-webster:merriam-webster quality PATO:0001173 obsolete urine glucose composition value true quality PATO:0001174 obsolete urine composition true quality PATO:0001175 obsolete urine composition true quality PATO:0001176 obsolete deaf true quality PATO:0001177 obsolete blind true A resistance quality inhering in a bearer by virtue of the bearer's resistance to a stimulus. resistant quality PATO:0001178 resistant to A resistance quality inhering in a bearer by virtue of the bearer's resistance to a stimulus. PATOC:GVG quality PATO:0001179 obsolete immune true quality PATO:0001180 obsolete relative response true quality PATO:0001181 obsolete absolute response true quality PATO:0001182 obsolete relative response true quality PATO:0001183 obsolete absolute response value true quality PATO:0001184 obsolete maturity value true A maturity quality inhering in a bearer by virtue of the bearer's indirect development, undergoing metamorphosis. quality PATO:0001185 larval A maturity quality inhering in a bearer by virtue of the bearer's indirect development, undergoing metamorphosis. Wikipedia:http://en.wikipedia.org/wiki/Larval A maturity quality inhering in a bearer by virtue of the bearer's being at the age immediately before puberty. quality PATO:0001186 prepubescent A maturity quality inhering in a bearer by virtue of the bearer's being at the age immediately before puberty. WordNet:WordNet A maturity quality inhering in a insect by virtue of the bearer's being in the chrysalis (cocoon) or post larval stage. quality PATO:0001187 pupal A maturity quality inhering in a insect by virtue of the bearer's being in the chrysalis (cocoon) or post larval stage. WordNet:WordNet A maturity quality inhering in a bearer by virtue of the bearer's being in an inactive stage in the development of some insects, between the larval and the pupal stages. quality PATO:0001188 prepupal A maturity quality inhering in a bearer by virtue of the bearer's being in an inactive stage in the development of some insects, between the larval and the pupal stages. WordNet:WordNet A maturity quality inhering in a bearer by virtue of the bearer's being between the onset of puberty and maturity. quality PATO:0001189 adolescent A maturity quality inhering in a bearer by virtue of the bearer's being between the onset of puberty and maturity. WordNet:WordNet A maturity quality inhering in a bearer by virtue the bearer's being not fully grown or developed. quality PATO:0001190 juvenile A maturity quality inhering in a bearer by virtue the bearer's being not fully grown or developed. thefreedictionary.com:thefreedictionary.com A spatial quality inhering in a bearer by virtue of the bearer's being located toward the middle relative to another entity. quality PATO:0001191 medial to A spatial quality inhering in a bearer by virtue of the bearer's being located toward the middle relative to another entity. PATOC:nw A response quality inhering in a bearer by virtue of the bearer's excessive reaction to a stimulus or an agent. hyperresponsive increased responsivity quality PATO:0001192 hyperresponsive to A response quality inhering in a bearer by virtue of the bearer's excessive reaction to a stimulus or an agent. PATOC:GVG A spatial quality inhering in a bearer by virtue of the bearer's being located toward the side relative to another entity. lateral quality PATO:0001193 lateral to A spatial quality inhering in a bearer by virtue of the bearer's being located toward the side relative to another entity. PATOC:GVG A response quality inhering in a bearer by virtue of the bearer's limited reaction to a stimulus or an agent. decreased responsivity hyporesponsive quality PATO:0001194 hyporesponsive to A response quality inhering in a bearer by virtue of the bearer's limited reaction to a stimulus or an agent. PATOC:GVG A spatial quality inhering in a bearer by virtue of the bearer's being located more centrally than another entity. quality PATO:0001195 proximal to A spatial quality inhering in a bearer by virtue of the bearer's being located more centrally than another entity. PATOC:nw A spatial quality inhering in a bearer by virtue of the bearer's being located toward the abdomen of an organism relative to another entity. quality PATO:0001196 ventral to A spatial quality inhering in a bearer by virtue of the bearer's being located toward the abdomen of an organism relative to another entity. PATOC:nw quality PATO:0001197 obsolete modified direction true quality PATO:0001198 obsolete unmodified direction true A shape quality inhering in a bearer by virtue of the bearer's being narrow, with the two opposite margins parallel. quality PATO:0001199 linear A shape quality inhering in a bearer by virtue of the bearer's being narrow, with the two opposite margins parallel. ISBN:0881923214 A concave 3-D shape quality inhering in a bearer by virtue of the bearer's being shaped in the form of the letter T. quality PATO:0001200 T-shaped A concave 3-D shape quality inhering in a bearer by virtue of the bearer's being shaped in the form of the letter T. WordNet:WordNet A concave 3-D shape quality inhering in a bearer by virtue of the bearer's being shaped in the form of the letter Y. quality PATO:0001201 Y-shaped A concave 3-D shape quality inhering in a bearer by virtue of the bearer's being shaped in the form of the letter Y. WordNet:WordNet true true quality PATO:0001204 obsolete not enlarged true A surface feature shape quality inhering in a bearer by virtue of the bearer's having toothlike projections in the margin. dentate toothed quality PATO:0001205 dentated A surface feature shape quality inhering in a bearer by virtue of the bearer's having toothlike projections in the margin. WordNet:WordNet A shape quality inhering in a bearer by virtue of having sharp straight-edged teeth pointing to the apex. serrate quality PATO:0001206 serrated A shape quality inhering in a bearer by virtue of having sharp straight-edged teeth pointing to the apex. ISBN:0881923214 quality PATO:0001207 obsolete absolute compatability true An odor quality inhering in a bearer by virtue of the bearer's lacking odour. quality PATO:0001208 odorless An odor quality inhering in a bearer by virtue of the bearer's lacking odour. PATOC:GVG quality PATO:0001209 obsolete absolute function true quality PATO:0001210 obsolete plane_angle_quantity true quality PATO:0001211 obsolete solid_angle_quantity true quality PATO:0001212 obsolete length_unit true quality PATO:0001213 obsolete mass_unit true quality PATO:0001214 obsolete temparature_unit true quality PATO:0001215 obsolete time_unit true quality PATO:0001216 obsolete volume_unit true quality PATO:0001217 obsolete energy_unit true quality PATO:0001218 obsolete substance_unit true quality PATO:0001219 obsolete area_unit true quality PATO:0001220 obsolete angle_unit true quality PATO:0001221 obsolete plane_angle_unit true quality PATO:0001222 obsolete solid_angle_unit true quality PATO:0001223 obsolete quantitative value true quality PATO:0001224 obsolete real number true quality PATO:0001225 obsolete relational number true true A variability quality inhering in a bearer by virtue of whether the bearer exhibits variation or change. variable quality PATO:0001227 variant A variability quality inhering in a bearer by virtue of whether the bearer exhibits variation or change. Dictionary:http://dictionary.reference.com/ quality PATO:0001228 obsolete dull true A color saturation which is of high purity. bright quality vivid PATO:0001229 high saturation A color saturation which is of high purity. PATOC:MAH A quality inhering in a bearer by virtue of the bearer's power or force. quality PATO:0001230 strength A quality inhering in a bearer by virtue of the bearer's power or force. thefreedictionary.com:thefreedictionary.com quality PATO:0001231 obsolete cold insensitive true quality PATO:0001232 obsolete heat insentive true A spatial quality inhering in a bearer by virtue of the bearer's being located toward the back or upper surface of an organism relative to another entity. dorsal posterior_to (human torso) superior_to (human head) quality PATO:0001233 dorsal to A spatial quality inhering in a bearer by virtue of the bearer's being located toward the back or upper surface of an organism relative to another entity. PATOC:nw A spatial quality inhering in a bearer by virtue of the bearer's being located further from a more centrally located entity. distal quality PATO:0001234 distal to A spatial quality inhering in a bearer by virtue of the bearer's being located further from a more centrally located entity. PATOC:nw quality PATO:0001235 obsolete strength value true A quality which inheres in an process. PATO:0001239 PATO:0001240 quality of a process quality of occurrent quality of process relational quality of occurrent quality PATO:0001236 See comments of relational quality of a physical entity. process quality A quality which inheres in an process. PATOC:GVG true true true true A quality which inheres in a continuant. PATO:0001237 PATO:0001238 snap:Quality monadic quality of a continuant multiply inhering quality of a physical entity quality of a continuant quality of a single physical entity quality of an object quality of continuant monadic quality of an object monadic quality of continuant quality PATO:0001241 Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles. physical object quality A quality which inheres in a continuant. PATOC:GVG A physical quality which is equal to the distance between repeating units of a wave pattern. quality PATO:0001242 wavelength A physical quality which is equal to the distance between repeating units of a wave pattern. PATOC:GVG A color consisting of blue hue and high brightness. quality PATO:0001243 light blue A color consisting of blue hue and high brightness. PATOC:GVG A color consisting of blue hue and low brightness. quality PATO:0001244 dark blue A color consisting of blue hue and low brightness. PATOC:GVG A color consisting of brown hue and low brightness. quality PATO:0001245 dark brown A color consisting of brown hue and low brightness. PATOC:GVG A color consisting of brown hue and high brightness. quality PATO:0001246 light brown A color consisting of brown hue and high brightness. PATOC:GVG A color consisting of cyan hue and high brightness. quality PATO:0001247 light cyan A color consisting of cyan hue and high brightness. PATOC:GVG A color consisting of cyan hue and low brightness. quality PATO:0001248 dark cyan A color consisting of cyan hue and low brightness. PATOC:GVG A color consisting of green hue and low brightness. quality PATO:0001249 dark green A color consisting of green hue and low brightness. PATOC:GVG A color consisting of green hue and high brightness. quality PATO:0001250 light green A color consisting of green hue and high brightness. PATOC:GVG A color consisting of grey color and low brightness. quality PATO:0001251 dark grey A color consisting of grey color and low brightness. PATOC:GVG A color consisting of grey color and high brightness. quality PATO:0001252 light grey A color consisting of grey color and high brightness. PATOC:GVG A color consisting of magenta color and high brightness. quality PATO:0001253 light magenta A color consisting of magenta color and high brightness. PATOC:GVG A color consisting of magenta with low brightness. quality PATO:0001254 dark magenta A color consisting of magenta with low brightness. PATOC:GVG A color consisting of orange hue and high brightness. quality PATO:0001255 light orange A color consisting of orange hue and high brightness. PATOC:GVG A color consisting of orange color and low brightness. quality PATO:0001256 dark orange A color consisting of orange color and low brightness. PATOC:GVG Pink color having high brightness and moderate saturation. quality PATO:0001257 light deep pink Pink color having high brightness and moderate saturation. PATOC:GVG Pink color having medium brightness and moderate saturation. quality PATO:0001258 deep pink Pink color having medium brightness and moderate saturation. PATOC:MAH A color consisting of purple color and low brightness. quality PATO:0001259 dark purple A color consisting of purple color and low brightness. PATOC:GVG A color consisting of purple color and high brightness. quality PATO:0001260 light purple A color consisting of purple color and high brightness. PATOC:GVG A color consisting of red hue and low brightness. quality PATO:0001261 dark red A color consisting of red hue and low brightness. PATOC:GVG A color consisting of red hue and high brightness. quality PATO:0001262 light red A color consisting of red hue and high brightness. PATOC:GVG A color consisting of yellow hue and low brightness. quality PATO:0001263 dark yellow A color consisting of yellow hue and low brightness. PATOC:GVG A color consisting of yellow hue and high brightness. quality blond PATO:0001264 light yellow A color consisting of yellow hue and high brightness. PATOC:GVG A color consisting of blue hue and high saturation. quality bright blue PATO:0001265 saturated blue A color consisting of blue hue and high saturation. PATOC:GVG A color consisting of blue hue and low saturation. pale blue quality PATO:0001266 desaturated blue A color consisting of blue hue and low saturation. PATOC:GVG A color consisting of brown hue and high saturation. quality bright brown PATO:0001267 saturated brown A color consisting of brown hue and high saturation. PATOC:GVG A color consisting of brown hue and low saturation. pale brown quality PATO:0001268 desaturated brown A color consisting of brown hue and low saturation. PATOC:GVG A color consisting of cyan colour and high saturation. quality bright cyan PATO:0001269 saturated cyan A color consisting of cyan colour and high saturation. PATOC:GVG A color consisting of cyan colour and low saturation. pale cyan quality PATO:0001270 desaturated cyan A color consisting of cyan colour and low saturation. PATOC:GVG A color consisting of green hue and high saturation. quality bright green PATO:0001271 saturated green A color consisting of green hue and high saturation. PATOC:GVG A color consisting of green hue and low saturation. pale green quality PATO:0001272 desaturated green A color consisting of green hue and low saturation. PATOC:GVG A color consisting of grey color and high saturation. quality PATO:0001273 obsolete bright grey true A color consisting of grey color and high saturation. PATOC:GVG A color consisting of grey color and low saturation. quality PATO:0001274 obsolete pale grey true A color consisting of grey color and low saturation. PATOC:GVG A color consisting of magenta color and high saturation. quality bright magenta PATO:0001275 saturated magenta A color consisting of magenta color and high saturation. PATOC:GVG A color consisting of magenta color and low saturation. pale magenta quality PATO:0001276 desaturated magenta A color consisting of magenta color and low saturation. PATOC:GVG A color consisting of orange hue and high saturation. quality bright orange PATO:0001277 saturated orange A color consisting of orange hue and high saturation. PATOC:GVG A color consisting of orange hue and low saturation. pale orange quality PATO:0001278 desaturated orange A color consisting of orange hue and low saturation. PATOC:GVG true Pink color having medium brightness and low saturation. PATO:0001279 quality bright pink PATO:0001280 dark pale pink Pink color having medium brightness and low saturation. PATOC:GVG A color consisting of purple color and high saturation. quality bright purple PATO:0001281 saturated purple A color consisting of purple color and high saturation. PATOC:GVG A color consisting of purple color and low saturation. pale purple quality PATO:0001282 desaturated purple A color consisting of purple color and low saturation. PATOC:GVG A color consisting of red hue and high saturation. quality bright red PATO:0001283 saturated red A color consisting of red hue and high saturation. PATOC:GVG A color consisting of red hue and low saturation. pale red quality PATO:0001284 desaturated red A color consisting of red hue and low saturation. PATOC:GVG A color consisting of yellow hue and high saturation. quality bright yellow PATO:0001285 saturated yellow A color consisting of yellow hue and high saturation. PATOC:GVG A color consisting of yellow hue and low saturation. pale yellow quality PATO:0001286 desaturated yellow A color consisting of yellow hue and low saturation. PATOC:GVG A color consisting of red and brown hue. quality PATO:0001287 red brown A color consisting of red and brown hue. PATOC:GVG A color consisting of red and brown hue and low brightness. quality PATO:0001288 dark red brown A color consisting of red and brown hue and low brightness. PATOC:GVG A color consisting of red and brown hue and high brightness. quality PATO:0001289 light red brown A color consisting of red and brown hue and high brightness. PATOC:GVG A fluorescence quality inhering in a bearer by virtue of emitting light during exposure to radiation from an external source. quality PATO:0001290 fluorescent A fluorescence quality inhering in a bearer by virtue of emitting light during exposure to radiation from an external source. web:www.thefreedictionary.com/ A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation. quality PATO:0001291 electromagnetic (EM) radiation quality A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation. Wikipedia:http://en.wikipedia.org/wiki/Electromagnetic_radiation An EM radiation quality that is independent of the EM wavelength range. quality PATO:0001292 full-spectrum EM radiation quality An EM radiation quality that is independent of the EM wavelength range. PATOC:GVG A scalar EM radiation quality which obtains by the capacity of the bearer to retain radiation. quality PATO:0001293 absorption quality A scalar EM radiation quality which obtains by the capacity of the bearer to retain radiation. PATOC:GVG A scalar EM radiation quality which obtains by the capacity of the bearer to scatter or reflect radiation. quality PATO:0001294 radiation reflective quality A scalar EM radiation quality which obtains by the capacity of the bearer to scatter or reflect radiation. PATOC:GVG A reflective quality restricted to a particular wavelength. quality PATO:0001295 Typically used for light, but also applied to full EM spectrum. albedo A reflective quality restricted to a particular wavelength. PATOC:cjm A scalar optical quality which obtains by the magnitude of the light emitted by the bearer. quality PATO:0001296 luminous flux A scalar optical quality which obtains by the magnitude of the light emitted by the bearer. PATOC:GVG A radiation reflective quality inhering in a bearer by virtue of the ratio of the energy of a wave reflected from its surface to the energy possessed by the wave striking the bearer's surface. quality PATO:0001297 reflectivity A radiation reflective quality inhering in a bearer by virtue of the ratio of the energy of a wave reflected from its surface to the energy possessed by the wave striking the bearer's surface. PATOC:GVG A fluorescence in which the emittence continues after the absorption has ceased. quality PATO:0001298 phosphorescence A fluorescence in which the emittence continues after the absorption has ceased. PATOC:GVG A scalar EM radiation quality which obtains by the capacity of the bearer to emit radiation. quality PATO:0001299 radiation emitting quality A scalar EM radiation quality which obtains by the capacity of the bearer to emit radiation. PATOC:GVG An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light. quality PATO:0001300 optical quality An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light. PATOC:GVG An optical quality that is the mixture, purity or pattern of wavelengths of light perceived by the observer. quality PATO:0001301 chromatic property An optical quality that is the mixture, purity or pattern of wavelengths of light perceived by the observer. PATOC:MAH A color consisting of red and orange hue with a slight amount of gray. quality PATO:0001302 vermilion A color consisting of red and orange hue with a slight amount of gray. PATOC:GVG A quality inhering in a bearer by virtue of the bearer's disposition to varying or changing. quality variability of a physical quality PATO:0001303 variability A quality inhering in a bearer by virtue of the bearer's disposition to varying or changing. Dictionary:http://dictionary.reference.com/ A variability quality inhering in a bearer by virtue of whether the bearer exhibits temperature variation or change. quality PATO:0001304 variability of temperature A variability quality inhering in a bearer by virtue of whether the bearer exhibits temperature variation or change. PATO:GVG A temperature which is relatively high. PATO:0000678 high temperature hot quality PATO:0001305 increased temperature A temperature which is relatively high. PATOC:GVG A temperature which is relatively low. PATO:0000677 cold low temperature quality PATO:0001306 decreased temperature A temperature which is relatively low. PATOC:GVG A variability of temperature which is relatively low. low variability of temperature quality PATO:0001307 decreased variability of temperature A variability of temperature which is relatively low. PATOC:GVG A variability of temperature which is relatively high. high variability of temperature quality PATO:0001308 increased variability of temperature A variability of temperature which is relatively high. PATOC:GVG A process quality inhering in a bearer by virtue of the bearer's magnitude of the temporal extent between the starting and ending point. PATO:0000081 period quality time PATO:0001309 duration A process quality inhering in a bearer by virtue of the bearer's magnitude of the temporal extent between the starting and ending point. PATOC:mellybelly A duration quality of a process inhering in a bearer by virtue of the bearer's duration of exhibition of thermal energy. quality PATO:0001310 TODO: obsolete? I don't know what this means. duration of temperature A duration quality of a process inhering in a bearer by virtue of the bearer's duration of exhibition of thermal energy. PATOC:GVG A duration of temperature which is lesser relative to the normal or average enduring or continuing in time. quality PATO:0001311 decreased duration of temperature A duration of temperature which is lesser relative to the normal or average enduring or continuing in time. PATOC:GVG A duration of temperature which is greater relative to the normal or average in respect to the quality of temperature of enduring or continuing in time. high duration of temperature quality PATO:0001312 increased duration of temperature A duration of temperature which is greater relative to the normal or average in respect to the quality of temperature of enduring or continuing in time. PATOC:GVG A variability quality inhering in a bearer by virtue of the bearer's lacking or not exhibiting variation of temperature. quality PATO:0001313 invariant temperature A variability quality inhering in a bearer by virtue of the bearer's lacking or not exhibiting variation of temperature. PATO:GVG A variability quality inhering in a bearer by virtue of the bearer's having or exhibiting variation of temperature. quality PATO:0001314 variant temperature A variability quality inhering in a bearer by virtue of the bearer's having or exhibiting variation of temperature. PATO:GVG A temperature which is increased by a low degree. quality PATO:0001315 mild increased temperature A temperature which is increased by a low degree. PATOC:GVG A temperature which is increased by a medium degree. quality PATO:0001316 moderate increased temperature A temperature which is increased by a medium degree. PATOC:GVG A temperature which is increased by a high degree. quality PATO:0001317 severe increased temperature A temperature which is increased by a high degree. PATOC:GVG A discrimination quality in a bearer by virtue of the bearer's being incapable perceiving differences between two or more stimuli. quality PATO:0001318 indiscriminate A discrimination quality in a bearer by virtue of the bearer's being incapable perceiving differences between two or more stimuli. PATOC:GVG A discrimination quality in a bearer by virtue of the bearer's being capable of perceiving differences between two or more stimuli. quality PATO:0001319 discriminate A discrimination quality in a bearer by virtue of the bearer's being capable of perceiving differences between two or more stimuli. PATOC:GVG A pilosity quality of being covered with short hairs or soft down. quality PATO:0001320 pubescent hair A pilosity quality of being covered with short hairs or soft down. PATOC:GVG An angle which is 90 degrees to another entity. quality PATO:0001321 right angle to An angle which is 90 degrees to another entity. thesaurus.math:thesaurus.math An angle which is 180 degrees to another entity. quality PATO:0001322 TODO: decide on correct parentage. straight angle to An angle which is 180 degrees to another entity. thesaurus.maths:thesaurus.maths A 2-D extent quality inhering in a bearer by virtue of the bearer's two dimensional extent. quality PATO:0001323 area A 2-D extent quality inhering in a bearer by virtue of the bearer's two dimensional extent. Wikipedia:http://en.wikipedia.org/wiki/Area A symmetry quality inhering in a bearer by virtue of the bearer's being symmetric about a plane running from its frontal end to its caudal end (head to tail), and has nearly identical right and left halves. left-right symmetry quality pennate PATO:0001324 bilateral symmetry A symmetry quality inhering in a bearer by virtue of the bearer's being symmetric about a plane running from its frontal end to its caudal end (head to tail), and has nearly identical right and left halves. Wikipedia:http://en.wikipedia.org/wiki/Bilateral_symmetry pennate https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0002-2908-3327 A symmetry quality inhering in a bearer by virtue of the bearer's having equal proportion around a central point or axis. centric quality PATO:0001325 radial symmetry A symmetry quality inhering in a bearer by virtue of the bearer's having equal proportion around a central point or axis. PATOC:GVG centric https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0002-2908-3327 quality PATO:0001326 obsolete left-right symmetry true A symmetry quality inhering in a bearer by virtue of the bearer's being capable of division into symmetrical halves by only one longitudinal plane passing through the axis. quality PATO:0001327 zygomorphic A symmetry quality inhering in a bearer by virtue of the bearer's being capable of division into symmetrical halves by only one longitudinal plane passing through the axis. WordNet:WordNet A symmetry quality inhering in a bearer by virtue of the bearer's being capable of division into symmetrical halves by any longitudinal plane passing through the axis. quality PATO:0001328 actinomorphic A symmetry quality inhering in a bearer by virtue of the bearer's being capable of division into symmetrical halves by any longitudinal plane passing through the axis. WordNet:WordNet A flavor quality inhering in a bearer by virtue of the bearer's having flavour. quality PATO:0001329 flavourful A flavor quality inhering in a bearer by virtue of the bearer's having flavour. PATOC:GVG A flavor quality inhering in a bearer by virtue of the bearer's lacking flavour. quality PATO:0001330 flavourless A flavor quality inhering in a bearer by virtue of the bearer's lacking flavour. PATOC:GVG An odor quality inhering in a bearer by virtue of the bearer's having odour. quality PATO:0001331 odorous An odor quality inhering in a bearer by virtue of the bearer's having odour. PATOC:GVG A morphology quality inhering in a bearer by virtue of the bearer's lack of distinct morphology. quality PATO:0001332 amorphous A morphology quality inhering in a bearer by virtue of the bearer's lack of distinct morphology. PATOC:GVG A quality of a process which ends later than the natural end time. quality PATO:0001333 temporally extended A quality of a process which ends later than the natural end time. PATOC:melissa A length quality which is equal to the length of any straight line segment that passes through the center of a circle and whose endpoints are on the circular boundary. quality PATO:0001334 diameter A length quality which is equal to the length of any straight line segment that passes through the center of a circle and whose endpoints are on the circular boundary. Wikipedia:http://en.wikipedia.org/wiki/Diameter A mating type that indicates whether the F plasmid has integrated into the chromosome. quality PATO:0001335 bacterial mating type A mating type that indicates whether the F plasmid has integrated into the chromosome. MGED:MGED A biological sex quality inhering in an individual whose sex is unknown. quality PATO:0001336 Unknown is not a type of sex. obsolete unknown sex true A biological sex quality inhering in an individual whose sex is unknown. MGED:MGED A yeast mating type. quality PATO:0001337 yeast mating type A yeast mating type. PATOC:GVG A biological sex quality inhering in a population of multiple sexes. quality PATO:0001338 For example a mixture of females and male or males and hermaphrodites. mixed sex A biological sex quality inhering in a population of multiple sexes. MGED:MGED A composition quality inhering in an bearer by virtue of the bearer's homogeneity of a biomaterial. quality PATO:0001339 biomaterial purity A composition quality inhering in an bearer by virtue of the bearer's homogeneity of a biomaterial. MGED:MGED A biological sex quality inhering in an organism or a population with both male and female sexual organs in one individual. hermaphroditic intersex quality PATO:0001340 hermaphrodite A biological sex quality inhering in an organism or a population with both male and female sexual organs in one individual. MGED:MGED A S. cerevisiae mating type cells that secrete a pheromone that in alpha haploids stimulates processes that lead to mating. a quality PATO:0001341 a mating type (yeast) A S. cerevisiae mating type cells that secrete a pheromone that in alpha haploids stimulates processes that lead to mating. MGED:MGED A S. cerevisiae mating type. quality PATO:0001342 Saccharomyces cerevisiae mating type A S. cerevisiae mating type. PATOC:GVG A S. pombe mating type determined by the gene configuration on the mat1 locus. quality PATO:0001343 Schizosaccharomyces pombe mating type A S. pombe mating type determined by the gene configuration on the mat1 locus. PATOC:GVG A S. cerevisiae mating type cells that secrete a pheromone that stimulates a haploids. alpha quality PATO:0001344 alpha mating type (yeast) A S. cerevisiae mating type cells that secrete a pheromone that stimulates a haploids. MGED:MGED A S. pombe mating type determined by the mat1-Mc and mat1-Mi on the mat1 locus. M h - quality PATO:0001345 h minus A S. pombe mating type determined by the mat1-Mc and mat1-Mi on the mat1 locus. PATOC:GVG A S. pombe mating type determined by the mat1-Pc and mat1-Pi on the mat1 locus. P h+ quality PATO:0001346 h plus A S. pombe mating type determined by the mat1-Pc and mat1-Pi on the mat1 locus. PATOC:GVG A bacterial mating type indicating the presence of F plasmid in a bacterial cell. quality PATO:0001347 F mating type A bacterial mating type indicating the presence of F plasmid in a bacterial cell. MGED:MGED A bacterial mating type indicating the absence of F plasmid in a bacterial cell. F- quality PATO:0001348 F minus mating type A bacterial mating type indicating the absence of F plasmid in a bacterial cell. MGED:MGED A mating type that indicates that the F plasmid has integrated into the chromosome. Hfr quality PATO:0001349 high frequency recombinant A mating type that indicates that the F plasmid has integrated into the chromosome. MGED:MGED A physical quality inhering in a bearer by virtue of the rate of change of the bearer's angular velocity. quality PATO:0001350 angular acceleration A physical quality inhering in a bearer by virtue of the rate of change of the bearer's angular velocity. Wikipedia:http://en.wikipedia.org/wiki/Angular_acceleration A density quality which inheres in a bearer by virtue of some influence exerted by the bearer's mass on a given area. quality PATO:0001351 area density A density quality which inheres in a bearer by virtue of some influence exerted by the bearer's mass on a given area. Wikipedia:http://en.wikipedia.org/wiki/Area_density A density quality which is equal to the mass exerting an influence on a one-dimensional object. quality PATO:0001352 linear density A density quality which is equal to the mass exerting an influence on a one-dimensional object. Wikipedia:http://en.wikipedia.org/wiki/Linear_density A density quality which inheres in a bearer by virtue of some influence exerted by the bearer's mass on a given volume. quality PATO:0001353 volumetric density A density quality which inheres in a bearer by virtue of some influence exerted by the bearer's mass on a given volume. Wikipedia:http://en.wikipedia.org/wiki/Mass_density A optical quality inhering in a bearer by virtue of the bearer's exhibiting low opacity. quality PATO:0001354 translucent A optical quality inhering in a bearer by virtue of the bearer's exhibiting low opacity. PATOC:GVG A shape quality that obtains by virtue of the bearer having inward facing edges; having a surface or boundary that curves or bulges outward, as the exterior of a sphere. quality PATO:0001355 convex A shape quality that obtains by virtue of the bearer having inward facing edges; having a surface or boundary that curves or bulges outward, as the exterior of a sphere. PATOC:GVG A shape quality inhering in a cell by virtue of the bearer's ability to take on two or more different shapes during its life cycle. quality PATO:0001356 pleomorphic A shape quality inhering in a cell by virtue of the bearer's ability to take on two or more different shapes during its life cycle. PATOC:GVG A convex 3-D shape quality inhering in a bearer by virtue of the bearer's being shaped like a cushion or has a marked convex cushion-like form. quality PATO:0001357 pulvinate A convex 3-D shape quality inhering in a bearer by virtue of the bearer's being shaped like a cushion or has a marked convex cushion-like form. PATOC:GVG A quality inhering in a bearer by virtue of the bearer's having a knob or knoblike protuberance. quality PATO:0001358 umbonate A quality inhering in a bearer by virtue of the bearer's having a knob or knoblike protuberance. PATOC:GVG A surface feature shape quality inhering in a bearer by virtue of the bearer's having many wrinkles or creases on the surface. quality PATO:0001359 rugose A surface feature shape quality inhering in a bearer by virtue of the bearer's having many wrinkles or creases on the surface. PATOC:GVG A shape quality inhering in a bearer by virtue of the bearer's having thin filamentous extensions at its edge. quality PATO:0001360 filamentous A shape quality inhering in a bearer by virtue of the bearer's having thin filamentous extensions at its edge. PATOC:GVG A texture quality inhering in a bearer by virtue of the bearer's being covered with warts or projections that resemble warts resulting in a hard rough surface. quality PATO:0001361 warty A texture quality inhering in a bearer by virtue of the bearer's being covered with warts or projections that resemble warts resulting in a hard rough surface. PATOC:GVG A structural quality inhering in a bearer by virtue of the bearer's disposition to being easily damaged or destroyed. quality PATO:0001362 fragile A structural quality inhering in a bearer by virtue of the bearer's disposition to being easily damaged or destroyed. WordNet:WordNet true A quality inhering in a bearer by virtue of the bearer's having root like extensions radiating from its center. quality PATO:0001364 rhizoidal A quality inhering in a bearer by virtue of the bearer's having root like extensions radiating from its center. PATOC:GVG A surface feature shape quality inhering in a bearer by virtue of the bearer's having spines, thorns or similar thin projections on its surface. quality PATO:0001365 spiny A surface feature shape quality inhering in a bearer by virtue of the bearer's having spines, thorns or similar thin projections on its surface. PATOC:GVG A shape quality inhering in a bearer by virtue of the bearer's being small and resembling a point. quality PATO:0001366 punctiform A shape quality inhering in a bearer by virtue of the bearer's being small and resembling a point. PATOC:GVG A surface feature shape quality inhering in a bearer by virtue of the bearer's having deeply undulating edges forming lobes. quality PATO:0001367 lobate A surface feature shape quality inhering in a bearer by virtue of the bearer's having deeply undulating edges forming lobes. PATOC:GVG A surface feature shape quality inhering in a bearer by virtue of the bearer's having an irregularly toothed edge. quality jagged PATO:0001368 erose A surface feature shape quality inhering in a bearer by virtue of the bearer's having an irregularly toothed edge. PATOC:GVG A shape quality inhering in a colony by virtue of the bearer's appearing above the medium surface with terraced edges. quality PATO:0001369 raised A shape quality inhering in a colony by virtue of the bearer's appearing above the medium surface with terraced edges. PATOC:GVG A coating quality which is sticky or clammy. quality PATO:0001370 viscid A coating quality which is sticky or clammy. PATOC:GVG A composition quality inhering in an bearer by virtue of the bearer's consistency of mucus. quality mucinous mucous PATO:0001371 mucoid A composition quality inhering in an bearer by virtue of the bearer's consistency of mucus. PATOC:GVG A physical quality that inheres in propagating wave (light or sound) virtue of the bearer's change in direction when passing from one medium to another. quality PATO:0001372 refractivity A physical quality that inheres in propagating wave (light or sound) virtue of the bearer's change in direction when passing from one medium to another. WordNet:WordNet A reflectivity quality inhering in a bearer by virtue of the bearer's reflecting lots of light. glossy shiny quality PATO:0001373 glistening A reflectivity quality inhering in a bearer by virtue of the bearer's reflecting lots of light. PATOC:GVG A cellular quality inhering in a bearer by virtue of the bearer's number of homologous sets of chromosomes in the nucleus or primary chromosome-containing compartment of the cell, each set essentially coding for all the biological traits of the organism. quality PATO:0001374 ploidy A cellular quality inhering in a bearer by virtue of the bearer's number of homologous sets of chromosomes in the nucleus or primary chromosome-containing compartment of the cell, each set essentially coding for all the biological traits of the organism. Wikipedia:http://en.wikipedia.org/wiki/Ploidy A ploidy quality inhering in a bearer by virtue of the bearer's containing a single set of homologous chromosomes. quality PATO:0001375 haploid A ploidy quality inhering in a bearer by virtue of the bearer's containing a single set of homologous chromosomes. Wikipedia:http://en.wikipedia.org/wiki/Haploid A ploidy quality inhering in a bearer by virtue of the bearer's containing a single set of unique homologous chromosomes. quality PATO:0001376 monoploid A ploidy quality inhering in a bearer by virtue of the bearer's containing a single set of unique homologous chromosomes. Wikipedia:http://en.wikipedia.org/wiki/Monoploid A ploidy quality inhering in a bearer by virtue of the bearer's containing more than two homologous sets of chromosomes. quality PATO:0001377 polyploid A ploidy quality inhering in a bearer by virtue of the bearer's containing more than two homologous sets of chromosomes. Wikipedia:http://en.wikipedia.org/wiki/Polyploid A polyploidy quality inhering in a bearer by virtue of the bearer's containing chromosomes derived from a single species. quality PATO:0001378 autopolyploid A polyploidy quality inhering in a bearer by virtue of the bearer's containing chromosomes derived from a single species. Wikipedia:http://en.wikipedia.org/wiki/Autopolyploid A polyploidy quality inhering in a bearer by virtue of the bearer's containing chromosomes derived from different species. quality PATO:0001379 allopolyploidy A polyploidy quality inhering in a bearer by virtue of the bearer's containing chromosomes derived from different species. Wikipedia:http://en.wikipedia.org/wiki/Allopolyploidy A polyploidy quality inhering in a bearer by virtue of the bearer's having an ancient polyploid ancestor. quality PATO:0001380 paleopolyploid A polyploidy quality inhering in a bearer by virtue of the bearer's having an ancient polyploid ancestor. Wikipedia:http://en.wikipedia.org/wiki/Paleopolyploid A polyploidy quality inhering in a bearer by virtue of the bearer's containing three homologous sets of chromosomes. quality PATO:0001381 triploid A polyploidy quality inhering in a bearer by virtue of the bearer's containing three homologous sets of chromosomes. Wikipedia:http://en.wikipedia.org/wiki/Triploid A polyploidy quality inhering in a bearer by virtue of the bearer's containing four homologous sets of chromosomes. quality PATO:0001382 tetraploid A polyploidy quality inhering in a bearer by virtue of the bearer's containing four homologous sets of chromosomes. Wikipedia:http://en.wikipedia.org/wiki/Tetraploid A polyploidy quality inhering in a bearer by virtue of the bearer's containing five homologous sets of chromosomes. quality PATO:0001383 pentaploid A polyploidy quality inhering in a bearer by virtue of the bearer's containing five homologous sets of chromosomes. Wikipedia:http://en.wikipedia.org/wiki/Pentaploid A polyploidy quality inhering in a bearer by virtue of the bearer's containing six homologous sets of chromosomes. quality PATO:0001384 hexaploid A polyploidy quality inhering in a bearer by virtue of the bearer's containing six homologous sets of chromosomes. Wikipedia:http://en.wikipedia.org/wiki/Hexaploid A ploidy quality inhering in a bearer by virtue of the bearer's containing a non-integral multiple of the monoploid number, due to extra or missing chromosomes. quality PATO:0001385 aneuploid A ploidy quality inhering in a bearer by virtue of the bearer's containing a non-integral multiple of the monoploid number, due to extra or missing chromosomes. Wikipedia:http://en.wikipedia.org/wiki/Aneuploid An aneuploidy quality inhering in a bearer by virtue of the bearer's containing only one chromosome from a pair in a cell's nucleus. quality PATO:0001386 monosomy An aneuploidy quality inhering in a bearer by virtue of the bearer's containing only one chromosome from a pair in a cell's nucleus. Wikipedia:http://en.wikipedia.org/wiki/Monosomy An aneuploidy quality inhering in a bearer by virtue of the bearer's containing only two chromosome from a pair in a cell's nucleus. quality PATO:0001387 For diploid organisms, such as humans, it is the normal condition, whilst for organisms that are normally triploid or above, disomy is an aneuploidy. disomy An aneuploidy quality inhering in a bearer by virtue of the bearer's containing only two chromosome from a pair in a cell's nucleus. Wikipedia:http://en.wikipedia.org/wiki/Disomy A disomy quality inhering in a bearer by virtue of the bearer's containing two copies of the chromosome from one of the parents (with no contribution from the other parent). quality PATO:0001388 uniparental disomy A disomy quality inhering in a bearer by virtue of the bearer's containing two copies of the chromosome from one of the parents (with no contribution from the other parent). Wikipedia:http://en.wikipedia.org/wiki/Uniparental_disomy An aneuploidy quality inhering in a bearer by virtue of the bearer's containing three, instead of two, chromosomes of a particular numbered type in an organism. quality PATO:0001389 trisomy An aneuploidy quality inhering in a bearer by virtue of the bearer's containing three, instead of two, chromosomes of a particular numbered type in an organism. Wikipedia:http://en.wikipedia.org/wiki/Trisomy A trisomy quality inhering in a bearer when part of the bearer's extra chromosome is attached to one of the other chromosomes, or if one of the bearer's chromosomes has two copies of part of its chromosome. quality PATO:0001390 partial trisomy A trisomy quality inhering in a bearer when part of the bearer's extra chromosome is attached to one of the other chromosomes, or if one of the bearer's chromosomes has two copies of part of its chromosome. Wikipedia:http://en.wikipedia.org/wiki/Partial_trisomy A trisomy quality inhering in a bearer by virtue of the bearer's having extra chromosomal material in only some of it's cells. quality PATO:0001391 mosaic trisomy A trisomy quality inhering in a bearer by virtue of the bearer's having extra chromosomal material in only some of it's cells. PATOC:GVG A polyploidy quality inhering in a bearer by virtue of the bearer's chromosome number being increased by endomitosis and for which the degree of ploidy is proportional to the number of times that endomitosis has taken place. quality PATO:0001392 endopolyploid A polyploidy quality inhering in a bearer by virtue of the bearer's chromosome number being increased by endomitosis and for which the degree of ploidy is proportional to the number of times that endomitosis has taken place. Wikipedia:http://en.wikipedia.org/wiki/Endopolyploid A ploidy quality inhering in a bearer by virtue of the bearer's containing an integral multiple of the monoploid number, possibly excluding the sex-determining chromosomes. quality PATO:0001393 euploid A ploidy quality inhering in a bearer by virtue of the bearer's containing an integral multiple of the monoploid number, possibly excluding the sex-determining chromosomes. Wikipedia:http://en.wikipedia.org/wiki/Euploid A ploidy quality inhering in a bearer by virtue of the bearer's having two copies (homologs) of each chromosome, usually one from the mother and one from the father. quality PATO:0001394 The exact number may be one or two different from the 2n number and still be classified as diploidy (although with aneuploidy). Nearly all mammals are diploid organisms, although all individuals have some small fraction of cells that are polyploidy. diploid A ploidy quality inhering in a bearer by virtue of the bearer's having two copies (homologs) of each chromosome, usually one from the mother and one from the father. Wikipedia:http://en.wikipedia.org/wiki/Diploid A diploidy quality inhering in a bearer in by virtue of belonging in a species whose one of the sexes has haploid cells and the other has diploid cells. quality PATO:0001395 haplodiploid A diploidy quality inhering in a bearer in by virtue of belonging in a species whose one of the sexes has haploid cells and the other has diploid cells. Wikipedia:http://en.wikipedia.org/wiki/Haplodiploid A monadic quality of continuant that exists at the cellular level of organisation. quality PATO:0001396 cellular quality A monadic quality of continuant that exists at the cellular level of organisation. PATOC:GVG A cellular quality that arises by virtue of whether the bearer's disposition to differentiate into one or more mature cell types. quality PATO:0001397 cellular potency A cellular quality that arises by virtue of whether the bearer's disposition to differentiate into one or more mature cell types. PATOC:GVG A cellular quality inhering in a bearer by virtue of the bearer's having the ability to go through numerous cycles of cell division while maintaining the undifferentiated state. quality PATO:0001398 self-renewal A cellular quality inhering in a bearer by virtue of the bearer's having the ability to go through numerous cycles of cell division while maintaining the undifferentiated state. PATOC:GVG A cellular potency that is the capacity to produce differentiated cell types of all three primary germ layers and extraembryonic cell types. quality PATO:0001399 totipotent A cellular potency that is the capacity to produce differentiated cell types of all three primary germ layers and extraembryonic cell types. Wikipedia:http://en.wikipedia.org/wiki/Totipotent A cellular potency that is the capacity to produce only one differentiated cell type. quality PATO:0001400 Unipotent cells have the quality of self-renewal which distinguishes them from non-stem cells. unipotent A cellular potency that is the capacity to produce only one differentiated cell type. Wikipedia:http://en.wikipedia.org/wiki/Unipotent A cellular potency that is the capacity to form multiple differentiated cell types of a specific lineage and lack self renewing capacity. quality PATO:0001401 Less potent than multipotent, often thought of as precursor or progenitor cell status. oligopotent A cellular potency that is the capacity to form multiple differentiated cell types of a specific lineage and lack self renewing capacity. PATOC:MAH A cellular potency that is the capacity to form multiple differentiated cell types. quality PATO:0001402 multipotent A cellular potency that is the capacity to form multiple differentiated cell types. Wikipedia:http://en.wikipedia.org/wiki/Multipotent A cellular potency that is the capacity to produce differentiated cell types of all three primary germ layers but not extraembryonic cell types. quality PATO:0001403 pluripotent A cellular potency that is the capacity to produce differentiated cell types of all three primary germ layers but not extraembryonic cell types. Wikipedia:http://en.wikipedia.org/wiki/Pluripotent A cellular quality inhering in a bearer by virtue of bearer's number of nuclei. quality PATO:0001404 nucleate quality A cellular quality inhering in a bearer by virtue of bearer's number of nuclei. PATOC:GVG A nucleate quality inhering in a bearer by virtue of the bearer's having no nucleus. quality PATO:0001405 anucleate A nucleate quality inhering in a bearer by virtue of the bearer's having no nucleus. Biology-online:Biology-online A nucleate quality inhering in a bearer by virtue of the bearer's having two nuclei. quality PATO:0001406 binucleate A nucleate quality inhering in a bearer by virtue of the bearer's having two nuclei. Biology-online:Biology-online A nucleate quality inhering in a bearer by virtue of the bearer's having one nucleus. quality PATO:0001407 mononucleate A nucleate quality inhering in a bearer by virtue of the bearer's having one nucleus. Biology-online:Biology-online A cellular quality inhering in a bearer by virtue of the bearer's having thin, tail-like projections extending outwards from the cell body. quality PATO:0001408 ciliatedness A cellular quality inhering in a bearer by virtue of the bearer's having thin, tail-like projections extending outwards from the cell body. Wikipedia:http://en.wikipedia.org/wiki/Ciliated A shape quality inhering in a bearer by virtue of the bearer's resembling a long tapered rod. quality PATO:0001409 spindle-shaped A shape quality inhering in a bearer by virtue of the bearer's resembling a long tapered rod. Biology-online:Biology-online A shape quality inhering in a bearer by virtue of the bearer's being marked by narrow lines or grooves, usually parallel. quality PATO:0001410 striated A shape quality inhering in a bearer by virtue of the bearer's being marked by narrow lines or grooves, usually parallel. Biology-online:Biology-online A structural quality inhering in a bearer by virtue of the bearer's having distinct structure. quality PATO:0001411 structured A structural quality inhering in a bearer by virtue of the bearer's having distinct structure. PATOC:GVG A structural quality inhering in a bearer by virtue of the bearer's lacking distinct structure. quality PATO:0001412 unstructured A structural quality inhering in a bearer by virtue of the bearer's lacking distinct structure. PATOC:GVG A physical quality inhering in a bearer by virtue of the rate of the bearer's angular movement about an axis; the angle rotated in a given time. quality PATO:0001413 angular velocity A physical quality inhering in a bearer by virtue of the rate of the bearer's angular movement about an axis; the angle rotated in a given time. Wikipedia:http://en.wikipedia.org/wiki/Angular_velocity A physical quality inhering in a catalyst by virtue of the amount of the catalyst's action. quality PATO:0001414 catalytic activity A physical quality inhering in a catalyst by virtue of the amount of the catalyst's action. PATOC:GVG A quality inhering in a population by virtue of the proportion of its members that are ill at a given time. quality PATO:0001415 morbidity A quality inhering in a population by virtue of the proportion of its members that are ill at a given time. PATOC:GVG A duration which has regular start and/or end times. quality PATO:0001416 regular duration A duration which has regular start and/or end times. PATOC:GVG A duration quality of a process inhering in a bearer by virtue of the bearer's duration which has irregular start and/or end times. quality PATO:0001417 irregular duration A duration quality of a process inhering in a bearer by virtue of the bearer's duration which has irregular start and/or end times. PATOC:melissa A behavioral quality inhering in a bearer by virtue of the bearer's being deficient in alertness or activity. quality PATO:0001418 lethargic A behavioral quality inhering in a bearer by virtue of the bearer's being deficient in alertness or activity. WordNet:WordNet A shape quality inhering in a bearer by virtue of the bearer's terminating in a point or edge. quality PATO:0001419 sharp A shape quality inhering in a bearer by virtue of the bearer's terminating in a point or edge. PATOC:GVG A physical quality inhering in a bearer by virtue of the bearer's disposition to rise or float in a fluid medium such as water or air. quality PATO:0001420 buoyancy A physical quality inhering in a bearer by virtue of the bearer's disposition to rise or float in a fluid medium such as water or air. PATOC:GVG A viability quality inhering in a bearer by virtue of the bearer's condition before death. quality PATO:0001421 alive A viability quality inhering in a bearer by virtue of the bearer's condition before death. PATOC:GVG A viability quality inhering in a bearer by virtue of the cessation of the bearer's life. quality PATO:0001422 dead A viability quality inhering in a bearer by virtue of the cessation of the bearer's life. PATOC:GVG A reflectivity quality inhering in the bearer by virtue of the bearer's ability to refract light. quality PATO:0001423 refractile A reflectivity quality inhering in the bearer by virtue of the bearer's ability to refract light. biology-online:biology-online A color hue with very low wavelength of that portion of the visible spectrum lying between reddish blue or bluish purple, evoked in the human observer by radiant energy with wavelengths of approximately 420 to 380 nanometers. quality PATO:0001424 violet A color hue with very low wavelength of that portion of the visible spectrum lying between reddish blue or bluish purple, evoked in the human observer by radiant energy with wavelengths of approximately 420 to 380 nanometers. Wikipedia:http://en.wikipedia.org/wiki/Violet A color hue consisting of red hue and yellow hue and high brightness. quality PATO:0001425 rosy A color hue consisting of red hue and yellow hue and high brightness. PATOC:GVG A color consisting of purple and brown hue. quality PATO:0001426 maroon A color consisting of purple and brown hue. Wikipedia:http://en.wikipedia.org/wiki/Maroon A concentration quality inhering in compound by virtue of the bearer's tendency to act as a hydron donor. quality PATO:0001427 compound acidity A concentration quality inhering in compound by virtue of the bearer's tendency to act as a hydron donor. chemicool:chemicool A concentration quality inhering in a medium by virtue of the bearer's tendency to hydronate a specific reference base. quality PATO:0001428 medium acidity A concentration quality inhering in a medium by virtue of the bearer's tendency to hydronate a specific reference base. chemicool:chemicool An medium acidity quality inhering in a solution by virtue of the bearer's a high concentration of H+ ions. quality PATO:0001429 acidic An medium acidity quality inhering in a solution by virtue of the bearer's a high concentration of H+ ions. chemicool:chemicool An medium acidity quality inhering in a solution by virtue of the bearer's a low concentration of H+ ions. quality PATO:0001430 alkaline An medium acidity quality inhering in a solution by virtue of the bearer's a low concentration of H+ ions. chemicool:chemicool An emergent molecular quality that arises by virtue of the bearer's disposition to exhibit molecular attraction to another entity in contact. adhesiveness quality stickiness PATO:0001431 The definition is general enough to cover adhesion arising from different kinds of chemical bonding/forces, although for PATO this term will most commonly used for cellular adhesion. See also GO:0031589 "cell-substrate adhesion". adhesivity An emergent molecular quality that arises by virtue of the bearer's disposition to exhibit molecular attraction to another entity in contact. PATOC:GVG A quality inhering in a bearer by virtue of the bearer's decomposition into component parts. quality PATO:0001432 decayed A quality inhering in a bearer by virtue of the bearer's decomposition into component parts. Medical-dictionary:Medical-dictionary A quality of a single process which describes the growth of an organism, structure, or group of organisms. PATO:0001489 quality growth quality of a process growth timing quality PATO:0001433 growth quality of occurrent A quality of a single process which describes the growth of an organism, structure, or group of organisms. PATOC:MAH An organismal quality inhering in a bearer by virtue of the bearer's ability to produce new life or offspring. quality PATO:0001434 reproductive quality An organismal quality inhering in a bearer by virtue of the bearer's ability to produce new life or offspring. WordNet:WordNet A structural quality inhering in a bearer by virtue of the bearer's having connection or association with another entity. quality PATO:0001435 attachment quality A structural quality inhering in a bearer by virtue of the bearer's having connection or association with another entity. PATOC:GVG An attachment quality inhering in a flower by virtue of the bearer's lacking a stalk, as in flowers or leaves that grow directly from the stem. quality PATO:0001436 sessile (sensu botany) An attachment quality inhering in a flower by virtue of the bearer's lacking a stalk, as in flowers or leaves that grow directly from the stem. Wikipedia:http://en.wikipedia.org/wiki/Sessility_(botany) A attachment quality inhering in a bearer by virtue of the bearer's inability to move about. quality PATO:0001437 sessile (sensu zoology) A attachment quality inhering in a bearer by virtue of the bearer's inability to move about. Wikipedia:http://en.wikipedia.org/wiki/Sessile_(zoology) A attachment quality inhering in a bearer by virtue of the bearer's having or being supported by a pedicel or pedicle. quality PATO:0001438 pedicellate A attachment quality inhering in a bearer by virtue of the bearer's having or being supported by a pedicel or pedicle. MedTerms:MedTerms A contractile quality inhering in a bearer by virtue of the bearer's elastic tension that facilitate response to stimuli. PATO:0001498 tone quality PATO:0001439 TODO: we need a clearer differentium between this and contractility - or merge? tonicity A contractile quality inhering in a bearer by virtue of the bearer's elastic tension that facilitate response to stimuli. WordNet:WordNet A cellular adhesivity quality inhering in a molecule in one cell by virtue of the bearer's attachment to an identical molecule in an adjacent cell. quality PATO:0001440 homophilic A cellular adhesivity quality inhering in a molecule in one cell by virtue of the bearer's attachment to an identical molecule in an adjacent cell. GO:GO A cellular adhesivity quality inhering in a molecule in one cell by virtue of the bearer's attachment to an nonidentical molecule in an adjacent cell. quality PATO:0001441 heterophilic A cellular adhesivity quality inhering in a molecule in one cell by virtue of the bearer's attachment to an nonidentical molecule in an adjacent cell. GO:GO A structural quality inhering in a bearer by virtue of whether the bearer includes all its components. quality PATO:0001442 wholeness A structural quality inhering in a bearer by virtue of whether the bearer includes all its components. thefreedictionary.com:thefreedictionary.com true A structural quality inhering in a bearer by virtue of the bearer's components no longer being in a single contiguous unit. PATO:0001443 PATO:0001820 fragmented fractured quality cracked hemorrhaged split torn PATO:0001444 broken A structural quality inhering in a bearer by virtue of the bearer's components no longer being in a single contiguous unit. https://orcid.org/0000-0003-4606-0597 A wholeness quality inhering in a bearer by virtue of the bearer's being taken apart into its constituent parts. quality PATO:0001445 disassembled A wholeness quality inhering in a bearer by virtue of the bearer's being taken apart into its constituent parts. thefreedictionary.com:thefreedictionary.com A wholeness quality inhering in a bearer by virtue of the bearer's including all its components. quality PATO:0001446 whole A wholeness quality inhering in a bearer by virtue of the bearer's including all its components. thefreedictionary.com:thefreedictionary.com A composition quality inhering in an bearer by virtue of the bearer's being encrusted or impregnated with calcium carbonate (CHEBI:3311). calcareous calcification quality PATO:0001447 calcified A composition quality inhering in an bearer by virtue of the bearer's being encrusted or impregnated with calcium carbonate (CHEBI:3311). thefreedictionary.com:thefreedictionary.com A composition quality inhering in an bearer by virtue of the bearer's being hardened by the deposition of calcium into bone. quality PATO:0001448 ossified A composition quality inhering in an bearer by virtue of the bearer's being hardened by the deposition of calcium into bone. MAMMALOGY:MAMMALOGY A composition quality inhering in an bearer by virtue of the bearer's cartilage quantities. quality PATO:0001449 Cartilage is a type of dense connective tissue. It is composed of specialized cells called chondrocytes (CL:0000138) that produce a large amount of extracellular matrix composed of collagen fibers, abundant ground substance rich in proteoglycan, and elastin fibers. cartilaginous A composition quality inhering in an bearer by virtue of the bearer's cartilage quantities. Wikipedia:http://en.wikipedia.org/wiki/Cartilaginous A structural quality which is held by a bearer when the latter exhibits an excessive accumulation of extracellular fluid. edemic oedematous oedemic edema oedema quality PATO:0001450 edematous A structural quality which is held by a bearer when the latter exhibits an excessive accumulation of extracellular fluid. thefreedictionary.com:thefreedictionary.com An extended swelling in plant organs caused primarily by an excessive accumulation of water. quality edemic oedematous oedemic PATO:0001451 obsolete edematous (sensu botany) true An extended swelling in plant organs caused primarily by an excessive accumulation of water. thefreedictionary.com:thefreedictionary.com true An attachment quality inhering in a bearer by virtue of the bearer's lacking connection or association with another entity. detached quality PATO:0001453 detached from An attachment quality inhering in a bearer by virtue of the bearer's lacking connection or association with another entity. PATOC:GVG A sensitivity quality inhering in a bearer by virtue of the bearer's dependence on oxygen. quality PATO:0001454 sensitivity to oxygen A sensitivity quality inhering in a bearer by virtue of the bearer's dependence on oxygen. PATOC:GVG A quality inhering in a bearer by virtue of the bearer's dependence on oxygen. quality PATO:0001455 aerobic A quality inhering in a bearer by virtue of the bearer's dependence on oxygen. PATOC:GVG A quality inhering in a bearer by virtue of the bearer's independence on oxygen. quality PATO:0001456 anaerobic A quality inhering in a bearer by virtue of the bearer's independence on oxygen. PATOC:GVG A quality of a process inhering in bearer by virtue of the bearer's disposition to respond to stimulation. sensitivity of occurrent quality PATO:0001457 sensitivity of a process A quality of a process inhering in bearer by virtue of the bearer's disposition to respond to stimulation. PATOC:GVG A sensitivity of a process quality inhering in a bearer by virtue of the bearer's unfolding in a location with or without oxygen. sensitivity of occurrent to oxygen quality PATO:0001458 sensitivity of a process to oxygen A sensitivity of a process quality inhering in a bearer by virtue of the bearer's unfolding in a location with or without oxygen. PATOC:GVG A sensitivity of a process inhering in a biological process by virtue of the process unfolding in a location with oxygen. quality PATO:0001459 aerobic (for occurrence) A sensitivity of a process inhering in a biological process by virtue of the process unfolding in a location with oxygen. PATOC:GVG A sensitivity of a process inhering in a biological process by virtue of the process unfolding in a location without oxygen. quality PATO:0001460 anaerobic (for occurrence) A sensitivity of a process inhering in a biological process by virtue of the process unfolding in a location without oxygen. PATOC:GVG A physical quality inhering in a liquid by virtue of the bearer's ability to attraction of molecules at its surface as a result of unbalanced molecular cohesive forces. quality PATO:0001461 surface tension A physical quality inhering in a liquid by virtue of the bearer's ability to attraction of molecules at its surface as a result of unbalanced molecular cohesive forces. Wikipedia:http://en.wikipedia.org/wiki/Surface_tension A quality inhering in a cell's plasma membrane by virtue of the electrical potential difference across it. quality PATO:0001462 membrane potential A quality inhering in a cell's plasma membrane by virtue of the electrical potential difference across it. Wikipedia:http://en.wikipedia.org/wiki/Membrane_potential A quality inhering in a cell's plasma membrane by virtue of a brief fluctuation in the bearer's potential caused by the rapid opening and closing of voltage-gated ion channels. quality PATO:0001463 action potential A quality inhering in a cell's plasma membrane by virtue of a brief fluctuation in the bearer's potential caused by the rapid opening and closing of voltage-gated ion channels. Wikipedia:http://en.wikipedia.org/wiki/Action_potential A quality that is equal to the potential energy per unit charge associated with a static (time-invariant) electric field, also called the electrostatic potential. quality PATO:0001464 electric potential A quality that is equal to the potential energy per unit charge associated with a static (time-invariant) electric field, also called the electrostatic potential. Wikipedia:http://en.wikipedia.org/wiki/Electric_potential A malformed quality inhering in a bearer by virtue of the bearer's all-encompassing, grotesque morphological defects. quality PATO:0001465 monstrous A malformed quality inhering in a bearer by virtue of the bearer's all-encompassing, grotesque morphological defects. PATOC:GVG A curvature quality inhering in a bearer by virtue of the bearer's being curved towards the front of an organism. curved anterior curved superior (human torso) quality PATO:0001466 curved rostral A curvature quality inhering in a bearer by virtue of the bearer's being curved towards the front of an organism. PATOC:GVG A curvature quality inhering in a bearer by virtue of the bearer's being curved towards the part of the body from which the tail arises. curved inferior (human torso) curved posterior quality PATO:0001467 curved caudal A curvature quality inhering in a bearer by virtue of the bearer's being curved towards the part of the body from which the tail arises. PATOC:GVG A curvature quality inhering in a bearer by virtue of the bearer's being curved towards the back or upper surface of an organism. curved posterior (human torso) curved superior (human head) quality PATO:0001468 curved dorsal A curvature quality inhering in a bearer by virtue of the bearer's being curved towards the back or upper surface of an organism. PATOC:GVG A curvature quality inhering in a bearer by virtue of the bearer's being curved towards the abdomen of an organism. curved anterior (human torso) curved inferior (human head) quality PATO:0001469 curved ventral A curvature quality inhering in a bearer by virtue of the bearer's being curved towards the abdomen of an organism. PATOC:GVG A quality inhering in a bearer by virtue of the bearer's magnitude in respect to a related entity. proportion proportionality quotient ratio quality rate PATO:0001470 Examples: height to weight; brain size to body size. These could all be children of proportionality. Proportions can be measured as ratios. Some measures may be dimensionless. Not all ratios measure proportionality, eg m/s measures velocity which is not a proportion in the sense defined above, it is a quality in its own right. proportionality to A quality inhering in a bearer by virtue of the bearer's magnitude in respect to a related entity. PATOC:nw true A depth which is relatively low. PATO:0001692 low depth shallow quality PATO:0001472 decreased depth A depth which is relatively low. PATOC:GVG A quality inhering in a bearer by virtue of the bearer's being present in two copies. doubled quality PATO:0001473 duplicated A quality inhering in a bearer by virtue of the bearer's being present in two copies. Dictionary.com:Dictionary.com An oriented quality inhering in a bearer by virtue of the bearer's axis being positioned forward. quality PATO:0001474 anteverted An oriented quality inhering in a bearer by virtue of the bearer's axis being positioned forward. bdid:bdid A position which is relatively high. quality high position PATO:0001475 increased position A position which is relatively high. PATOC:GVG A positional which is relatively low. quality low position PATO:0001476 decreased position A positional which is relatively low. PATOC:GVG A positional quality inhering in a bearer by virtue of the bearer's being drawn in or pulled back from any given point. moved quality retruded PATO:0001477 retracted A positional quality inhering in a bearer by virtue of the bearer's being drawn in or pulled back from any given point. Dictionary.com:Dictionary.com A structural quality inhering in a bearer by virtue of the bearer's being broken down; caved in. quality PATO:0001478 collapsed A structural quality inhering in a bearer by virtue of the bearer's being broken down; caved in. Dictionary.com:Dictionary.com true A structural quality inhering in a bearer by virtue of the bearer's resembling a sponge in elasticity, absorbency, or porousness. quality PATO:0001480 spongy A structural quality inhering in a bearer by virtue of the bearer's resembling a sponge in elasticity, absorbency, or porousness. Answers.com:Answers.com A shape quality inhering in a bearer by virtue of the bearer's having an oblique or slanted direction. quality PATO:0001481 sloped A shape quality inhering in a bearer by virtue of the bearer's having an oblique or slanted direction. WordNet:WordNet A quality inhering in a bearer by virtue of the bearer's standing out or projecting beyond a surface or line. quality PATO:0001482 prominent A quality inhering in a bearer by virtue of the bearer's standing out or projecting beyond a surface or line. Dictionary.com:Dictionary.com Absence of an organ, tissue or cell due to failure to develop from a primordium or precursor cell. aplasia undeveloped quality PATO:0001483 With aplasia, the primordium or precursor develops, but does not proceed in its development to a mature structure aplastic Absence of an organ, tissue or cell due to failure to develop from a primordium or precursor cell. PATOC:GVG PATOC:PortlandMeetingFeb2015 A quality of a process which occurs near to or not long before the present. quality PATO:0001484 recent A quality of a process which occurs near to or not long before the present. WordNet:WordNet A structural quality inhering in a bearer by virtue of the bearer's being thicker or more closely packed together; pressed tightly together. PATO:0001840 compact compressed squashed quality dense PATO:0001485 condensed A structural quality inhering in a bearer by virtue of the bearer's being thicker or more closely packed together; pressed tightly together. PATOC:GVG An age quality that exists by virtue of the time (years and months) that the bearer has existed. quality PATO:0001486 chronological age An age quality that exists by virtue of the time (years and months) that the bearer has existed. WordNet:Wordnet A time quality inhering in a bearer by virtue of the bearer's growing old; aging. quality PATO:0001487 senescent A time quality inhering in a bearer by virtue of the bearer's growing old; aging. answers.com:answers.com A cellular quality inhering in a cell by virtue of whether the bearer exhibits the ability to move spontaneously. quality PATO:0001488 Term should be obsoleted and the GO term cellular motility should be used instead. cellular motility A cellular quality inhering in a cell by virtue of whether the bearer exhibits the ability to move spontaneously. thefreedictionary.com:thefreedictionary.com true A growth quality of a process inhering in an organism, structure, or group of organisms by virtue of the bearer's reduced or increased growth. quality PATO:0001490 heterochronic growth A growth quality of a process inhering in an organism, structure, or group of organisms by virtue of the bearer's reduced or increased growth. PATOC:MAH A paedomorphic growth quality which is due to a reduced rate. neotenic growth quality PATO:0001491 neotenous growth A paedomorphic growth quality which is due to a reduced rate. PATOC:mh quality PATO:0001492 This term will be obsoleted; Use GO:growth and PATO:rate. growth rate quality PATO:0001493 This term will be obsoleted; Use GO:growth and PATO:rate. hypertrophic growth quality PATO:0001494 This term will be obsoleted; Use GO:growth and PATO:rate. hypotrophic growth A concave quality inhering in a bearer by virtue of the bearer's shape being a V-shaped cut. quality indented PATO:0001495 notched A concave quality inhering in a bearer by virtue of the bearer's shape being a V-shaped cut. thefreedictionary.com:thefreedictionary.com A reproductive quality inhering in the young of an animal by virtue of the bearer's being cared for at one time. quality PATO:0001496 brood quality A reproductive quality inhering in the young of an animal by virtue of the bearer's being cared for at one time. WordNet:WordNet A reproductive quality inhering in the young of an animal by virtue of the bearer's disposition to survive and develop normally. quality PATO:0001497 brood viability A reproductive quality inhering in the young of an animal by virtue of the bearer's disposition to survive and develop normally. PATOC:GVG true A spheroid quality inhering in a bearer by virtue of the bearer's resembling a ball (a sphere whose equatorial diameter is equal to the polar diameter). PATO:0000408 globular quality rotund PATO:0001499 spherical A spheroid quality inhering in a bearer by virtue of the bearer's resembling a ball (a sphere whose equatorial diameter is equal to the polar diameter). WordNet:WordNet A shape quality inhering in a bearer by virtue of the bearer's being gradually narrower or thinner toward one end. taper quality PATO:0001500 tapered A shape quality inhering in a bearer by virtue of the bearer's being gradually narrower or thinner toward one end. WordNet:WordNet A quality inhering in a bearer by virtue of the bearer's lacking complete growth, differentiation, or development. quality underdeveloped PATO:0001501 immature A quality inhering in a bearer by virtue of the bearer's lacking complete growth, differentiation, or development. Merriam-Webster:Merriam-Webster A monadic quality of continuant inhering in a bearer by virtue of the bearer's being intricate and compounded. quality PATO:0001502 TODO: obsolete this. complexity A monadic quality of continuant inhering in a bearer by virtue of the bearer's being intricate and compounded. WordNet:WordNet A complexity quality in a bearer by virtue of the bearer's having few parts or being complicated or compound. quality PATO:0001503 simple A complexity quality in a bearer by virtue of the bearer's having few parts or being complicated or compound. WordNet:WordNet A complexity quality inhering in a bearer by virtue of the bearer's being intricate and compounded. quality PATO:0001504 complex A complexity quality inhering in a bearer by virtue of the bearer's being intricate and compounded. WordNet:WordNet A structural quality inhering in a bearer by virtue of the bearer's not being in contact with another entity, or of no longer being connected or joined with another entity. quality discontiguous divided_from splitted from PATO:0001505 separated from A structural quality inhering in a bearer by virtue of the bearer's not being in contact with another entity, or of no longer being connected or joined with another entity. WordNet:WordNet A structural quality inhering in a bearer by virtue of the bearer's separation of normally joined parts, such as the separation of adjacent bones without fracture or of certain abdominal muscles during pregnancy. quality PATO:0001506 diastatic A structural quality inhering in a bearer by virtue of the bearer's separation of normally joined parts, such as the separation of adjacent bones without fracture or of certain abdominal muscles during pregnancy. answers.com:answers.com A quality of a single process inhering in a bearer by virtue of the bearer's being interrupted of its normal course. quality PATO:0001507 disrupted A quality of a single process inhering in a bearer by virtue of the bearer's being interrupted of its normal course. PATOC:GVG true A quality of a single physical entity that arises by virtue of whether the bearer exhibits the ability to perform a regular function(s). quality PATO:0001509 functionality A quality of a single physical entity that arises by virtue of whether the bearer exhibits the ability to perform a regular function(s). PATOC:MAH A functionality quality held by the bearer when the latter is able to perform a regular function(s). quality PATO:0001510 functional A functionality quality held by the bearer when the latter is able to perform a regular function(s). PATOC:MAH A disfunctional quality held by the bearer when the latter is unable to perform a regular function(s). PATO:0001640 disfunctional functional failure quality defective failure PATO:0001511 non-functional A disfunctional quality held by the bearer when the latter is unable to perform a regular function(s). PATC:MAH A pattern inhering in a surface by virtue of the bearer's being marked by the presence of dots, punctures, points or pits. quality dotted spotted stippled PATO:0001512 punctate A pattern inhering in a surface by virtue of the bearer's being marked by the presence of dots, punctures, points or pits. medical-dictionary:medical-dictionary true A structural quality inhering in a bearer by virtue of the bearer's lacking some outer layer. quality PATO:0001514 delaminated A structural quality inhering in a bearer by virtue of the bearer's lacking some outer layer. PATOC:cjm A color quality inhering in a bearer by virtue of the bearer's being uneven in color. quality murky PATO:0001515 variable color A color quality inhering in a bearer by virtue of the bearer's being uneven in color. PATOC:NC An optical quality where light rays originating from a point on the object converge. quality PATO:0001516 focus An optical quality where light rays originating from a point on the object converge. Wikipedia:http://en.wikipedia.org/wiki/Focus_(optics) An optical quality inhering in a bearer by virtue of the bearer's having focus. quality PATO:0001517 focused An optical quality inhering in a bearer by virtue of the bearer's having focus. PATOC:GVG An optical quality inhering in a bearer by virtue of the bearer's lacking focus. quality PATO:0001518 blurry An optical quality inhering in a bearer by virtue of the bearer's lacking focus. PATOC:NC A quality inhering in a bearer by virtue of vibration, as perceived by the sense of hearing. quality PATO:0001519 sound quality A quality inhering in a bearer by virtue of vibration, as perceived by the sense of hearing. Wikipedia:http://en.wikipedia.org/wiki/Sound_quality The frequency of transmitted vibrations. quality PATO:0001520 sound frequency The frequency of transmitted vibrations. thefreedictionary.com:thefreedictionary.com A physical quality inhering in a sound wave by virtue of the maximum magnitude (value without regard to sign) of its disturbance. loudness quality PATO:0001521 sound amplitude A physical quality inhering in a sound wave by virtue of the maximum magnitude (value without regard to sign) of its disturbance. answers.com:answers.com A physical quality inhering in sound by virtue of the bearer's travelling speed in a given medium under specified conditions. quality PATO:0001522 sound speed A physical quality inhering in sound by virtue of the bearer's travelling speed in a given medium under specified conditions. Wikipedia:http://en.wikipedia.org/wiki/Sound_speed A physical quality which is equal to the quotient of the speed of a sound wave divided by its wavelength. quality PATO:0001523 sound wavelength A physical quality which is equal to the quotient of the speed of a sound wave divided by its wavelength. Wikipedia:http://en.wikipedia.org/wiki/Sound_wavelength A sound frequency in the range of 0-20 Hz. quality PATO:0001524 intrasonic A sound frequency in the range of 0-20 Hz. studyphysics:studyphysics A sound frequency in the range of 20 to 20.000 Hz. quality PATO:0001525 sonic A sound frequency in the range of 20 to 20.000 Hz. url:http://www.studyphysics.ca/ A sound frequency in the range of 20 000 + Hz. quality PATO:0001526 ultrasonic A sound frequency in the range of 20 000 + Hz. studyphysics:studyphysics A sound amplitude which is relatively low. quality PATO:0001527 quiet A sound amplitude which is relatively low. PATOC:GVG A sound amplitude which is relatively high. quality PATO:0001528 loud A sound amplitude which is relatively high. PATOC:GVG A spatiotemporal quality inhering in a cell. quality PATO:0001529 cellular spatiotemporal quality A spatiotemporal quality inhering in a cell. PATOC:GVG A quality of a single process inhering in a bearer by virtue of the bearer's behavior. behavioral quality of occurrent quality PATO:0001530 behavioral quality of a process A quality of a single process inhering in a bearer by virtue of the bearer's behavior. PATOC:GVG A cellular quality that exists by virtue of the disposition of the cell to adhere to other cells and molecules, through the emergent action of the molecular parts of the cell surface. quality PATO:0001531 cellular adhesivity A cellular quality that exists by virtue of the disposition of the cell to adhere to other cells and molecules, through the emergent action of the molecular parts of the cell surface. PATOC:cjm A color pattern inhering in a bearer by virtue of the bearer's having one hue. evenly colored homogeneously colored uniformly colored quality homogenously pigmented PATO:0001532 mono-colored A color pattern inhering in a bearer by virtue of the bearer's having one hue. PATOC:GVG A color pattern inhering in a bearer by virtue of bearer's having two or more hues or degrees of saturation. variegated quality PATO:0001533 multi-colored A color pattern inhering in a bearer by virtue of bearer's having two or more hues or degrees of saturation. PATOC:GVG A color pattern inhering in a bearer by virtue of bearer's having 3 or more hues or degrees of saturations. quality PATO:0001534 motley A color pattern inhering in a bearer by virtue of bearer's having 3 or more hues or degrees of saturations. merriam-webster.:merriam-webster. A color pattern inhering in a bearer by virtue of bearer's being marked with small spots, patches, or specks of hue or degree of saturation differing from that of the background. quality speckled PATO:0001535 dappled A color pattern inhering in a bearer by virtue of bearer's being marked with small spots, patches, or specks of hue or degree of saturation differing from that of the background. merriam-webster.:merriam-webster. A molecular quality that inheres in a molecular entity by virtue of the bearer's disposition to dissolve in a liquid. quality PATO:0001536 solubility A molecular quality that inheres in a molecular entity by virtue of the bearer's disposition to dissolve in a liquid. edp:edp A solubility quality inhering in a substance by virtue of the bearer's disposition to dissolve in a liquid. soluble quality PATO:0001537 soluble in A solubility quality inhering in a substance by virtue of the bearer's disposition to dissolve in a liquid. edp:edp A solubility quality inhering in a substance by virtue of the bearer's inability of a substance to dissolve in a liquid. insoluble quality PATO:0001538 insoluble in A solubility quality inhering in a substance by virtue of the bearer's inability of a substance to dissolve in a liquid. edp:edp A compositional quality inhering in an bearer by virtue of the bearer's quantities or relative ratios of amylose of the inhering entity. amylose compositionality quality PATO:0001539 amylose composition A compositional quality inhering in an bearer by virtue of the bearer's quantities or relative ratios of amylose of the inhering entity. PATOC:GVG An amylose composition quality inhering in an bearer by virtue of the bearer's having negligible or no amylose content. quality PATO:0001540 glutinous An amylose composition quality inhering in an bearer by virtue of the bearer's having negligible or no amylose content. TO:TO An amylose composition quality inhering in an bearer by virtue of the bearer's having high amount of amylose content. quality PATO:0001541 non-glutinous An amylose composition quality inhering in an bearer by virtue of the bearer's having high amount of amylose content. TO:TO A phase which starts later than natural start point. quality PATO:0001542 delayed phase A phase which starts later than natural start point. PATOC:GVG A physical quality inhering in a bearer by virtue of the bearer's disposition to being turned, bowed, or twisted without breaking. quality PATO:0001543 flexibility A physical quality inhering in a bearer by virtue of the bearer's disposition to being turned, bowed, or twisted without breaking. merriam-webster:merriam-webster A physical quality inhering in a bearer by virtue of the bearer's ability of being turned, bowed, or twisted without breaking. bendy quality PATO:0001544 flexible A physical quality inhering in a bearer by virtue of the bearer's ability of being turned, bowed, or twisted without breaking. merriam-webster:merriam-webster A physical quality inhering in a bearer by virtue of the bearer's inability of being turned, bowed, or twisted without breaking. stiff quality stiffness PATO:0001545 inflexible A physical quality inhering in a bearer by virtue of the bearer's inability of being turned, bowed, or twisted without breaking. merriam-webster:merriam-webster A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity characterized by particles arranged such that their shape and volume are relatively stable. solidity quality PATO:0001546 quality of a solid A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity characterized by particles arranged such that their shape and volume are relatively stable. Chemistry:http://chemistry.about.com/od/chemistryglossary/a/soliddefinition.htm A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity consisting of particles that have neither a defined volume nor defined shape. gaseous quality PATO:0001547 quality of a gas A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity consisting of particles that have neither a defined volume nor defined shape. Chemistry:http://chemistry.about.com/od/chemistryglossary/a/gasdefinition.htm PATOC:GVG A physical quality inhering in an entity exhibiting the physical characteristics of an amorphous (non-crystalline) form of matter between a gas and a solid that has a definite volume, but no definite shape. liquidity quality PATO:0001548 quality of a liquid A physical quality inhering in an entity exhibiting the physical characteristics of an amorphous (non-crystalline) form of matter between a gas and a solid that has a definite volume, but no definite shape. url:http://www.chemistry-dictionary.com/definition/liquid.php A sensitivity toward an external stimulus which is higher than normal/average. high sensitivity toward increased sensitivity quality PATO:0001549 increased sensitivity toward A sensitivity toward an external stimulus which is higher than normal/average. PATO:GVG A sensitivity toward an external stimulus which is lower than normal/average. decreased sensitivity low sensitivity toward quality PATO:0001550 decreased sensitivity toward A sensitivity toward an external stimulus which is lower than normal/average. PATO:GVG A sensitivity of a process which is higher than normal or average. high sensitivity of occurrent increased sensitivity of occurrent quality PATO:0001551 increased sensitivity of a process A sensitivity of a process which is higher than normal or average. PATO:GVG A sensitivity of a process which is lower than normal or average. decreased sensitivity of occurrent low sensitivity of occurrent quality PATO:0001552 decreased sensitivity of a process A sensitivity of a process which is lower than normal or average. PATO:GVG A sensitivity of occurrent to oxygen which is higher than normal or average. high sensitivity of occurrent to oxygen quality PATO:0001553 increased sensitivity of a process to oxygen A sensitivity of occurrent to oxygen which is higher than normal or average. PATO:GVG A sensitivity of a process to oxygen which is lower than normal or average. low sensitivity of occurrent to oxygen quality PATO:0001554 decreased sensitivity of a process to oxygen A sensitivity of a process to oxygen which is lower than normal or average. PATO:GVG The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts. OBO_REL:has_part extra or missing physical or functional parts has or lacks parts of type mereological quality number of quality cardinality number PATO:0001555 has number of The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts. PATOC:CJM true true A quality of a process inhering in a bearer by virtue of the bearer's lacking a processual part as specified by the additional entity. quality PATO:0001558 lacking processual parts A quality of a process inhering in a bearer by virtue of the bearer's lacking a processual part as specified by the additional entity. PATOC:GVG A functionality quality which is held by the bearer when the latter is able to perform additional or different function(s). having supernumerary functions quality PATO:0001559 having extra function A functionality quality which is held by the bearer when the latter is able to perform additional or different function(s). PATO:MAH true A quality of a process inhering in a bearer by virtue of the bearer's having additional processual parts. having supernumerary processual parts quality PATO:0001561 having extra processual parts A quality of a process inhering in a bearer by virtue of the bearer's having additional processual parts. PATOC:GVG A mass which is lower than normal or average. PATO:0000579 low mass small mass quality PATO:0001562 decreased mass A mass which is lower than normal or average. PATO:GVG A mass which is higher than normal or average. PATO:0000578 high mass large mass quality PATO:0001563 increased mass A mass which is higher than normal or average. PATO:GVG A quality of a process inhering in a bearer by virtue of the bearer's processual parts. quality PATO:0001564 extra or missing processual parts A quality of a process inhering in a bearer by virtue of the bearer's processual parts. PATOC:GVG true A spatial pattern inhering in a bearer by virtue of the bearer's being spread out or scattered about or divided up. PATO:0001513 diffuse scattered quality PATO:0001566 distributed A spatial pattern inhering in a bearer by virtue of the bearer's being spread out or scattered about or divided up. WordNet:WordNet A spatial pattern inhering in a bearer by virtue of the bearer's not being spread out or scattered about or divided up. quality PATO:0001567 undistributed A spatial pattern inhering in a bearer by virtue of the bearer's not being spread out or scattered about or divided up. WordNet:WordNet true true A quality of a process inhering in a bearer by virtue of the bearer's having fewer processual parts. quality PATO:0001570 having decreased processual parts A quality of a process inhering in a bearer by virtue of the bearer's having fewer processual parts. PATO:GVG A size quality inhering in a bearer by virtue of the bearer's being made wider or larger in all dimensions. quality PATO:0001571 dilated A size quality inhering in a bearer by virtue of the bearer's being made wider or larger in all dimensions. WordNet:WordNet true A symmetry quality inhering in a bearer by virtue of the bearer's having equal dimensions or measurements. quality PATO:0001573 isometrical A symmetry quality inhering in a bearer by virtue of the bearer's having equal dimensions or measurements. WordNet:WordNet A physical quality inhering in a bearer by virtue of the bearer's motion characteristic. quality PATO:0001574 flow rate A physical quality inhering in a bearer by virtue of the bearer's motion characteristic. WordNet:WordNet A pressure which is relatively low. low pressure quality PATO:0001575 decreased pressure A pressure which is relatively low. PATO:GVG A pressure which is relatively high. high pressure quality PATO:0001576 increased pressure A pressure which is relatively high. PATO:GVG A permeability which is relatively high. high permeability quality PATO:0001577 increased permeability A permeability which is relatively high. PATO:GVG A permeability which is relatively low. low permeability quality PATO:0001578 decreased permeability A permeability which is relatively low. PATO:GVG A physical quality that is the ability to contract or shrink. quality PATO:0001579 contractility A physical quality that is the ability to contract or shrink. WordNet:WordNet A contractility which is relatively high. high contractility quality PATO:0001580 increased contractility A contractility which is relatively high. PATO:GVG A contractility which is relatively low. low contractility quality PATO:0001581 decreased contractility A contractility which is relatively low. PATO:GVG A spatial quality inhering in an inactive muscle or muscle fibers by virtue of the bearer's exhibiting gradual lengthening. quality PATO:0001582 GO has now relevant relation terms which should be used instead. obsolete relaxational quality true A spatial quality inhering in an inactive muscle or muscle fibers by virtue of the bearer's exhibiting gradual lengthening. WordNet:WordNet A variability which is relatively low. low variability quality PATO:0001583 decreased variability A variability which is relatively low. PATO:GVG A variability which is relatively high. high variability quality PATO:0001584 increased variability A variability which is relatively high. PATO:GVG A physical quality inhering in a bearer by virtue of the bearer's disposition to transmit of an entity through a medium. quality PATO:0001585 Examples could be heat or electricity or sound. conductivity A physical quality inhering in a bearer by virtue of the bearer's disposition to transmit of an entity through a medium. PATOC:GVG A variability quality inhering in a bearer by virtue of whether the bearer exhibits rate variation or change. quality PATO:0001586 variability of rate A variability quality inhering in a bearer by virtue of whether the bearer exhibits rate variation or change. PATO:GVG A variability of rate which is relatively high. high variability of rate quality PATO:0001587 increased variability of rate A variability of rate which is relatively high. PATO:GVG A variability of rate which is relatively low. low variability of rate quality PATO:0001588 decreased variability of rate A variability of rate which is relatively low. PATO:GVG Increased, intensified. PATO:0002017 quality PATO:0001589 Obsoleted because it used to be a child of behavioral quality, which really meant increased magnitude of a given behavior. Now this can be done by using increased magnitude with another quality. obsolete enhanced true Increased, intensified. PATOC:GVG A structural quality inhering in a bearer by virtue of the bearer's coinciding spatially, partially or wholly with another entity. overlap quality PATO:0001590 overlap with A structural quality inhering in a bearer by virtue of the bearer's coinciding spatially, partially or wholly with another entity. PATO:GVG A surface shape quality inhering in a bearer by virtue of the bearer's exhibiting a degree of bending. quality PATO:0001591 curvature A surface shape quality inhering in a bearer by virtue of the bearer's exhibiting a degree of bending. WordNet:WordNet A curvature which is relatively high. quality PATO:0001592 increased curvature A curvature which is relatively high. PATO:GVG A curvature which is relatively low. quality PATO:0001593 decreased curvature A curvature which is relatively low. PATO:GVG A concave quality inhering in a bearer by virtue of the bearer's forming or resembling an arch. quality PATO:0001594 arched A concave quality inhering in a bearer by virtue of the bearer's forming or resembling an arch. WordNet:WordNet A 1-D extent quality inhering in a bearer by virtue of the bearer's downward or backward or inward dimension. quality PATO:0001595 depth A 1-D extent quality inhering in a bearer by virtue of the bearer's downward or backward or inward dimension. WordNet:WordNet A depth quality which is relatively high. PATO:0001666 deep quality PATO:0001596 increased depth A depth quality which is relatively high. PATO:GVG An oriented quality inhering in a bearer by virtue of the bearer's being turned outward in placement. quality PATO:0001597 everted An oriented quality inhering in a bearer by virtue of the bearer's being turned outward in placement. thefreedictionary:thefreedictionary A quality inhering in a bearer by virtue of the bearer's extending out above or beyond a surface or boundary. PATO:0001644 protruding relational protruding quality quality PATO:0001598 protruding A quality inhering in a bearer by virtue of the bearer's extending out above or beyond a surface or boundary. WordNet:WordNet An oriented quality inhering in a bearer by virtue of the bearer's being relocated around an axis. rotation quality PATO:0001599 rotated An oriented quality inhering in a bearer by virtue of the bearer's being relocated around an axis. answers.com:answers.com A rotation quality inhering in a bearer by virtue of being rotated towards the rear of organism. quality PATO:0001600 posteriorly rotated A rotation quality inhering in a bearer by virtue of being rotated towards the rear of organism. PATOC:GVG A rotation quality inhering in a bearer by virtue of being rotated towards the front of an organism. quality PATO:0001601 anteriorly rotated A rotation quality inhering in a bearer by virtue of being rotated towards the front of an organism. PATOC:GVG A size quality inhering in a bearer by virtue of the bearer's being abnormally expanded or increased in size. quality expanded PATO:0001602 distended A size quality inhering in a bearer by virtue of the bearer's being abnormally expanded or increased in size. WordNet:WordNet A life span which is relatively high. high life span quality PATO:0001603 increased life span A life span which is relatively high. PATO:GVG A life span which is relatively low. low life span quality PATO:0001604 decreased life span A life span which is relatively low. PATO:GVG A spatial pattern inhering in a bearer by virtue of the bearer's being in disarray; extremely disorderly. quality PATO:0001605 disheveled A spatial pattern inhering in a bearer by virtue of the bearer's being in disarray; extremely disorderly. WordNet:WordNet A coating which is oily and slippery. quality PATO:0001606 greasy A coating which is oily and slippery. .answers.com:.answers.com A tangled quality inhering in a bearer by virtue of the bearer's being not possible to unravel. quality PATO:0001607 matted A tangled quality inhering in a bearer by virtue of the bearer's being not possible to unravel. PATOC:MAH A spatial pattern inhering in a bearer by virtue of the bearer's being marked by, consisting of, or diversified with patches. quality PATO:0001608 patchy A spatial pattern inhering in a bearer by virtue of the bearer's being marked by, consisting of, or diversified with patches. Merriam-Webster:Merriam-Webster A spatial pattern inhering in a bearer by virtue of the bearer's being scattered; spread irregularly, and at a distance from each other. quality PATO:0001609 sparse A spatial pattern inhering in a bearer by virtue of the bearer's being scattered; spread irregularly, and at a distance from each other. biology.lsu:biology.lsu true A variability quality inhering in a bearer by virtue of whether the bearer exhibits color variation or change. quality PATO:0001611 variability of color A variability quality inhering in a bearer by virtue of whether the bearer exhibits color variation or change. PATO:GVG A variability of color which is relatively high. high variability of color quality PATO:0001612 increased variability of color A variability of color which is relatively high. PATO:GVG A variability of color which is relatively low. low variability of color quality PATO:0001613 decreased variability of color A variability of color which is relatively low. PATO:GVG A variability quality inhering in a bearer by virtue of the bearer's lacking or not exhibiting variation of color. quality PATO:0001614 invariant color A variability quality inhering in a bearer by virtue of the bearer's lacking or not exhibiting variation of color. PATO:GVG A variability quality inhering in a bearer by virtue of the bearer's having or exhibiting variation of colour. quality PATO:0001615 variant color A variability quality inhering in a bearer by virtue of the bearer's having or exhibiting variation of colour. PATO:GVG true A morphological quality inhering in a bearer by virtue of the bearer's being distorted in form. quality disfigured distorted PATO:0001617 deformed A morphological quality inhering in a bearer by virtue of the bearer's being distorted in form. thefreedictionary.com:thefreedictionary.com A tonicity which is relatively high. high tonicity quality PATO:0001618 increased tonicity A tonicity which is relatively high. PATO:GVG A tonicity which is relatively low. low tonicity quality PATO:0001619 decreased tonicity A tonicity which is relatively low. PATO:GVG A structural quality inhering in a cell or blood vessel or capillary by virtue of the bearer's being in a rigid state of fullness resulting from pressure of the contents against the wall or membrane. quality PATO:0001620 turgor A structural quality inhering in a cell or blood vessel or capillary by virtue of the bearer's being in a rigid state of fullness resulting from pressure of the contents against the wall or membrane. WordNet:WordNet A turgor which is relatively low. low turgor quality PATO:0001621 decreased turgor A turgor which is relatively low. PATO:GVG A turgor which is relatively high. high turgor quality PATO:0001622 increased turgor A turgor which is relatively high. PATO:GVG A size quality inhering in a bearer by virtue of a part or parts of the bearer's being decreased in size due to reduction in tissue mass through wasting. atrophic quality PATO:0001623 atrophied A size quality inhering in a bearer by virtue of a part or parts of the bearer's being decreased in size due to reduction in tissue mass through wasting. Wiikipedia:Wasting Wikipedia:Atrophy A functionality quality held by the bearer when the latter exhibits decreased ability to perform a regular function(s). PATO:0001556 PATO:0001568 PATO:0001641 PATO:0001642 dysfunction dysfunctional having decreased function lacks function of type low functionality partial functionality quality impaired PATO:0001624 decreased functionality A functionality quality held by the bearer when the latter exhibits decreased ability to perform a regular function(s). PATO:MAH A functional quality held by the bearer when the latter exhibits increased ability to perform a regular function(s). high functionality quality PATO:0001625 increased functionality A functional quality held by the bearer when the latter exhibits increased ability to perform a regular function(s). PATO:MAH A structural quality inhering in a bearer by virtue of whether the bearer has enough functionality. quality adequacy PATO:0001626 This term and children should probably be obsoleted. sufficiency A structural quality inhering in a bearer by virtue of whether the bearer has enough functionality. PATO:GVG A wholeness quality inhering in a bearer by virtue of the bearer's has enough functionality. quality adequate PATO:0001627 sufficient A wholeness quality inhering in a bearer by virtue of the bearer's has enough functionality. PATO:GVG A wholeness quality inhering in a bearer by virtue of the bearer's lacks enough functionality. quality inadequate PATO:0001628 insufficient A wholeness quality inhering in a bearer by virtue of the bearer's lacks enough functionality. PATO:GVG A spatial pattern inhering in a bearer by virtue of the bearer's being gathered or tending to gather into a mass or whole. clumped clustered quality PATO:0001629 aggregated A spatial pattern inhering in a bearer by virtue of the bearer's being gathered or tending to gather into a mass or whole. WordNet:WordNet A positional quality inhering in a bearer by virtue of the bearer's being distributed or spread over a considerable extent. quality PATO:0001630 dispersed A positional quality inhering in a bearer by virtue of the bearer's being distributed or spread over a considerable extent. WordNet:WordNet true A spatial quality inhering in a bearer by virtue of the bearer's being located toward the front of an organism relative to another entity. preceding quality PATO:0001632 anterior to A spatial quality inhering in a bearer by virtue of the bearer's being located toward the front of an organism relative to another entity. PATOC:nw A spatial quality inhering in a bearer by virtue of the bearer's being located toward the rear of an organism relative to another entity. posterior (human torso) superior (human head) quality PATO:0001633 posterior to A spatial quality inhering in a bearer by virtue of the bearer's being located toward the rear of an organism relative to another entity. PATOC:nw A quality of a single physical entity inhering in a bearer by virtue of whether the bearer is essential or indispensable. quality PATO:0001634 necessity (continuant) A quality of a single physical entity inhering in a bearer by virtue of whether the bearer is essential or indispensable. WordNet:WordNet A necessity quality (continuant) inhering in a bearer by virtue of the bearer's being essential or indispensable. quality PATO:0001635 necessary (continuant) A necessity quality (continuant) inhering in a bearer by virtue of the bearer's being essential or indispensable. WordNet:WordNet A necessity quality (continuant) inhering in a bearer by virtue of the bearer's being non-essential or dispensable. quality PATO:0001636 unnecessary (continuant) A necessity quality (continuant) inhering in a bearer by virtue of the bearer's being non-essential or dispensable. WordNet:WordNet A quality of single process inhering in a bearer by virtue of whether the bearer is essential or indispensable. quality PATO:0001637 necessity of occurrent A quality of single process inhering in a bearer by virtue of whether the bearer is essential or indispensable. PATO:GVG A necessity quality inhering in a process by virtue of the bearer's being essential or indispensable. quality PATO:0001638 necessary (occurrent) A necessity quality inhering in a process by virtue of the bearer's being essential or indispensable. PATO:GVG A necessity quality inhering in a process by virtue of the bearer's being non-essential or dispensable. quality PATO:0001639 unnecessary (occurrent) A necessity quality inhering in a process by virtue of the bearer's being non-essential or dispensable. PATO:GVG true true true A size quality inhering in a bearer by virtue of the bearer's having a short, stocky build. quality PATO:0001643 stubby A size quality inhering in a bearer by virtue of the bearer's having a short, stocky build. thefreedictionary.com:thefreedictionary.com true A quality inhering into a bearer by virtue of the bearer's extending out above or beyond its surface or boundary into the surface or boundary of another entity. quality PATO:0001645 protruding into A quality inhering into a bearer by virtue of the bearer's extending out above or beyond its surface or boundary into the surface or boundary of another entity. PATOC:nc A quality inhering into a bearer by virtue of the bearer's extending out above or beyond its surface or boundary and outwards in relation to the physical space occupied by another entity. extruding from quality exits through exposed PATO:0001646 protruding out of A quality inhering into a bearer by virtue of the bearer's extending out above or beyond its surface or boundary and outwards in relation to the physical space occupied by another entity. PATOC:nc true An 1-D extent quality which is equal to the length of the closed curve of a circle. quality PATO:0001648 circumference An 1-D extent quality which is equal to the length of the closed curve of a circle. WordNet:WordNet A curvature quality inhering in a bearer by virtue of the bearer's being curved towards the side. quality PATO:0001649 curved lateral A curvature quality inhering in a bearer by virtue of the bearer's being curved towards the side. PATOC:GVG A resistance to a stimulus which is relatively high. high resistance to increased resistance quality PATO:0001650 increased resistance to A resistance to a stimulus which is relatively high. PATOC:GVG A resistance to a stimulus which is relatively low. decreased resistance low resistance to quality PATO:0001651 decreased resistance to A resistance to a stimulus which is relatively low. PATOC:GVG A spatial quality inhering in a bearer by virtue of the bearer's spatial positioning with respect to an additional entity. quality PATO:0001652 alignment A spatial quality inhering in a bearer by virtue of the bearer's spatial positioning with respect to an additional entity. PATOC:GVG An alignment quality inhering in a bearer by virtue of the bearer's being in a proper spatial positioning with respect to an additional entity. aligned quality aligned to PATO:0001653 aligned with An alignment quality inhering in a bearer by virtue of the bearer's being in a proper spatial positioning with respect to an additional entity. PATO:GVG An alignment quality inhering in a bearer by virtue of the bearer's being in a improper spatial positioning with respect to an additional entity. misaligned unaligned with quality PATO:0001654 misaligned with An alignment quality inhering in a bearer by virtue of the bearer's being in a improper spatial positioning with respect to an additional entity. PATOC:GVG A concentration quality inhering in a bearer by virtue of the bearer's amount of osmoles of solute per liter of solution. quality PATO:0001655 osmolarity A concentration quality inhering in a bearer by virtue of the bearer's amount of osmoles of solute per liter of solution. Wikipedia:http://en.wikipedia.org/wiki/Osmolarity A osmolarity which is relatively low. low osmolarity quality PATO:0001656 decreased osmolarity A osmolarity which is relatively low. PATOC:GVG A osmolarity which is relatively high. high osmolarity quality PATO:0001657 increased osmolarity A osmolarity which is relatively high. PATOC:GVG A rotation quality inhering in a bearer by virtue of being rotated towards the back or upper surface of an organism. quality PATO:0001658 dorsally rotated A rotation quality inhering in a bearer by virtue of being rotated towards the back or upper surface of an organism. PATOC:GVG A rotation quality inhering in a bearer by virtue of being rotated towards the abdomen of an organism. quality PATO:0001659 ventrally rotated A rotation quality inhering in a bearer by virtue of being rotated towards the abdomen of an organism. PATOC:GVG An action potential which is relatively low. low action potential quality PATO:0001660 obsolete decreased action potential true An action potential which is relatively low. PATOC:GVG An action potential which is relatively high. high action potential quality PATO:0001661 obsolete increased action potential true An action potential which is relatively high. PATOC:GVG A structural quality inhering in a bearer by virtue of the bearer's disposition to being damaged or destroyed. quality PATO:0001662 fragility A structural quality inhering in a bearer by virtue of the bearer's disposition to being damaged or destroyed. WordNet:WordNet A solubility which is relatively high. high solubility quality PATO:0001663 increased solubility A solubility which is relatively high. PATO:GVG A solubility which is relatively low. low solubility quality PATO:0001664 decreased solubility A solubility which is relatively low. PATO:GVG A spatial pattern inhering in a bearer by virtue of the bearer's being located near a surface. PATO:0001471 superficial to quality PATO:0001665 superficial A spatial pattern inhering in a bearer by virtue of the bearer's being located near a surface. Dictionary.com:Dictionary.com true An attachment quality inhering in a bearer by virtue of the bearer's connection or association with another entity. attached quality affixed to PATO:0001667 attached to An attachment quality inhering in a bearer by virtue of the bearer's connection or association with another entity. PATOC:GVG A structural quality inhering in a bearer by virtue of the bearer's being in close proximity and physically interacting with another entity. associated quality PATO:0001668 associated with A structural quality inhering in a bearer by virtue of the bearer's being in close proximity and physically interacting with another entity. PATOC:GVG A susceptibility toward an external stimulus which is higher than normal/average. high susceptibility toward increased susceptibility quality PATO:0001669 increased susceptibility toward A susceptibility toward an external stimulus which is higher than normal/average. PATOC:GVG A susceptibility toward an external stimulus which is lower than normal/average. decreased susceptibility low susceptibility toward quality PATO:0001670 decreased susceptibility toward A susceptibility toward an external stimulus which is lower than normal/average. PATOC:GVG A distribution which is relatively high. high distribution quality PATO:0001671 increased distribution A distribution which is relatively high. PATOC:GVG A distribution which is relatively low. low distribution quality PATO:0001672 decreased distribution A distribution which is relatively low. PATOC:GVG Structure quality that is the presence of at least one sac-like closed membranous structure containing one or more liquid or solid organism substances. cysts quality PATO:0001673 Cystic is an abnormal condition. cystic Structure quality that is the presence of at least one sac-like closed membranous structure containing one or more liquid or solid organism substances. PATOC:MAH A concentration quality inhering in a bearer by virtue of the bearer's catalytic activity divided by the volume of the system. quality PATO:0001674 catalytic (activity) concentration A concentration quality inhering in a bearer by virtue of the bearer's catalytic activity divided by the volume of the system. IUPAC:IUPAC An efficiency which is relatively low. low efficiency quality PATO:0001675 decreased efficiency An efficiency which is relatively low. PATOC:GVG An efficiency which is relatively high. high efficiency quality PATO:0001676 increased efficiency An efficiency which is relatively high. PATOC:GVG An efficiency quality inhering in a bearer by virtue of the bearer's lacking efficiency. quality PATO:0001677 inefficient An efficiency quality inhering in a bearer by virtue of the bearer's lacking efficiency. PATOC:GVG An efficiency quality inhering in a bearer by virtue of the bearer's having efficiency. quality PATO:0001678 efficient An efficiency quality inhering in a bearer by virtue of the bearer's having efficiency. PATOC:GVG A volume quality inhering in a mass of substance by virtue of the amount of 3-dimensional space it occupies. quality PATO:0001679 The reciprocal of density. specific volume A volume quality inhering in a mass of substance by virtue of the amount of 3-dimensional space it occupies. Wikipedia:http://en.wikipedia.org/wiki/Specific_volume A volume quality inhering in a homogeneous substance containing 6.02 x 1023 atoms or molecules by virtue of the amount of 3-dimensional space it occupies. quality PATO:0001680 molar volume A volume quality inhering in a homogeneous substance containing 6.02 x 1023 atoms or molecules by virtue of the amount of 3-dimensional space it occupies. Wikipedia:http://en.wikipedia.org/wiki/Molar_volume A physical quality that inheres in a homogeneous substance containing 6.02 x 1023 atoms or molecules. quality PATO:0001681 molar mass A physical quality that inheres in a homogeneous substance containing 6.02 x 1023 atoms or molecules. Wikipedia:http://en.wikipedia.org/wiki/Molar_mass A physical quality inhering in a bearer by virtue of the bearer's disposition to exert an attractive or repulsive force on other entities. quality PATO:0001682 magnetism A physical quality inhering in a bearer by virtue of the bearer's disposition to exert an attractive or repulsive force on other entities. Wikipedia:http://en.wikipedia.org/wiki/Magnetism A magnetism which is relatively high. high magnetism quality PATO:0001683 increased magnetism A magnetism which is relatively high. PATOC:GVG A magnetism which is relatively low. low magnetism quality PATO:0001684 decreased magnetism A magnetism which is relatively low. PATOC:GVG A magnetic quality inhering in a bearer by virtue of the bearer's ability to exert magnitism. quality PATO:0001685 magnetic A magnetic quality inhering in a bearer by virtue of the bearer's ability to exert magnitism. PATOC:GVG A magnetic quality inhering in a bearer by virtue of the bearer's inability to exert magnitism. quality PATO:0001686 non-magnetic A magnetic quality inhering in a bearer by virtue of the bearer's inability to exert magnitism. PATOC:GVG A positional quality inhering in a bearer by virtue of the bearer's vertical distance of a point above or below a reference surface. quality PATO:0001687 elevation A positional quality inhering in a bearer by virtue of the bearer's vertical distance of a point above or below a reference surface. Trailillustrated:Trailillustrated An elevation which is relatively high. high elevation quality elevated PATO:0001688 increased elevation An elevation which is relatively high. PATOC:GVG An elevation which is relatively low. low elevation quality PATO:0001689 decreased elevation An elevation which is relatively low. PATOC:GVG A contractility quality inhering in a bearer by virtue of the bearer's ability of contracting or being contracted. quality PATO:0001690 This refers to the disposition of the bearer. contractile A contractility quality inhering in a bearer by virtue of the bearer's ability of contracting or being contracted. PATOC:GVG A contractility quality inhering in a bearer by virtue of the bearer's inability of contracting or being contracted. quality PATO:0001691 This refers to the disposition of the bearer. non-contractile A contractility quality inhering in a bearer by virtue of the bearer's inability of contracting or being contracted. PATOC:GVG true A viscosity which relatively high. high viscosity quality PATO:0001693 increased viscosity A viscosity which relatively high. PATOC:GVG A viscosity which relatively low. low viscosity quality PATO:0001694 decreased viscosity A viscosity which relatively low. PATOC:GVG A fecundity which is relatively high. high fecundity quality PATO:0001695 increased fecundity A fecundity which is relatively high. PATOC:GVG A fecundity which is relatively low. low fecundity quality PATO:0001696 decreased fecundity A fecundity which is relatively low. PATOC:GVG A photosensitivity which is relatively low. low photosensitivity quality PATO:0001697 decreased photosensitivity A photosensitivity which is relatively low. PATOC:GVG A photosensitivity which is relatively high. high photosensitivity quality PATO:0001698 increased photosensitivity A photosensitivity which is relatively high. PATOC:GVG A sleep pattern which has regular start and/or end times. quality PATO:0001699 regular sleep pattern A sleep pattern which has regular start and/or end times. PATOC:GVG A sleep pattern which has irregular start and/or end times. quality PATO:0001700 irregular sleep pattern A sleep pattern which has irregular start and/or end times. PATOC:GVG A quality inhering in a bearer by virtue of the bearer's exhibiting complete growth, differentiation, or development. quality PATO:0001701 mature A quality inhering in a bearer by virtue of the bearer's exhibiting complete growth, differentiation, or development. Merriam-Webster:Merriam-Webster A color consisting of violet hue and high saturation. quality bright violet PATO:0001702 saturated violet A color consisting of violet hue and high saturation. PATOC:GVG A color consisting of violet hue and low saturation. pale violet quality PATO:0001703 desaturated violet A color consisting of violet hue and low saturation. PATOC:GVG A color consisting of violet hue and high brightness. quality PATO:0001704 light violet A color consisting of violet hue and high brightness. PATOC:GVG A color consisting of violet hue and low brightness. quality PATO:0001705 dark violet A color consisting of violet hue and low brightness. PATOC:GVG A behavioral quality inhering in a bearer by virtue of the bearer's disposition to lack activity. quality PATO:0001706 behavioural inactive A behavioral quality inhering in a bearer by virtue of the bearer's disposition to lack activity. PATOC:GVG A behavioral quality of a process inhering in a bearer by virtue of the bearer's exhibiting marked activity. quality PATO:0001707 behavioural active A behavioral quality of a process inhering in a bearer by virtue of the bearer's exhibiting marked activity. PATOC:GVG A size quality inhering in an bearer by virtue of the bearer's extension in one dimension. 1-D size quality PATO:0001708 1-D extent A size quality inhering in an bearer by virtue of the bearer's extension in one dimension. PATOC:GVG A size quality inhering in an bearer by virtue of the bearer's extension in two dimensions. 2-D size quality PATO:0001709 2-D extent A size quality inhering in an bearer by virtue of the bearer's extension in two dimensions. PATOC:GVG A size quality inhering in an bearer by virtue of the bearer's extension in three dimensions. 3D size quality PATO:0001710 3-D extent A size quality inhering in an bearer by virtue of the bearer's extension in three dimensions. PATOC:GVG An 1-D extent quality inhering in two-dimensional bearer by virtue of being equal to the distance around it. quality PATO:0001711 perimeter An 1-D extent quality inhering in two-dimensional bearer by virtue of being equal to the distance around it. Wikipedia:http://en.wikipedia.org/wiki/Perimeter A perimeter which is relatively high. quality PATO:0001712 increased perimeter A perimeter which is relatively high. PATOC:GVG A perimeter which is relatively low. quality PATO:0001713 decreased perimeter A perimeter which is relatively low. PATOC:GVG A diameter which is relatively large. quality PATO:0001714 increased diameter A diameter which is relatively large. PATOC:GVG A diameter which is relatively small. quality PATO:0001715 decreased diameter A diameter which is relatively small. PATOC:GVG A structural quality inhering in a bearer by virtue of the bearer's ability to withstand great strain without tearing or breaking. quality resilient strong tough PATO:0001716 non-fragile A structural quality inhering in a bearer by virtue of the bearer's ability to withstand great strain without tearing or breaking. thefreedictionary.com:thefreedictionary.com A radiation emitting quality which obtains by the intensity of the bearer emitted radiation. quality PATO:0001717 radiation emitting intensity quality A radiation emitting quality which obtains by the intensity of the bearer emitted radiation. PATOC:GVG A quality that exists by virtue of the luminous intensity per unit area projected in a given direction. quality PATO:0001718 luminance A quality that exists by virtue of the luminous intensity per unit area projected in a given direction. Wikipedia:http://en.wikipedia.org/wiki/Luminance A behavioral quality which holds by virtue of whether the bearer exhibits the ability to receive another agentitive entity. quality PATO:0001719 receptivity A behavioral quality which holds by virtue of whether the bearer exhibits the ability to receive another agentitive entity. PATOC:cjm A behavioral quality which holds by virtue of extent of the receptiveness of a female to male advances. quality PATO:0001720 female receptivity A behavioral quality which holds by virtue of extent of the receptiveness of a female to male advances. GO:GO A behavioral quality which holds by virtue of extent of the receptiveness of a male to female advances. quality PATO:0001721 male receptivity A behavioral quality which holds by virtue of extent of the receptiveness of a male to female advances. PATOC:GVG true A female receptivity which is relatively high. high female receptivity quality PATO:0001723 increased female receptivity A female receptivity which is relatively high. PATOC:GVG A female receptivity which is relatively low. low female receptivity quality PATO:0001724 decreased female receptivity A female receptivity which is relatively low. PATOC:GVG A male receptivity which is relatively high. high male receptivity quality PATO:0001725 increased male receptivity A male receptivity which is relatively high. PATOC:GVG A male receptivity which is relatively low. low male receptivity quality PATO:0001726 decreased male receptivity A male receptivity which is relatively low. PATOC:GVG A quality inhering in a bearer by virtue of the bearer's prevailing tendency, mood, or inclination. quality tendency PATO:0001727 disposition A quality inhering in a bearer by virtue of the bearer's prevailing tendency, mood, or inclination. Merriam-Webster:Merriam-Webster A disposition inhering in a multi-cellular organism. quality PATO:0001728 multi-cellular organismal disposition A disposition inhering in a multi-cellular organism. PATOC:GVG An organismal quality inhering in a bearer by virtue of the bearer's disposition to lose an entity by natural process. quality PATO:0001729 shedability An organismal quality inhering in a bearer by virtue of the bearer's disposition to lose an entity by natural process. PATOC:GVG A quality inhering in a bearer by virtue of the bearer's disposition to shed body parts. quality PATO:0001730 deciduous (generic) A quality inhering in a bearer by virtue of the bearer's disposition to shed body parts. PATOC:GVG A quality inhering in a plant by virtue of the bearer's disposition to shed foliage. quality PATO:0001731 deciduous (plant) A quality inhering in a plant by virtue of the bearer's disposition to shed foliage. PATOC:cjm A quality inhering in a plant by virtue of the bearer's disposition to not shed any body part. quality PATO:0001732 non-deciduous (any body part) A quality inhering in a plant by virtue of the bearer's disposition to not shed any body part. PATOC:GVG A quality inhering in a plant by virtue of the bearer's disposition to retain foliage. quality PATO:0001733 evergreen (plant) A quality inhering in a plant by virtue of the bearer's disposition to retain foliage. PATOC:GVG A quality inhering in a plant by virtue of the bearer's disposition to being between evergeen and deciduous. quality PATO:0001734 semi-deciduous(plant) A quality inhering in a plant by virtue of the bearer's disposition to being between evergeen and deciduous. PATOC:cjm A physical quality inhering in a bearer by virtue of the bearer's parts having the arrangement which exhibits characteristics of liquids. liquid quality PATO:0001735 liquid configuration A physical quality inhering in a bearer by virtue of the bearer's parts having the arrangement which exhibits characteristics of liquids. PATOC:GVG A physical quality inhering in a bearer by virtue of the bearer's parts having the arrangement which exhibits characteristics of solids. solid quality PATO:0001736 solid configuration A physical quality inhering in a bearer by virtue of the bearer's parts having the arrangement which exhibits characteristics of solids. PATOC:GVG A physical quality inhering in a bearer by virtue of the bearer's parts having the arrangement which exhibits characteristics of gases. gas quality PATO:0001737 gaseus configuration A physical quality inhering in a bearer by virtue of the bearer's parts having the arrangement which exhibits characteristics of gases. PATOC:GVG A structural quality inhering in a bearer by virtue of the bearer's lacking physically interaction with another entity. dissociated quality PATO:0001738 dissociated from A structural quality inhering in a bearer by virtue of the bearer's lacking physically interaction with another entity. PATOC:GVG A quality that inheres in an bearer by virtue of how that bearer interacts with radiation. quality PATO:0001739 radiation quality A quality that inheres in an bearer by virtue of how that bearer interacts with radiation. PATOC:GVG A radiation quality inhering in a radioactive substance by virtue of its transformation (disintegration) rate. radioactivity quality PATO:0001740 activity (of a radionuclide) A radiation quality inhering in a radioactive substance by virtue of its transformation (disintegration) rate. PATOC:GVG A radiation quality inhering in bearer by virtue of the bearer's exhibiting or being caused by radioactivity. quality PATO:0001741 radioactive A radiation quality inhering in bearer by virtue of the bearer's exhibiting or being caused by radioactivity. WordNet:WordNet A radioactivity which is relatively low. high radioactivity quality PATO:0001742 increased radioactivity A radioactivity which is relatively low. PATOC:GVG A radioactivity which is relatively high. low radioactivity quality PATO:0001743 decreased radioactivity A radioactivity which is relatively high. PATOC:GVG A radiation quality inhering in a bearer by virtue of what the bearer receives as a result of being exposed to ionizing radiation. quality PATO:0001744 radiation exposure A radiation quality inhering in a bearer by virtue of what the bearer receives as a result of being exposed to ionizing radiation. hps:hps A radiation exposure quality inhering in a substance by virtue of the radiation energy "deposited" in a kilogram of a substance. quality PATO:0001745 radiation absorbed dose A radiation exposure quality inhering in a substance by virtue of the radiation energy "deposited" in a kilogram of a substance. arpansa:arpansa A radiation exposure quality inhering in a tissue by virtue of the relation between the absorbed dose to the effective biological damage of the radiation to that tissue. quality PATO:0001746 radiation equivalent dose A radiation exposure quality inhering in a tissue by virtue of the relation between the absorbed dose to the effective biological damage of the radiation to that tissue. arpansa:arpansa A radiation exposure quality inhering in an organ by virtue of the multiplication of an equivalent dose to that organ multiplied by the tissue weighting factor for that organ. quality PATO:0001747 radiation effective dose A radiation exposure quality inhering in an organ by virtue of the multiplication of an equivalent dose to that organ multiplied by the tissue weighting factor for that organ. arpansa:arpansa A shape quality in which a portion of the outermost boundary of an entity folds in space such that a portion that was originally convex is now concave. quality PATO:0001748 invaginated A shape quality in which a portion of the outermost boundary of an entity folds in space such that a portion that was originally convex is now concave. PATOC:GVG A heterochronic growth quality inhering in an organism, structure, or group of organisms by virtue of the bearer's reduced growth. hypoplastic growth pedomorphic growth quality PATO:0001749 paedomorphic growth A heterochronic growth quality inhering in an organism, structure, or group of organisms by virtue of the bearer's reduced growth. PATOC:mh A paedomorphic growth quality which is due to a delayed onset. quality PATO:0001750 postdisplaced growth A paedomorphic growth quality which is due to a delayed onset. PATOC:mh A paedomorphic growth quality which is due to an earlier offset. quality PATO:0001751 progenetic growth A paedomorphic growth quality which is due to an earlier offset. PATOC:mh A heterochronic growth quality inhering in an organism, structure, or group of organisms by virtue of the bearer's increased growth. hyperplastic growth quality PATO:0001752 peramorphic growth A heterochronic growth quality inhering in an organism, structure, or group of organisms by virtue of the bearer's increased growth. PATOC:mh A peramorphic growth quality which is due to an increased rate. quality PATO:0001753 accelerated growth A peramorphic growth quality which is due to an increased rate. PATOC:mh A peramorphic growth quality which is due to an earlier onset. precocious growth quality PATO:0001754 predisplaced growth A peramorphic growth quality which is due to an earlier onset. PATOC:mh A peramorphic growth quality which is due to a delayed offset. quality PATO:0001755 hypermorphic growth A peramorphic growth quality which is due to a delayed offset. PATOC:mh A conductivity quality inhering in a bearer by virtue of the bearer's disposition to spontaneous transfer of thermal energy from a region of higher temperature to a region of lower temperature. thermal conduction quality PATO:0001756 heat conductivity A conductivity quality inhering in a bearer by virtue of the bearer's disposition to spontaneous transfer of thermal energy from a region of higher temperature to a region of lower temperature. Wikipedia:http://en.wikipedia.org/wiki/Heat_conduction A conductivity quality inhering in a bearer by virtue of the bearer's ability to convey electricity. quality PATO:0001757 electrical conductivity A conductivity quality inhering in a bearer by virtue of the bearer's ability to convey electricity. Wikipedia:http://en.wikipedia.org/wiki/Electrical_conduction A conductivity quality inhering in motor and sensory nerves by virtue of the bearer's ability to convey electricity. quality PATO:0001758 nerve conductivity A conductivity quality inhering in motor and sensory nerves by virtue of the bearer's ability to convey electricity. PATOC:GVG A composition quality inhering in a bearer by virtue of the bearer's containing granules. quality PATO:0001759 granular A composition quality inhering in a bearer by virtue of the bearer's containing granules. thefreedictionary.com:thefreedictionary.com quality PATO:0001760 female semi-fertile quality PATO:0001761 male semi-fertile quality PATO:0001762 male semi-sterile quality PATO:0001763 female semi-sterile An age which is high relative to the normal or average. high age quality PATO:0001764 increased age An age which is high relative to the normal or average. PATOC:GVG An age which is low relative to the normal or average. low age quality PATO:0001765 decreased age An age which is low relative to the normal or average. PATOC:GVG A cellular quality inhering in a cell by virtue of its anisotropic intracellular organization. PATO:0001769 quality PATO:0001766 obsolete cellular polarity true A cellular quality inhering in a cell by virtue of its anisotropic intracellular organization. PATOC:GVG quality PATO:0001767 semi-fertile A viability quality inhering in a bearer or a population by virtue of some of it's members' inability to survive to reproduce. quality PATO:0001768 semi-lethal (sensu genetics) A viability quality inhering in a bearer or a population by virtue of some of it's members' inability to survive to reproduce. PATOC:CVC A positional quality inhering in a bearer by virtue of the bearer's location of features or characteristics along an axis. quality cellular polarity PATO:0001769 positional polarity A positional quality inhering in a bearer by virtue of the bearer's location of features or characteristics along an axis. PATOC:MAH cellular polarity PATOC:MAH A viability quality inhering in a population by virtue of some of it's members' ability to survive. quality PATO:0001770 semi-viable A viability quality inhering in a population by virtue of some of it's members' ability to survive. PATOC:CVC true A spatial quality inhering in a bearer by virtue of the bearer's being extended on all sides of another entity simultaneously. encircling enclosing wrapping quality PATO:0001772 Nedd to add reciprocal of relationship to 'surrounded by' PATO:0005016. surrounding A spatial quality inhering in a bearer by virtue of the bearer's being extended on all sides of another entity simultaneously. thefreedictionary.com:thefreedictionary.com A quality inhering in a bearer by virtue of the bearer's having only one phase or stage. quality PATO:0001773 monophasic A quality inhering in a bearer by virtue of the bearer's having only one phase or stage. hefreedictionary.com:hefreedictionary.com A quality inhering in a bearer by virtue of the bearer's having or existing in many phases. quality PATO:0001774 polyphasic A quality inhering in a bearer by virtue of the bearer's having or existing in many phases. PATOC:GVG A positional quality inhering in a bearer by virtue of the bearer's location of features or characteristics along the dorsal-ventral axis. quality PATO:0001775 dorsal-ventral polarity A positional quality inhering in a bearer by virtue of the bearer's location of features or characteristics along the dorsal-ventral axis. PATOC:MAH A flexibility which is relatively high. high flexibility quality PATO:0001776 increased flexibility A flexibility which is relatively high. PATOC:GVG A flexibility which is relatively low. low flexibility quality PATO:0001777 decreased flexibility A flexibility which is relatively low. PATOC:GVG A strength which is relatively high. high strength quality PATO:0001778 increased strength A strength which is relatively high. PATOC:GVG A strength which is relatively low. weak quality PATO:0001779 decreased strength A strength which is relatively low. PATOC:GVG A size quality inhering in a bearer by virtue of the bearer's being abnormally developed, usually due to malnutrition. dystrophied quality dystrophy PATO:0001780 dystrophic A size quality inhering in a bearer by virtue of the bearer's being abnormally developed, usually due to malnutrition. Wiikipedia:Wiikipedia A thickness quality which lacks pattern. quality PATO:0001781 irregular thickness A thickness quality which lacks pattern. PATOC:GVG An intensity which is relatively high. high intensity quality PATO:0001782 increased intensity An intensity which is relatively high. PATOC:GVG An intensity which is relatively low. low intensity quality PATO:0001783 decreased intensity An intensity which is relatively low. PATOC:GVG A branched quality inhering in a bearer by virtue of the bearer's being divided into two branches. PATO:0001572 bifid quality forked PATO:0001784 bifurcated A branched quality inhering in a bearer by virtue of the bearer's being divided into two branches. thefreedictionary.com:thefreedictionary.com A curvature quality inhering in a bearer by virtue of the bearer's being curved outward. quality PATO:0001785 TODO: obsolete, definition too ambiguous. splayed A curvature quality inhering in a bearer by virtue of the bearer's being curved outward. PATOC:GVG A shape quality inhering in a bearer by virtue of the bearer's being divided or broken up into parts or divisions. clefted septate quality divided forked subdivided PATO:0001786 split A shape quality inhering in a bearer by virtue of the bearer's being divided or broken up into parts or divisions. die.net:die.net A curvature quality inhering in a bearer by virtue of the bearer's being curved around an axis. quality PATO:0001787 rotational curvature A curvature quality inhering in a bearer by virtue of the bearer's being curved around an axis. PATOC:GVG A density which is higher relative to the normal or average. high density quality PATO:0001788 increased mass density A density which is higher relative to the normal or average. PATOC:GVG A curvature quality inhering in a bearer by virtue of the bearer's having a shape resembling a dome. quality PATO:0001789 domed A curvature quality inhering in a bearer by virtue of the bearer's having a shape resembling a dome. PATOC:GVG A density which is lower relative to the normal or average. low density quality PATO:0001790 decreased mass density A density which is lower relative to the normal or average. PATOC:GVG A spatial pattern inhering in a bearer by virtue of the bearer's being confined or restricted to multiple locations. multi-focal quality PATO:0001791 multi-localised A spatial pattern inhering in a bearer by virtue of the bearer's being confined or restricted to multiple locations. PATOC:GVG A spatial quality inhering in a bearer by virtue of the bearer's being located on left side of from the a another entity. quality PATO:0001792 left side of A spatial quality inhering in a bearer by virtue of the bearer's being located on left side of from the a another entity. PATOC:GVG A spatial quality inhering in a bearer by virtue of the bearer's being located on right side of a another entity. quality PATO:0001793 right side of A spatial quality inhering in a bearer by virtue of the bearer's being located on right side of a another entity. PATOC:GVG A shape quality inhering in a bearer by virtue of the bearer's being wound in a continuous series of loops. quality PATO:0001794 coiling A shape quality inhering in a bearer by virtue of the bearer's being wound in a continuous series of loops. Online_Dictionary:Online_Dictionary A coiling which is relatively high. high coiling quality PATO:0001795 increased coiling A coiling which is relatively high. PATOC:GVG A coiling which is relatively low. low coiling quality PATO:0001796 decreased coiling A coiling which is relatively low. PATOC:GVG true A shape quality inhering in a bearer by virtue of the bearer's having multiple angles in its length. quality tightly curled twisted PATO:0001798 kinked A shape quality inhering in a bearer by virtue of the bearer's having multiple angles in its length. thefreedictionary.com:thefreedictionary.com A shape quality inhering in a bearer by virtue of the bearer's exhibiting disturbance of its smoothness or regularity. quality PATO:0001799 ruffled A shape quality inhering in a bearer by virtue of the bearer's exhibiting disturbance of its smoothness or regularity. .thefreedictionary.com:.thefreedictionary.com A composition quality inhering in an bearer by virtue of the quantities or relative ratios of water of the inhering entity. quality PATO:0001800 water composition A composition quality inhering in an bearer by virtue of the quantities or relative ratios of water of the inhering entity. PATOC:GVG A composition quality inhering in an bearer by virtue of the reduction in amount of water the bearer contains. dehydrated quality dry PATO:0001801 decreased water composition A composition quality inhering in an bearer by virtue of the reduction in amount of water the bearer contains. Wikipedia:http://en.wikipedia.org/wiki/Dehydrated A pattern quality inhering in a bearer by virtue of the bearer's not being compact or dense in arrangement. quality PATO:0001802 loose A pattern quality inhering in a bearer by virtue of the bearer's not being compact or dense in arrangement. answers.com:answers.com A photosensitivity quality inhering in a bearer by virtue of the bearer's disposition to being susceptible to damage by light. quality PATO:0001803 phototoxic A photosensitivity quality inhering in a bearer by virtue of the bearer's disposition to being susceptible to damage by light. answers.com:answers.com A texture quality inhering in a bearer by virtue of the bearer's being covered or partially covered with scales. quality squamous PATO:0001804 scaly A texture quality inhering in a bearer by virtue of the bearer's being covered or partially covered with scales. answers.com:answers.com A texture quality inhering in a bearer by virtue of the bearer's formed or tending to form flakes or thin, crisp fragments. quality PATO:0001805 flaky A texture quality inhering in a bearer by virtue of the bearer's formed or tending to form flakes or thin, crisp fragments. answers.com:answers.com A sensitivity quality inhering in a bearer by virtue of the bearer's exposure to radiation. quality PATO:0001806 sensitivity to irradiation A sensitivity quality inhering in a bearer by virtue of the bearer's exposure to radiation. PATOC:GVG A sensitivity to irradiation which is relatively low. low sensitivity to irradiation quality PATO:0001807 decreased sensitivity to irradiation A sensitivity to irradiation which is relatively low. PATOC:GVG A sensitivity to irradiation which is relatively high. high sensitivity to irradiation quality PATO:0001808 increased sensitivity to irradiation A sensitivity to irradiation which is relatively high. PATOC:GVG A pattern quality inhering in a bearer by virtue of the bearer's being compact or dense in arrangement. quality PATO:0001809 tight A pattern quality inhering in a bearer by virtue of the bearer's being compact or dense in arrangement. PATOC:GVG A grooved texture quality inhering in a bearer by virtue of the bearer's being marked by one or more creases in a normally smooth surface. quality PATO:0001810 wrinkled A grooved texture quality inhering in a bearer by virtue of the bearer's being marked by one or more creases in a normally smooth surface. url:http://www.thefreedictionary.com/wrinkled A relaxation which is relatively high. high relaxation quality PATO:0001811 GO has now relevant relation terms which should be used instead. obsolete increased relaxation true A relaxation which is relatively high. PATOC:GVG A relaxation which is relatively low. low relaxation quality PATO:0001812 GO has now relevant relation terms which should be used instead. obsolete decreased relaxation true A relaxation which is relatively low. PATOC:GVG A structural quality inhering in a bearer by virtue of the bearer's lack elastic tension that facilitate response to stimuli. quality PATO:0001813 atonicity A structural quality inhering in a bearer by virtue of the bearer's lack elastic tension that facilitate response to stimuli. PATOC:GVG A structural quality inhering in a bearer by virtue of the bearer's impaired elastic tension that facilitate response to stimuli. quality PATO:0001814 dystonicity A structural quality inhering in a bearer by virtue of the bearer's impaired elastic tension that facilitate response to stimuli. PATOC:GVG A strength quality inhering in a bearer by virtue of the bearer's disposition to lose strength. quality PATO:0001815 fatigability A strength quality inhering in a bearer by virtue of the bearer's disposition to lose strength. WordNet:WordNet A fatigability which is relatively high. high fatigability quality PATO:0001816 increased fatigability A fatigability which is relatively high. PATOC:GVG A fatigability which is relatively low. low fatigability quality PATO:0001817 decreased fatigability A fatigability which is relatively low. PATOC:GVG A quality of a single process inhering in a bearer by virtue of the bearer's increasing over time. quality PATO:0001818 progressive A quality of a single process inhering in a bearer by virtue of the bearer's increasing over time. PATOC:GVG A morphological quality inhering in a bearer by virtue of the bearer's absence or closure of a normal body orifice or tubular passage. atresia quality PATO:0001819 atretic A morphological quality inhering in a bearer by virtue of the bearer's absence or closure of a normal body orifice or tubular passage. answers.com:answers.com true A structural quality inhering in a bearer by virtue of the bearer's having no opening. unperforated quality PATO:0001821 imperforate A structural quality inhering in a bearer by virtue of the bearer's having no opening. thefreedictionary.com:thefreedictionary.com A quality inhering in a bearer by virtue of whether the bearer's being covered by a liquid. quality PATO:0001822 wetness A quality inhering in a bearer by virtue of whether the bearer's being covered by a liquid. wordreference.com:wordreference.com A wetness quality inhering in a bearer by virtue of the bearer's being covered by a liquid. quality PATO:0001823 wet A wetness quality inhering in a bearer by virtue of the bearer's being covered by a liquid. PATOC:GVG A wetness quality inhering in a bearer by virtue of the bearer's not being covered by a liquid. quality PATO:0001824 dry A wetness quality inhering in a bearer by virtue of the bearer's not being covered by a liquid. PATOC:GVG A wetness quality that is relatively high. quality PATO:0001825 increased wetness A wetness quality that is relatively high. PATOC:GVG A wetness quality that is relatively low. low wetness quality PATO:0001826 decreased wetness A wetness quality that is relatively low. PATOC:GVG A biological sex quality inhering in an individual or a population by virtue of having internal reproductive organs of one sex and external sexual characteristics of the other sex. quality PATO:0001827 pseudohermaphrodite A biological sex quality inhering in an individual or a population by virtue of having internal reproductive organs of one sex and external sexual characteristics of the other sex. WordNet:WordNet A biological sex quality inhering in an individual or a population by virtue of having internal reproductive organs of male and external sexual characteristics of female. quality PATO:0001828 male pseudohermaphrodite A biological sex quality inhering in an individual or a population by virtue of having internal reproductive organs of male and external sexual characteristics of female. PATOC:GVG A biological sex quality inhering in an individual or a population by virtue of having internal reproductive organs of female and external sexual characteristics of male. quality PATO:0001829 female pseudohermaphrodite A biological sex quality inhering in an individual or a population by virtue of having internal reproductive organs of female and external sexual characteristics of male. PATOC:GVG A female fertility which is relatively low. low female fertility quality PATO:0001830 decreased female fertility A female fertility which is relatively low. PATOC:GVG A female fertility which is relatively high. high female fertility quality PATO:0001831 increased female fertility A female fertility which is relatively high. PATOC:GVG A male fertility which is relatively high. high male fertility quality PATO:0001832 increased male fertility A male fertility which is relatively high. PATOC:GVG A male fertility which is relatively low. low male fertility quality PATO:0001833 decreased male fertility A male fertility which is relatively low. PATOC:GVG A fertility which is relatively low. low fertility quality PATO:0001834 decreased fertility A fertility which is relatively low. PATOC:GVG A fertility which is relatively high. high fertility quality PATO:0001835 increased fertility A fertility which is relatively high. PATOC:GVG A structural quality inhering in a bearer with some kind of aperture or opening that is blocked or clogged. quality PATO:0001836 congested A structural quality inhering in a bearer with some kind of aperture or opening that is blocked or clogged. answers.com:answers.com true A flow that is relatively low. low flow quality PATO:0001838 decreased fluid flow A flow that is relatively low. PATOC:GVG A fluid flow that is relatively high. high flow quality PATO:0001839 increased fluid flow A fluid flow that is relatively high. PATOC:GVG true An intensity which is characterized by temporary abatement in severity. quality PATO:0001841 remittent intensity An intensity which is characterized by temporary abatement in severity. answers.com:answers.com A concentration quality inhering in a bearer by virtue of the bearer's containing acid (hydrogen ions). pH quality PATO:0001842 acidity A concentration quality inhering in a bearer by virtue of the bearer's containing acid (hydrogen ions). biology-online:biology-online An acidity which is relatively low. low acidity quality PATO:0001843 decreased acidity An acidity which is relatively low. PATOC:GVG An acidity which is relatively high. high acidity quality PATO:0001844 increased acidity An acidity which is relatively high. PATOC:GVG A rhythm quality inhering in a bearer by virtue of the bearer's lacking rhythm lacking pattern. quality PATO:0001845 irregular rhythm A rhythm quality inhering in a bearer by virtue of the bearer's lacking rhythm lacking pattern. PATOC:GVG A structural quality inhering in a bearer by virtue of the bearer's being entwined and difficult to unravel. quality PATO:0001846 tangled A structural quality inhering in a bearer by virtue of the bearer's being entwined and difficult to unravel. answers.com:answers.com A structural quality inhering in a bearer by virtue of the bearer's being drawn together, compressed or squeezed physically. PATO:0001837 stenosis stenotic stricture quality PATO:0001847 constricted A structural quality inhering in a bearer by virtue of the bearer's being drawn together, compressed or squeezed physically. WordNet:WordNet A curvature quality inhering in a bearer by virtue of the bearer's being curved asymmetrically. quality PATO:0001848 asymmetrically curved A curvature quality inhering in a bearer by virtue of the bearer's being curved asymmetrically. PATOC:GVG A texture quality inhering in a bearer by virtue of a portion of the bearer's surface being scraped away. quality PATO:0001849 abrased A texture quality inhering in a bearer by virtue of a portion of the bearer's surface being scraped away. answers.com:answers.com A structural quality inhering in a bearer by virtue of the bearer's being fibrous tissue that replaces normal tissue destroyed by injury or disease. quality PATO:0001850 scarred A structural quality inhering in a bearer by virtue of the bearer's being fibrous tissue that replaces normal tissue destroyed by injury or disease. answers.com:answers.com A structure quality inhering in a bearer by virtue of the bearer's exhibiting transient abnormal enlargement, not due to cell proliferation. swelling quality PATO:0001851 swollen A structure quality inhering in a bearer by virtue of the bearer's exhibiting transient abnormal enlargement, not due to cell proliferation. thefreedictionary.com:thefreedictionary.com A positional quality inhering in a bearer by virtue of the bearer's being out of its usual or proper place, or position. PATO:0001479 PATO:0002158 PATO:0002159 dislocation luxated luxation relational dislocated quality quality PATO:0001852 dislocated A positional quality inhering in a bearer by virtue of the bearer's being out of its usual or proper place, or position. thefreedictionary.com:thefreedictionary.com A structural quality which is held by a bearer when the latter exhibits an excessive accumulation of cerebral spinal fluid. quality PATO:0001853 hydrocephalic A structural quality which is held by a bearer when the latter exhibits an excessive accumulation of cerebral spinal fluid. PATOC:mh A spatial pattern inhering in a bearer by virtue of the bearer's being situated at right angles to the horizon. quality PATO:0001854 vertical A spatial pattern inhering in a bearer by virtue of the bearer's being situated at right angles to the horizon. thefreedictionary.com:thefreedictionary.com A positional quality inhering in a bearer by virtue of the bearer's being in the plane of the horizon. quality PATO:0001855 horizontal A positional quality inhering in a bearer by virtue of the bearer's being in the plane of the horizon. thefreedictionary.com:thefreedictionary.com An oriented quality inhering in a bearer by virtue of the bearer's being turned inward upon itself. quality PATO:0001856 For example, a tubular organ or part. introverted An oriented quality inhering in a bearer by virtue of the bearer's being turned inward upon itself. die.net:die.net A shape quality in a bearer by virtue of the bearer's curving inward. quality PATO:0001857 concave A shape quality in a bearer by virtue of the bearer's curving inward. WordNet:WordNet A functionality quality inhering in a bearer by virtue of being not completely paralysed. quality PATO:0001858 partially paralysed A functionality quality inhering in a bearer by virtue of being not completely paralysed. PATOC:GVG A coordination which is relatively high. high coordination quality PATO:0001859 increased coordination A coordination which is relatively high. PATOC:GVG A coordination which is relatively low. low coordination quality PATO:0001860 decreased coordination A coordination which is relatively low. PATOC:GVG A structural quality inhering in a bearer by virtue of the bearer's forming a bundle of aligned anatomical fibers, as of muscle or nerve. fascicled quality PATO:0001861 fasciculated A structural quality inhering in a bearer by virtue of the bearer's forming a bundle of aligned anatomical fibers, as of muscle or nerve. answers.com:answers.com A fertility quality inhering in a bearer by virtue of the bearer's disposition to make its offspring sterile. quality grandchildless PATO:0001862 lack of fertility in offspring A fertility quality inhering in a bearer by virtue of the bearer's disposition to make its offspring sterile. PATOC:GVG A duration quality of a process inhering in a bearer by virtue of the bearer's having slow progressive course of indefinite duration. quality PATO:0001863 chronic A duration quality of a process inhering in a bearer by virtue of the bearer's having slow progressive course of indefinite duration. PATOC:cjm true A convex 3-D shape quality inhering in a bearer by virtue of the bearer's having a quadric surface in three dimensions obtained by rotating an ellipse about one of its principal axes. Includes spheres and oblate/prolate spheroids. PATO:0001864 quality sphericality PATO:0001865 spheroid A convex 3-D shape quality inhering in a bearer by virtue of the bearer's having a quadric surface in three dimensions obtained by rotating an ellipse about one of its principal axes. Includes spheres and oblate/prolate spheroids. Wikipedia:http://en.wikipedia.org/wiki/Spheroid A spheroid quality inhering in a bearer by virtue of the bearer's exhibiting a polar diameter longer than its equatorial diameter. Image:http://upload.wikimedia.org/wikipedia/commons/8/88/ProlateSpheroid.png quality prolate spheroid PATO:0001866 prolate A spheroid quality inhering in a bearer by virtue of the bearer's exhibiting a polar diameter longer than its equatorial diameter. Wikipedia:http://en.wikipedia.org/wiki/Prolate A shape quality inhering in a bearer by virtue of it being a quadrilateral polygon in which all four angles are right angles. Image:http://upload.wikimedia.org/wikipedia/en/e/ee/Shaperec.svg quality PATO:0001867 rectangular A shape quality inhering in a bearer by virtue of it being a quadrilateral polygon in which all four angles are right angles. Wikipedia:http://en.wikipedia.org/wiki/Rectangular A fluorescence quality inhering in a bearer by virtue of the bearer's exhibiting fluorescence which is self-induced. quality PATO:0001868 autofluorescence A fluorescence quality inhering in a bearer by virtue of the bearer's exhibiting fluorescence which is self-induced. PATOC:mb A quality inhering in a bearer by virtue of the bearer's being abnormal and having a destructive effect on living tissue. quality PATO:0001869 pathological A quality inhering in a bearer by virtue of the bearer's being abnormal and having a destructive effect on living tissue. PATOC:cjm A shape quality inhering in a circular disk by virtue of the bearer's having a segment of another circle removed from its edge, so that what remains is a shape enclosed by two circular arcs of different diameters which intersect at two points (usually in such a manner that the enclosed shape does not include the center of the original circle). Image:http://upload.wikimedia.org/wikipedia/commons/7/74/Crescent.svg crescentic quality bow-shaped lunate PATO:0001870 crescent-shaped A shape quality inhering in a circular disk by virtue of the bearer's having a segment of another circle removed from its edge, so that what remains is a shape enclosed by two circular arcs of different diameters which intersect at two points (usually in such a manner that the enclosed shape does not include the center of the original circle). Wikipedia:http://en.wikipedia.org/wiki/Crescent A concave 3-D shape quality inhering in a bearer by virtue of the bearer's having the shape of a kidney. kidney-shaped quality bean shaped PATO:0001871 reniform A concave 3-D shape quality inhering in a bearer by virtue of the bearer's having the shape of a kidney. ISBN:0881923214 A convex 3-D shape quality inhering in a bearer by virtue of the bearer's resemblance to a cube (a 3-D shape with a square cross section). cuboidal quality block-like PATO:0001872 cuboid A convex 3-D shape quality inhering in a bearer by virtue of the bearer's resemblance to a cube (a 3-D shape with a square cross section). PATOC:MAH A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section. PATO:0001203 rod-like rod-shaped tubulate quality PATO:0001873 cylindrical A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section. PATOC:MAH A shape quality inhering in a bearer by virtue of the bearer's being cylindrical, in which the height is less than the diameter. disc-shaped disk-shaped quality PATO:0001874 discoid A shape quality inhering in a bearer by virtue of the bearer's being cylindrical, in which the height is less than the diameter. PATOC:cjm A shape quality inhering in a bearer by virtue of the bearer's having three angles. deltoid quality delta shaped triangle triangle-shaped PATO:0001875 triangular A shape quality inhering in a bearer by virtue of the bearer's having three angles. wordreference:wordreference A concave 3-D shape quality inhering in a bearer by virtue of the bearer's having two parts, roughly spherical and of equal size, connected by a bar. quality PATO:0001876 dumbbell-shaped A concave 3-D shape quality inhering in a bearer by virtue of the bearer's having two parts, roughly spherical and of equal size, connected by a bar. PATOC:GVG A shape quality inhering in a bearer by virtue of the bearer's being shaped like a lance-head, considerably longer than wide, tapering towards the tip from below the middle; attached at the broad end. spear-shaped quality PATO:0001877 lanceolate A shape quality inhering in a bearer by virtue of the bearer's being shaped like a lance-head, considerably longer than wide, tapering towards the tip from below the middle; attached at the broad end. PATOC:GVG A shape quality inhering in a bearer by virtue of the bearer's consisting of two curves, in opposite directions. S-shaped. S-shaped sigmoidal quality PATO:0001878 sigmoid A shape quality inhering in a bearer by virtue of the bearer's consisting of two curves, in opposite directions. S-shaped. PATOC:CJM A concave 3-D shape quality inhering in a bearer by virtue of the bearer's being shaped in the form of the letter U. horseshoe shaped horseshoe quality PATO:0001879 U-shaped A concave 3-D shape quality inhering in a bearer by virtue of the bearer's being shaped in the form of the letter U. WordNet:WordNet A quality inhering in a bearer by virtue of the bearer's having a tail or tail-like projection. caudal quality tailed PATO:0001880 caudate A quality inhering in a bearer by virtue of the bearer's having a tail or tail-like projection. PATOC:cjm A shape quality inhering in a bearer by virtue of the bearer's forming two equal obtuse triangles with a short side in common. sagittate quality PATO:0001881 Gradually enlarged at the base, like the head of an arrow. arrow-shaped A shape quality inhering in a bearer by virtue of the bearer's forming two equal obtuse triangles with a short side in common. ISBN:0881923214 RKC:RKC A concave 3-D shape quality inhering in a bearer by virtue of the bearer's resembling a slug. quality PATO:0001882 limaciform A concave 3-D shape quality inhering in a bearer by virtue of the bearer's resembling a slug. PATOC:CJM A concave 3-D shape quality inhering in a bearer by virtue of the bearer's gradually becoming thicker towards the end. PATO:0001797 club-like club-shaped clubbed quality PATO:0001883 clavate A concave 3-D shape quality inhering in a bearer by virtue of the bearer's gradually becoming thicker towards the end. MP:0000576 A physical quality inhering in a bearer by virtue the bearer's disposition to being water-repellent; tending to repel and not absorb water. quality PATO:0001884 hydrophobicity A physical quality inhering in a bearer by virtue the bearer's disposition to being water-repellent; tending to repel and not absorb water. WordNet:WordNet A quality inhering in a bearer by virtue of the bearer's lacking affinity for water; tending to repel and not absorb water; tending not to dissolve in or mix with or be wetted by water. quality PATO:0001885 hydrophobic A quality inhering in a bearer by virtue of the bearer's lacking affinity for water; tending to repel and not absorb water; tending not to dissolve in or mix with or be wetted by water. WordNet:WordNet A physical quality inhering in a bearer by virtue the bearer's disposition to having an affinity for water; it is readily absorbing or dissolving in water. quality PATO:0001886 hydrophilicity A physical quality inhering in a bearer by virtue the bearer's disposition to having an affinity for water; it is readily absorbing or dissolving in water. answers.com:answers.com A quality inhering in a bearer by virtue of the bearer's disposition to having a strong affinity for water; tending to dissolve in, mix with, or be wetted by water. quality PATO:0001887 hydrophilic A quality inhering in a bearer by virtue of the bearer's disposition to having a strong affinity for water; tending to dissolve in, mix with, or be wetted by water. WordNet:WordNet A quality of a liquid inhering in a bearer by virtue of the bearer's ability to mix with (dissolve in) another liquid. quality PATO:0001888 miscibility A quality of a liquid inhering in a bearer by virtue of the bearer's ability to mix with (dissolve in) another liquid. Chemicool:Chemicool A surface feature shape quality inhering in a bearer by virtue of the bearer's having the border, edge, or outline cut into a series of segments of circles resembling a scallop-shell. crenate crenulate quality PATO:0001889 scalloped A surface feature shape quality inhering in a bearer by virtue of the bearer's having the border, edge, or outline cut into a series of segments of circles resembling a scallop-shell. Oxford:EnglishDictionary A concave 3-D shape quality inhering in a bearer by virtue of the bearer's being divided into three branches. trifurcate quality PATO:0001890 tripartite A concave 3-D shape quality inhering in a bearer by virtue of the bearer's being divided into three branches. InfoVisual:InfoVisual A spheroid quality inhering in a bearer by virtue of the bearer's exhibiting a continuous convex surface with an axis of symmetry and one axis longer than the other; egg-shaped. egg-shaped oval ovoid quality eccentric PATO:0001891 ovate A spheroid quality inhering in a bearer by virtue of the bearer's exhibiting a continuous convex surface with an axis of symmetry and one axis longer than the other; egg-shaped. PATOC:mc An odor quality of having decreased odor. quality PATO:0001892 decreased odor An odor quality of having decreased odor. PATOC:GVG An odor quality of having increased odor. quality PATO:0001893 increased odor An odor quality of having increased odor. PATOC:GVG An organismal quality inhering in a bearer by virtue of the bearer's physical expression of sexual characteristics. quality PATO:0001894 phenotypic sex A biological sex quality inhering in an individual or a population that undergo sexual reproduction. quality PATO:0001895 mating type A biological sex quality inhering in an individual or a population that undergo sexual reproduction. wikipedia:wikipedia A structure quality inhering in a bearer by virtue of the bearer's lacking of a three dimensional space surrounded by one or more anatomical structures and containing one or more anatomical substances. quality PATO:0001896 unlumenized A structure quality inhering in a bearer by virtue of the bearer's lacking of a three dimensional space surrounded by one or more anatomical structures and containing one or more anatomical substances. PATOC:MAH A structure quality inhering in a bearer by virtue of the bearer's having a three dimensional space surrounded by one or more anatomical structures and containing one or more anatomical substances. quality PATO:0001897 See GO term: GO:0031974 membrane-enclosed lumen [DEF:"The enclosed volume within a sealed membrane or between two sealed membranes"]. lumenized A structure quality inhering in a bearer by virtue of the bearer's having a three dimensional space surrounded by one or more anatomical structures and containing one or more anatomical substances. PATOC:MAH A circumference which is relatively high. quality PATO:0001898 increased circumference A circumference which is relatively high. PATOC:GVG A circumference which is relatively low. quality PATO:0001899 decreased circumference A circumference which is relatively low. PATOC:GVG A directional quality inhering in a bearer by virtue of the bearer's direction that is similar to the direction of an object to the south when it faces north. quality PATO:0001900 front A directional quality inhering in a bearer by virtue of the bearer's direction that is similar to the direction of an object to the south when it faces north. PATOC:GVG A directional quality inhering in a bearer by virtue of the bearer's direction that is similar to the direction of an object to the north when it faces south. quality PATO:0001901 back A directional quality inhering in a bearer by virtue of the bearer's direction that is similar to the direction of an object to the north when it faces south. PATOC:GVG A directional quality inhering in a bearer by virtue of the bearer's having one direction only. quality PATO:0001902 unidirectional A directional quality inhering in a bearer by virtue of the bearer's having one direction only. PATOC:GVG A directional quality inhering in a bearer by virtue of the bearer's having two directions. quality PATO:0001903 bi-directional A directional quality inhering in a bearer by virtue of the bearer's having two directions. PATOC:GVG A directional quality inhering in a bearer by virtue of the bearer's direction approximating the shape of a circle. quality PATO:0001904 circling direction A directional quality inhering in a bearer by virtue of the bearer's direction approximating the shape of a circle. PATOC:GVG The bearer of this quality has_part = n, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. having physical part quality PATO:0001905 has normal numbers of parts of type The bearer of this quality has_part = n, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. PATOC:CJM A physical quality inhering in a bearer by virtue of the bearer's participation in movement. quality PATO:0001906 movement quality A physical quality inhering in a bearer by virtue of the bearer's participation in movement. PATOC:GVG A surface feature shape quality inhering in a bearer by virtue of the bearer's being like the surface of a compact mass of grapes. quality PATO:0001907 botryoidal A surface feature shape quality inhering in a bearer by virtue of the bearer's being like the surface of a compact mass of grapes. PATOC:cvs A nucleate quality inhering in a bearer by virtue of the bearer's having more than one nucleus. quality PATO:0001908 multinucleate A nucleate quality inhering in a bearer by virtue of the bearer's having more than one nucleus. PATOC:GVG A nucleate quality inhering in a bearer by virtue of the bearer's having three nuclei. quality PATO:0001909 trinucleate A nucleate quality inhering in a bearer by virtue of the bearer's having three nuclei. thefreedictionary:thefreedictionary A surface feature shape quality inhering in a bearer by virtue of the bearer's one part being layered over another connected part. quality PATO:0001910 folded A surface feature shape quality inhering in a bearer by virtue of the bearer's one part being layered over another connected part. PATOC:cjm A behavioral quality inhering in a bearer by virtue of the bearer's exhibiting movement in a circular course. quality PATO:0001911 circling A behavioral quality inhering in a bearer by virtue of the bearer's exhibiting movement in a circular course. PATOC:mb A quality of a single process inhering in a bearer by virtue of the state of bearer's mechanical, physical, and biochemical processes. quality PATO:0001912 physiological state A quality of a single process inhering in a bearer by virtue of the state of bearer's mechanical, physical, and biochemical processes. PATOC:mb A physiological state which is characterized by periods of high-frequency high amplitude electrical activity in neuronal tissue. quality PATO:0001913 ictal A physiological state which is characterized by periods of high-frequency high amplitude electrical activity in neuronal tissue. PATOC:mb A physiological state which is characterized by normal electrical activity in neuronal tissue. quality PATO:0001914 non-ictal A physiological state which is characterized by normal electrical activity in neuronal tissue. PATOC:mb A spatial quality inhering in a bearer by virtue of the bearer's being located toward the front and upper surface of an organism relative to another entity. quality PATO:0001915 anterodorsal to A spatial quality inhering in a bearer by virtue of the bearer's being located toward the front and upper surface of an organism relative to another entity. PATOC:wd A spatial quality inhering in a bearer by virtue of the bearer's being located toward the rear and upper surface of an organism relative to another entity. quality PATO:0001916 posterodorsal to A spatial quality inhering in a bearer by virtue of the bearer's being located toward the rear and upper surface of an organism relative to another entity. PATOC:wd A spatial quality inhering in a bearer by virtue of the bearer's being located toward the front and abdomen of an organism relative to another entity. quality PATO:0001917 anteroventral to A spatial quality inhering in a bearer by virtue of the bearer's being located toward the front and abdomen of an organism relative to another entity. PATOC:wd A spatial quality inhering in a bearer by virtue of the bearer's being located toward the rear and abdomen of an organism relative to another entity. quality PATO:0001918 posteroventral to A spatial quality inhering in a bearer by virtue of the bearer's being located toward the rear and abdomen of an organism relative to another entity. PATOC:wd A positional quality inhering in a bearer by virtue of the bearer's being positioned towards the back or upper surface of an organism. quality PATO:0001919 mislocalised dorsally A positional quality inhering in a bearer by virtue of the bearer's being positioned towards the back or upper surface of an organism. PATOC:mb A positional quality inhering in a bearer by virtue of the bearer's being positioned towards the abdomen of an organism. quality PATO:0001920 mislocalised ventrally A positional quality inhering in a bearer by virtue of the bearer's being positioned towards the abdomen of an organism. PATOC:mb A positional quality inhering in a bearer by virtue of the bearer's being positioned towards the front of an organism. quality PATO:0001921 mislocalised anteriorly A positional quality inhering in a bearer by virtue of the bearer's being positioned towards the front of an organism. PATOC:mb A positional quality inhering in a bearer by virtue of the bearer's being positioned towards the rear of an organism. quality PATO:0001922 mislocalised posteriorly A positional quality inhering in a bearer by virtue of the bearer's being positioned towards the rear of an organism. PATOC:mb A positional quality inhering in a bearer by virtue of the bearer's being positioned towards the side of an organism. quality PATO:0001923 mislocalised laterally A positional quality inhering in a bearer by virtue of the bearer's being positioned towards the side of an organism. PATOC:mb A positional quality inhering in a bearer by virtue of the bearer's being positioned towards the middle of an organism. quality PATO:0001924 mislocalised medially A positional quality inhering in a bearer by virtue of the bearer's being positioned towards the middle of an organism. PATOC:mb A surface shape quality inhering in a bearer by virtue of the bearer's shape of features present on its surface or outer shell. quality PATO:0001925 This quality either inheres directly in the surface, or in the entity that has the surface. For example, to say that a particular fly wing is curved is shorthand for saying the wing has a surface which is curved. surface feature shape A surface shape quality inhering in a bearer by virtue of the bearer's shape of features present on its surface or outer shell. PATOC:CJM A fluorescence which is higher than normal. high fluorescence quality PATO:0001926 increased fluorescence A fluorescence which is higher than normal. PATOC:GVG A fluorescence which is lower than normal. low fluorescence quality PATO:0001927 decreased fluorescence A fluorescence which is lower than normal. PATOC:GVG A texture quality inhering in a bearer by virtue of a local accumulation of fluid underneath the surface of the bearer. blistering quality PATO:0001928 blistered A texture quality inhering in a bearer by virtue of a local accumulation of fluid underneath the surface of the bearer. PATOC:GVG A variability quality inhering in a bearer by virtue of whether the bearer exhibits shape variation or change. quality PATO:0001929 variability of shape A variability quality inhering in a bearer by virtue of whether the bearer exhibits shape variation or change. PATOC:GVG A quality inhering in a bearer by virtue the bearer's having or exhibiting variation its shape. quality PATO:0001930 variant shape A quality inhering in a bearer by virtue the bearer's having or exhibiting variation its shape. PATOC:GVG A quality inhering in a bearer by virtue of the bearer's lacking or not exhibiting variation of shape. quality PATO:0001931 invariant shape A quality inhering in a bearer by virtue of the bearer's lacking or not exhibiting variation of shape. PATOC:GVG A pattern quality inhering in a bearer by virtue of the bearer's being placed alternately one above the other. quality PATO:0001932 alternate placement A pattern quality inhering in a bearer by virtue of the bearer's being placed alternately one above the other. ISBN:0881923214 A positional quality inhering in a bearer by virtue of the bearer's being positioned on opposite sides on the same plane. quality PATO:0001933 opposite A positional quality inhering in a bearer by virtue of the bearer's being positioned on opposite sides on the same plane. ISBN:0881923214 A shape quality inhering in a bearer by virtue of the bearer's being perfectly circular. quality PATO:0001934 orbicular A shape quality inhering in a bearer by virtue of the bearer's being perfectly circular. ISBN:0881923214 A shape quality inhering in a bearer by virtue of the bearer's being roundish, a little inclining to be oblong. roundish quality PATO:0001935 obtuse A shape quality inhering in a bearer by virtue of the bearer's being roundish, a little inclining to be oblong. ISBN:0881923214 A spheroid quality inhering in a bearer by virtue of the bearer's being egg-shaped and flat, with the narrow end attached to the base. quality obovoid PATO:0001936 obovate A spheroid quality inhering in a bearer by virtue of the bearer's being egg-shaped and flat, with the narrow end attached to the base. wordreference:wordreference A shape quality inhering in a bearer by virtue of the bearer's being oblong, with the lower end very much attenuated. spathulate quality PATO:0001937 spatulate A shape quality inhering in a bearer by virtue of the bearer's being oblong, with the lower end very much attenuated. ISBN:0881923214 A spheroid quality inhering in a bearer by virtue of the bearer's being oval and a little angular in the middle. quality PATO:0001938 rhomboid A spheroid quality inhering in a bearer by virtue of the bearer's being oval and a little angular in the middle. ISBN:0881923214 true A size quality inhering in a bearer by virtue of the bearer's being many folds greater relative to the normal average. giant quality PATO:0001940 gigantic A size quality inhering in a bearer by virtue of the bearer's being many folds greater relative to the normal average. PATOC:UMH A color consisting of yellow and green hues. quality PATO:0001941 yellow green A color consisting of yellow and green hues. PATOC:GVG A color consisting of brown and green hues. olive green quality PATO:0001942 brown green A color consisting of brown and green hues. PATOC:GVG A purple color which has low saturation and low brightness. quality PATO:0001943 lilac A purple color which has low saturation and low brightness. PATOC:GVG A color consisting of yellow and orange hue. quality PATO:0001944 yellow orange A color consisting of yellow and orange hue. PATOC:GVG A moderate yellow-orange to orange color. quality PATO:0001945 ochre A moderate yellow-orange to orange color. wordreference:wordreference A color pattern inhering in a bearer by virtue of bearer's exhibiting transverse stripes of one hue or degree of saturation crossing another. striped quality PATO:0001946 banded A color pattern inhering in a bearer by virtue of bearer's exhibiting transverse stripes of one hue or degree of saturation crossing another. ISBN:0881923214 A color pattern inhering in a bearer by virtue of bearer's being covered with reticulated lines of a different hue or degree of saturation. net-like reticulated quality PATO:0001947 netted A color pattern inhering in a bearer by virtue of bearer's being covered with reticulated lines of a different hue or degree of saturation. ISBN:0881923214 A grooved texture quality inhering in a bearer by virtue of the bearer's being marked by two or more parallel channels. quality fluted PATO:0001948 furrowed A grooved texture quality inhering in a bearer by virtue of the bearer's being marked by two or more parallel channels. PATOC:JE A shape quality inhering in a bearer by virtue of the bearer's terminating abruptly in a little point. quality PATO:0001949 pointleted A shape quality inhering in a bearer by virtue of the bearer's terminating abruptly in a little point. ISBN:0881923214 A shape quality inhering in a bearer by virtue of the bearer's terminating gradually in a rounded end. quality PATO:0001950 blunt A shape quality inhering in a bearer by virtue of the bearer's terminating gradually in a rounded end. ISBN:0881923214 A spatial pattern inhering in a bearer by virtue of the bearer's being in opposition round a common axis. quality PATO:0001951 whorled A spatial pattern inhering in a bearer by virtue of the bearer's being in opposition round a common axis. ISBN:0881923214 A spatial quality inhering in a bearer by virtue of the bearer's being arranged in two opposite rows (and hence in the same plane). quality PATO:0001952 distichous A spatial quality inhering in a bearer by virtue of the bearer's being arranged in two opposite rows (and hence in the same plane). ISBN:0881923214 A pattern quality inhering in a bearer by virtue of the bearer's consisting of paired parts that alternately cross each other. crosscutting intercrossing intersecting quality PATO:0001953 decussate A pattern quality inhering in a bearer by virtue of the bearer's consisting of paired parts that alternately cross each other. ISBN:0881923214 A shape quality inhering in a bearer by virtue of the bearer's being linear, very narrow, tapering to a very fine point from a narrow base. awl-shaped needle-like quality PATO:0001954 subulate A shape quality inhering in a bearer by virtue of the bearer's being linear, very narrow, tapering to a very fine point from a narrow base. ISBN:0881923214 A shape quality inhering in a bearer by virtue of the bearer's being narrowly triangular, wider at the apex and tapering toward the base. wedge-shaped quality PATO:0001955 cuneate A shape quality inhering in a bearer by virtue of the bearer's being narrowly triangular, wider at the apex and tapering toward the base. wordreference:wordreference A variability quality inhering in a bearer by virtue of whether the bearer exhibits size variation or change. quality PATO:0001956 variability of size A variability quality inhering in a bearer by virtue of whether the bearer exhibits size variation or change. PATOC:GVG A variability of size which is relatively low. low variability of size quality PATO:0001957 decreased variability of size A variability of size which is relatively low. PATOC:GVG A variability of size which is relatively high. high variability of size quality PATO:0001958 increased variability of size A variability of size which is relatively high. PATOC:GVG A structural quality inhering in a bearer by virtue of the bearer's in which bundles of aligned anatomical fibers have become separated. quality PATO:0001959 defasciculated A structural quality inhering in a bearer by virtue of the bearer's in which bundles of aligned anatomical fibers have become separated. PATOC:mw A shape quality inhering in a bearer by virtue of the bearer's parts or projections being interlocked; for example, the fingers of two hands that are clasped. quality PATO:0001960 interdigitated A shape quality inhering in a bearer by virtue of the bearer's parts or projections being interlocked; for example, the fingers of two hands that are clasped. PATOC:wdahdul A structural quality inhering in a bearer by virtue of the bearer's touching another entity. quality contiguous PATO:0001961 in contact with A structural quality inhering in a bearer by virtue of the bearer's touching another entity. PATOC:wdahdul A curled quality inhering in a bearer by virtue of the bearer's edges of its surface being rolled inwards spirally on each side. quality PATO:0001962 involute A curled quality inhering in a bearer by virtue of the bearer's edges of its surface being rolled inwards spirally on each side. ISBN:0881923214 A curled quality inhering in a bearer by virtue of the bearer's edges of its surface being rolled backwards spirally on each side. quality PATO:0001963 revolute A curled quality inhering in a bearer by virtue of the bearer's edges of its surface being rolled backwards spirally on each side. ISBN:0881923214 A curled quality inhering in a bearer by virtue of the bearer's edges of its surface being rolled spirally downwards. quality PATO:0001964 circinate A curled quality inhering in a bearer by virtue of the bearer's edges of its surface being rolled spirally downwards. ISBN:0881923214 A curled quality inhering in a bearer by virtue of the bearer's edges of its surface being bent down upon their stalk. quality PATO:0001965 reclinate A curled quality inhering in a bearer by virtue of the bearer's edges of its surface being bent down upon their stalk. ISBN:0881923214 A curled quality inhering in a bearer by virtue of the bearer's one edge of its surface being wholly rolled up in another. quality PATO:0001966 convolute A curled quality inhering in a bearer by virtue of the bearer's one edge of its surface being wholly rolled up in another. ISBN:0881923214 A branched quality inhering in a bearer by virtue of the bearer's having three or more primary branches diverging radially from a single point. quality PATO:0001967 actinodromous A branched quality inhering in a bearer by virtue of the bearer's having three or more primary branches diverging radially from a single point. Hickey:1988 A branched quality inhering in a bearer by virtue of the bearer's having two or more parallel primary branches originate beside each other and converge apically. quality PATO:0001968 parallelodromous A branched quality inhering in a bearer by virtue of the bearer's having two or more parallel primary branches originate beside each other and converge apically. Hickey:1988 A branched quality inhering in a bearer by virtue of the bearer's having secondary branches terminating at the margin. quality PATO:0001969 craspedodromous A branched quality inhering in a bearer by virtue of the bearer's having secondary branches terminating at the margin. Hickey:1988 A branched quality inhering in a bearer by virtue of the bearer's having secondary branches joined together in a series of prominent arches. quality PATO:0001970 brochidodromous A branched quality inhering in a bearer by virtue of the bearer's having secondary branches joined together in a series of prominent arches. Hickey:1988 A branched quality inhering in a bearer by virtue of the bearer's having secondary branches freely branching toward the margin. quality PATO:0001971 cladodromous A branched quality inhering in a bearer by virtue of the bearer's having secondary branches freely branching toward the margin. Hickey:1988 A branched quality inhering in a bearer by virtue of the bearer's having secondary branches branching into a reticulum toward the margin. quality PATO:0001972 reticulodromous A branched quality inhering in a bearer by virtue of the bearer's having secondary branches branching into a reticulum toward the margin. Hickey:1988 A shape quality inhering in a bearer by virtue of the bearer's being tapering gradually into a rigid point. quality PATO:0001973 cuspidate A shape quality inhering in a bearer by virtue of the bearer's being tapering gradually into a rigid point. ISBN:0881923214 A shape quality inhering in a bearer by virtue of the bearer's terminating in a round end, the centre of which is depressed. quality PATO:0001974 retuse A shape quality inhering in a bearer by virtue of the bearer's terminating in a round end, the centre of which is depressed. ISBN:0881923214 A surface feature shape quality inhering in a bearer by virtue of the bearer's lacking sharp straight-edged teeth pointing to the apex. quality smooth PATO:0001975 unserrated A surface feature shape quality inhering in a bearer by virtue of the bearer's lacking sharp straight-edged teeth pointing to the apex. ISBN:0881923214 A surface feature shape quality inhering in a bearer by virtue of the bearer's having or lacking sharp straight-edged teeth pointing to the apex. quality PATO:0001976 serration A surface feature shape quality inhering in a bearer by virtue of the bearer's having or lacking sharp straight-edged teeth pointing to the apex. PATOC:GVG A shape quality inhering in a bearer by virtue of the bearer's having at least one salient angle on the margin. angulate quality PATO:0001977 angular A shape quality inhering in a bearer by virtue of the bearer's having at least one salient angle on the margin. PATOC:GVG A shape quality inhering in a bearer by virtue of the bearer's being regularly divided by deep incisions. incised quality PATO:0001978 cut A shape quality inhering in a bearer by virtue of the bearer's being regularly divided by deep incisions. ISBN:0881923214 A shape quality inhering in a bearer by virtue of the bearer's being partly divided into a determinate number of regions. quality PATO:0001979 lobed A shape quality inhering in a bearer by virtue of the bearer's being partly divided into a determinate number of regions. ISBN:0881923214 A shape quality inhering in a bearer by virtue of the bearer's having distinct parts arising from a common point or center. quality PATO:0001980 digitate A shape quality inhering in a bearer by virtue of the bearer's having distinct parts arising from a common point or center. thefreedictionary:thefreedictionary A shape quality inhering in a bearer by virtue of the bearer's having a shape resembling an ear. quality PATO:0001981 auriculate A shape quality inhering in a bearer by virtue of the bearer's having a shape resembling an ear. url:http://www.thefreedictionary.com/auriculate A shape quality inhering in a bearer by virtue of the bearer's gradually tapering to a slender point. quality PATO:0001982 attenuate A shape quality inhering in a bearer by virtue of the bearer's gradually tapering to a slender point. url:http://www.thefreedictionary.com/attenuate A structural quality inhering in a bearer by virtue of the bearer's two basal lobes being united together. quality PATO:0001983 perfoliate A structural quality inhering in a bearer by virtue of the bearer's two basal lobes being united together. ISBN:0881923214 A shape quality inhering in a bearer by virtue of the bearer's being prolonged below the point of insertion. quality PATO:0001984 decurrent A shape quality inhering in a bearer by virtue of the bearer's being prolonged below the point of insertion. ISBN:0881923214 A quality inhering in a bearer by virtue of the bearer's being kept below its freezing point. quality PATO:0001985 frozen A quality inhering in a bearer by virtue of the bearer's being kept below its freezing point. OBI:OBI A quality inhering in a bearer by virtue of the bearer's passing into solution. quality PATO:0001986 dissolved A quality inhering in a bearer by virtue of the bearer's passing into solution. PATOC:GVG A structural quality inhering in a bearer by virtue of the bearer's having a three dimensional cavity with a narrow or no opening, and often containing an anatomical substance. sacular quality PATO:0001987 saccular A structural quality inhering in a bearer by virtue of the bearer's having a three dimensional cavity with a narrow or no opening, and often containing an anatomical substance. PATOC:MAH A shape quality inhering in a bearer by virtue of the bearer's having four angles and four sides. quality PATO:0001988 quadrangular A shape quality inhering in a bearer by virtue of the bearer's having four angles and four sides. url:http://www.oed.com/ A curvature quality inhering in a bearer by virtue of the bearer's having many curves and turns. quality twisted PATO:0001989 sinuous A curvature quality inhering in a bearer by virtue of the bearer's having many curves and turns. PATOC:GVG A duration quality of a process inhering in a disease by virtue of the bearer's duration of an impairment of health or of a condition of abnormal functioning. quality PATO:0001990 MAH: I think this term should be obsoleted. Is it used? duration of disease A duration quality of a process inhering in a disease by virtue of the bearer's duration of an impairment of health or of a condition of abnormal functioning. PATOC:GVG A quality inhering in a bearer by virtue of the bearer's disposition to being capable of indefinite growth or division. quality PATO:0001991 immortal A quality inhering in a bearer by virtue of the bearer's disposition to being capable of indefinite growth or division. answers.com:answers.com An organismal quality inhering in a bearer by virtue of the bearer's consisting cells. quality PATO:0001992 cellularity An organismal quality inhering in a bearer by virtue of the bearer's consisting cells. PATOC:GVG A cellularity quality inhering in a bearer by virtue of the bearer's consisting of more than one cell. quality PATO:0001993 multicellular A cellularity quality inhering in a bearer by virtue of the bearer's consisting of more than one cell. PATOC:GVG A cellularity quality inhering in a bearer by virtue of the bearer's consisting of exactly one cell. quality PATO:0001994 unicellular A cellularity quality inhering in a bearer by virtue of the bearer's consisting of exactly one cell. PATOC:GVG A quality that inheres in an entire organism or part of an organism. quality PATO:0001995 organismal quality A quality that inheres in an entire organism or part of an organism. PATOC:CJM true An amount which is relatively low. PATO:0000419 PATO:0000468 decreased number present in fewer numbers in organism quality decreased reduced subnumerary PATO:0001997 decreased amount An amount which is relatively low. PATOC:GVG A quality inhering in a bearer by virtue of its visibility. quality PATO:0001998 This term was created as a grouping term for the 2 terms "conspicuous" and "inconspicuous". However, it is not clear if these terms should even remain in PATO. conspicuousness A quality inhering in a bearer by virtue of its visibility. PATOC:MAH The bearer of this quality has_part < n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. This case includes the limit case, where the bearer lacks all parts of the specified type. loss of quality PATO:0001999 lacks parts or has fewer parts of type The bearer of this quality has_part < n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. This case includes the limit case, where the bearer lacks all parts of the specified type. PATOC:CJM A quality of physical entities inhering in a bearer by virtue of the bearer's lacking a physical part as specified by the additional entity. PATO:0001557 OBO_REL:lacks_part lacks all physical parts of type quality PATO:0002000 Example: [E=organism Q=lacks_all_parts_of_type E2=Wing] - applies to an organism. A relational quality in which the bearer entity has no parts of the specified type. The bearer of this quality has_part = 0 of the indicated entity type, where a comparable organism usually has at least 1 part of the same type. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e lacks all parts of type X at time t, then there exists no instances x of X at t such that x part_of e that has no wings, where wings are normally present in that organism type. In OWL this is equivalent to a restriction on the OBO_REL:has_part relation with cardinality=0, i.e has_part 0 E2. lacks all parts of type A quality of physical entities inhering in a bearer by virtue of the bearer's lacking a physical part as specified by the additional entity. PATOC:CJM The bearer of this quality has_part < n AND has_part > 0 of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. PATO:0001569 decreased number of has decreased number of has fewer physical parts of type quality PATO:0002001 Example: [E=hand Q=has_fewer_parts_of_type E2=digit] - applies to an organism that has no less fingers than is normal for organisms of that type. has fewer parts of type The bearer of this quality has_part < n AND has_part > 0 of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. PATOC:CJM The bearer of this quality has_part > n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. PATO:0001560 has extra parts of has increased number of having extra physical parts having supernumerary physical parts increased number of quality PATO:0002002 In polydactyly, the bearer of the quality is the hand, and the entity type being counted is 'finger'. In EQ syntax, E=hand, Q=<this> E2=finger. has extra parts of type The bearer of this quality has_part > n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. PATOC:CJM A quality that inheres in an entire population or part of a population. quality PATO:0002003 population quality A quality that inheres in an entire population or part of a population. PATOC:GVG A shape that inheres in a part of a surface. An object can have different surface shapes on different parts of its surface. quality PATO:0002004 Consider PATO:0001925 obsolete surface shape true A shape that inheres in a part of a surface. An object can have different surface shapes on different parts of its surface. PATOC:CJM Surface shape that refers to the inward or outward curvature of the surface. quality PATO:0002005 concavity Surface shape that refers to the inward or outward curvature of the surface. PATOC:MAH A shape that inheres in a 2 dimensional entity, such as a cross section or projection of a 3 dimensional entity. quality 2-D projection cross-sectional PATO:0002006 2-D shape A shape that inheres in a 2 dimensional entity, such as a cross section or projection of a 3 dimensional entity. PATOC:CJM A complete three dimensional shape in which for every line connecting pair of points on the object is within the object. Or: a shape lacking cavities. Contrast: concave. Image:http://upload.wikimedia.org/wikipedia/commons/0/06/Convex_polygon_illustration1.png quality PATO:0002007 Use this term or an is_a child of this term when the entire shape of the object is known. convex 3-D shape A complete three dimensional shape in which for every line connecting pair of points on the object is within the object. Or: a shape lacking cavities. Contrast: concave. PATOC:CJM A complete three dimensional shape in which there is a line connecting pair of points on the object that lies outside the object. Or: a shape with cavities. Contrast: concave. Image:http://en.wikipedia.org/wiki/Image:Convex_polygon_illustration2.png quality PATO:0002008 concave 3-D shape A complete three dimensional shape in which there is a line connecting pair of points on the object that lies outside the object. Or: a shape with cavities. Contrast: concave. PATOC:CJM A shape quality inhering in a bearer by virtue of the degree to which there are subdivisions or offshoots in a bearer entity. quality PATO:0002009 branchiness A shape quality inhering in a bearer by virtue of the degree to which there are subdivisions or offshoots in a bearer entity. PATOC:MAH A texture quality inhering in a bearer by virtue of the bearer's bing full of small openings or gaps. quality PATO:0002010 looseness A texture quality inhering in a bearer by virtue of the bearer's bing full of small openings or gaps. url:http://www.wordreference.com/definition/loose A structural quality which is held by a bearer when the latter's disposition the presence of abnormally proliferating masses of cells. tumorous quality PATO:0002011 neoplastic A structural quality which is held by a bearer when the latter's disposition the presence of abnormally proliferating masses of cells. PATOC:MAH A texture quality that exists through a liquid cover on the surface of the bearer. quality PATO:0002012 coating A texture quality that exists through a liquid cover on the surface of the bearer. Wikipedia:Wikipedia A structural quality inhering in a bearer by virtue of whether the bearer forms a bundle of anatomical fibers, as of muscle or nerve. quality PATO:0002013 fasciculation A structural quality inhering in a bearer by virtue of whether the bearer forms a bundle of anatomical fibers, as of muscle or nerve. answers.com:http://www.answers.com/ A structural quality that inheres in a bearer by virtue of the bearer's containing hollow areas. quality PATO:0002014 structure, cavities A structural quality that inheres in a bearer by virtue of the bearer's containing hollow areas. PATOC:GVG true quality PATO:0002016 magnitude high magnitude quality PATO:0002017 increased magnitude low magnitude quality PATO:0002018 decreased magnitude A growth quality of occurrent in which the growth of an organism, structure or group of organisms does not occur. agenesis quality PATO:0002019 aplastic growth A growth quality of occurrent in which the growth of an organism, structure or group of organisms does not occur. PATOC:MAH Pink color having high brightness and low saturation. quality PATO:0002020 pale pink Pink color having high brightness and low saturation. PATOC:GVG A convex 3-D shape quality inhering in a bearer by virtue of the bearer's resembling a cone (a 3-D shape with a round cross section that tapers). Image:http://upload.wikimedia.org/wikipedia/commons/d/d2/Cone_3d.png cone-shaped quality PATO:0002021 conical A convex 3-D shape quality inhering in a bearer by virtue of the bearer's resembling a cone (a 3-D shape with a round cross section that tapers). Wikipedia:http://en.wikipedia.org/wiki/Cone_(geometry) A concave 3-D shape quality inhering in a bearer by virtue of the bearer's resembling a minute projection (villus). quality PATO:0002022 villiform A concave 3-D shape quality inhering in a bearer by virtue of the bearer's resembling a minute projection (villus). PATOC:PEM A positional quality inhering in a bearer by virtue of the bearer's location of features or characteristics along an apical-basal axis. quality PATO:0002023 apical-basal polarity A positional quality inhering in a bearer by virtue of the bearer's location of features or characteristics along an apical-basal axis. PATOC:MAH A positional quality inhering in a bearer by virtue of the bearer's location of features or characteristics along the anterior-posterior axis. rostral-caudal polarity superior-caudal polarity (human torso) quality PATO:0002024 anterior-posterior polarity A positional quality inhering in a bearer by virtue of the bearer's location of features or characteristics along the anterior-posterior axis. PATOC:MAH A convex angle that is formed by one side of a polygon and a line extended from an adjacent side. quality PATO:0002025 external angle A convex angle that is formed by one side of a polygon and a line extended from an adjacent side. http://en.wikipedia.org/wiki/Internal_angle A quality of a single process inhering in a bearer by virtue of the bearer's not increasing over time. george gkoutos 2008-12-18T12:49:19Z quality PATO:0002026 non-progressive A quality of a single process inhering in a bearer by virtue of the bearer's not increasing over time. PATOC:GVG A concentration quality inhering in a bearer by virtue of the bearer's amount of osmoles of solute per kilogram of solvent. george 2009-01-27T10:53:11Z quality PATO:0002027 osmolality A concentration quality inhering in a bearer by virtue of the bearer's amount of osmoles of solute per kilogram of solvent. Wikipedia:http://en.wikipedia.org/wiki/Osmolarity An osmolality which is relatively low. george 2009-01-27T10:55:33Z low osmolality quality PATO:0002028 decreased osmolality An osmolality which is relatively low. PATOC:GVG An osmolality which is relatively high. george 2009-01-27T10:56:19Z high osmolality quality PATO:0002029 increased osmolality An osmolality which is relatively high. PATOC:GVG A molecular quality that inheres in a molecular entity by virtue of whether the bearer exhibits the ability of a probe to react precisely with a specific target molecule. george 2009-01-27T11:13:52Z quality PATO:0002030 specificity to A molecular quality that inheres in a molecular entity by virtue of whether the bearer exhibits the ability of a probe to react precisely with a specific target molecule. PATOC:mc A curvature quality inhering in a bearer by virtue of the bearer's being curved or tilted such that the tip points upwards. george 2009-01-27T11:23:45Z quality PATO:0002031 upturned A curvature quality inhering in a bearer by virtue of the bearer's being curved or tilted such that the tip points upwards. PATOC:cjm A reflectivity quality inhering in light by virtue of the bearer's scattering occurring at small angle to the incident beam. george 2009-01-27T11:38:49Z quality PATO:0002032 forward scatter A reflectivity quality inhering in light by virtue of the bearer's scattering occurring at small angle to the incident beam. PATOC:mc A reflective quality that is the light scattering occurring at wide angle (around 90 degrees) to the incident beam. george 2009-01-27T11:39:36Z quality PATO:0002033 side scatter A reflective quality that is the light scattering occurring at wide angle (around 90 degrees) to the incident beam. PATOC:mc A shape quality inhering in a bearer by virtue of the bearer's being unseparated into parts or divisions. george 2009-01-27T11:53:46Z quality unseparated PATO:0002034 undivided A shape quality inhering in a bearer by virtue of the bearer's being unseparated into parts or divisions. PATOC:GVG A spatial quality inhering in a bearer by virtue of the bearer's being on the same side in relation to another structure. george 2009-02-01T02:04:11Z ipsilateral quality PATO:0002035 ipsilateral to A spatial quality inhering in a bearer by virtue of the bearer's being on the same side in relation to another structure. PATOC:GVG A spatial quality inhering in a bearer by virtue of the bearer's being located towards the central axis of the organism or an extremity. george 2009-02-01T02:06:20Z quality PATO:0002036 axial to A spatial quality inhering in a bearer by virtue of the bearer's being located towards the central axis of the organism or an extremity. PATOC:GVG A structural quality inhering in a bearer by virtue of the bearer exhibiting deterioration of its structure. george 2009-02-03T11:13:19Z quality PATO:0002037 degeneration A structural quality inhering in a bearer by virtue of the bearer exhibiting deterioration of its structure. PATOC:GVG A structural quality inhering in a bearer whose structure which does not deteriorate. george 2009-02-03T11:14:54Z not degenerate quality PATO:0002038 non-degenerate A structural quality inhering in a bearer whose structure which does not deteriorate. PATOC:GVG A concave quality inhering in a bearer by virtue of the bearer's curving inward on both sides or surfaces. quality PATO:0002039 biconcave A concave quality inhering in a bearer by virtue of the bearer's curving inward on both sides or surfaces. PATOC:GVG A shape quality inhering in a bearer by virtue of the bearer's being convex on both sides or surface. Image:http://www.thefreedictionary.com/_/viewer.aspx?path=hm&name=A4bicovx quality PATO:0002040 biconvex A shape quality inhering in a bearer by virtue of the bearer's being convex on both sides or surface. thefreedictionary:http://www.thefreedictionary.com/biconvexity A diameter that is along the anterior-posterior axis. quality PATO:0002041 anterior-posterior diameter A diameter that is along the anterior-posterior axis. PATOC:GVG An anterior-posterior diameter quality which is relatively small. low anterior-posterior diameter quality PATO:0002042 decreased anterior-posterior diameter An anterior-posterior diameter quality which is relatively small. PATOC:GVG An anterior-posterior diameter quality which is relatively large. high anterior-posterior diameter quality PATO:0002043 increased anterior-posterior diameter An anterior-posterior diameter quality which is relatively large. PATOC:GVG A shape quality inhering in a bearer by virtue of the bearer's being a quadrilateral with two parallel sides. trapezoidal quality PATO:0002044 trapezoid A shape quality inhering in a bearer by virtue of the bearer's being a quadrilateral with two parallel sides. PATOC:GVG A branched quality inhering in a bearer by virtue of the bearer's having smaller branches arising from larger branches. Resembling a tree in branching structure. george 2009-02-15T08:11:41Z dendriform dendroid dendroidal quality PATO:0002045 dendritic A branched quality inhering in a bearer by virtue of the bearer's having smaller branches arising from larger branches. Resembling a tree in branching structure. PATOC:cvs A spatial quality inhering in a bearer by virtue of the bearer's being away from or on the opposite side of the central axis. george gkoutos 2009-03-03T04:16:11Z quality PATO:0002046 abaxial to A spatial quality inhering in a bearer by virtue of the bearer's being away from or on the opposite side of the central axis. medical-dictionary:http://medical-dictionary.thefreedictionary.com/abaxial A spatial quality inhering in a bearer by virtue of the bearer's being located on the side nearest to the axis of an organ or organism. george gkoutos 2009-03-03T04:22:28Z quality PATO:0002047 adaxial to A spatial quality inhering in a bearer by virtue of the bearer's being located on the side nearest to the axis of an organ or organism. thefreedictionary:http://www.thefreedictionary.com/adaxial An organismal quality inhering in a bearer by virtue of the bearer's having two or more cell populations that differ in genetic makeup. This situation can affect any type of cell, including blood cells, gametes (egg and sperm cells), and skin. george gkoutos 2009-03-03T04:30:52Z quality heterogeneity PATO:0002048 mosaicism An organismal quality inhering in a bearer by virtue of the bearer's having two or more cell populations that differ in genetic makeup. This situation can affect any type of cell, including blood cells, gametes (egg and sperm cells), and skin. Medline:http://www.nlm.nih.gov/medlineplus A curvature quality inhering in a bearer by virtue of the bearer's being curved around an axis and towards the side. George Gkoutos 2009-03-13T12:36:14Z quality PATO:0002049 lateral and rotional curvature A curvature quality inhering in a bearer by virtue of the bearer's being curved around an axis and towards the side. PATOC:GVG An amount which normal. george 2009-03-20T11:16:22Z present in normal numbers in organism quality PATO:0002050 normal amount An amount which normal. PATOC:GVG An occurrence which is relatively high. George Gkoutos 2009-03-26T11:10:11Z increased incidence quality PATO:0002051 increased occurrence An occurrence which is relatively high. PATOC:GVG An occurrence which is relatively low. George Gkoutos 2009-03-26T11:12:35Z decreased incidence quality PATO:0002052 decreased occurrence An occurrence which is relatively low. PATOC:GVG A quality inhering in a bearer by virtue of the bearer's being flattened along dorso-ventral axis. George Gkoutos 2009-03-26T03:02:38Z quality PATO:0002053 dorso-ventrally flattened A quality inhering in a bearer by virtue of the bearer's being flattened along dorso-ventral axis. PATOC:MSP A quality inhering in a bearer by virtue of the bearer's being flattened along transverse axis. George Gkoutos 2009-03-26T03:03:37Z laterally flattened quality transversely flattened PATO:0002054 laterally compressed A quality inhering in a bearer by virtue of the bearer's being flattened along transverse axis. PATOC:msp A fragility which is relatively high. George Gkoutos 2009-03-26T04:01:37Z quality PATO:0002055 increased fragility A fragility which is relatively high. PATOC:GVG A fragility which is relatively low. George Gkoutos 2009-03-26T04:02:14Z quality PATO:0002056 decreased fragility A fragility which is relatively low. PATOC:GVG An area which is relatively high. George Gkoutos 2009-03-30T04:11:43Z quality PATO:0002057 increased area An area which is relatively high. PATOC:GVG An area which is relatively low. George Gkoutos 2009-03-30T04:12:11Z quality PATO:0002058 decreased area An area which is relatively low. PATOC:GVG The specific wavelength of light emitted by a fluorescent molecule, such as a labelled probe, upon absorption of light at the (higher) excitation wavelength. George Gkoutos 2009-05-27T02:25:33Z quality PATO:0002059 emmision wavelength The specific wavelength of light emitted by a fluorescent molecule, such as a labelled probe, upon absorption of light at the (higher) excitation wavelength. web:http://www.expertglossary.com/ The specific wavelength of radiation that can be retained by a bearer. George Gkoutos 2009-05-27T02:33:32Z quality PATO:0002060 absorption wavelength The specific wavelength of radiation that can be retained by a bearer. PATOC:GVG true george 2009-06-05T09:16:46Z quality PATO:0002062 physical quality of a process A shape inhering in a bearer by virtue of the bearer's being elongated and cylindrical. George Gkoutos 2009-07-01T01:44:06Z quality PATO:0002063 columnar A shape inhering in a bearer by virtue of the bearer's being elongated and cylindrical. PATOC:me A structure quality inhering in a bearer by virtue of the bearer's delimited by a surface with holes. George Gkoutos 2009-07-01T01:46:53Z quality PATO:0002064 fenestrated A structure quality inhering in a bearer by virtue of the bearer's delimited by a surface with holes. PATOC:me A shape quality inhering in a bearer by virtue of the bearer's being arranged like rays or radii; radiating from a common center. George Gkoutos 2009-07-01T01:48:19Z stellate quality PATO:0002065 star shaped A shape quality inhering in a bearer by virtue of the bearer's being arranged like rays or radii; radiating from a common center. PATOC:me A solid configuration inhering in a material entity by virtue of its constituent atoms, molecules, or ions being arranged in an orderly repeating pattern extending in all three spatial dimensions. George Gkoutos 2009-07-01T01:50:40Z quality PATO:0002066 crystal configuration A solid configuration inhering in a material entity by virtue of its constituent atoms, molecules, or ions being arranged in an orderly repeating pattern extending in all three spatial dimensions. Wikipedia:http://en.wikipedia.org/wiki/Crystal A spatial pattern inhering in a bearer by virtue of the bearer's layered configuration. George Gkoutos 2009-07-01T02:30:45Z quality PATO:0002067 stratification A spatial pattern inhering in a bearer by virtue of the bearer's layered configuration. PATOC:GVG A spatial pattern inhering in a bearer by virtue of the bearer's exhibiting a layered configuration. George Gkoutos 2009-07-01T02:31:53Z quality PATO:0002068 stratified A spatial pattern inhering in a bearer by virtue of the bearer's exhibiting a layered configuration. PATOC:GVG A spatial pattern inhering in a bearer by virtue of the bearer's lacking a layered configuration. George Gkoutos 2009-07-01T02:33:41Z quality PATO:0002069 unstratified A spatial pattern inhering in a bearer by virtue of the bearer's lacking a layered configuration. PATOC:GVG A molecular quality that arises from the molecular attraction exerted between two atoms or compounds. George Gkoutos 2009-09-18T01:16:16Z quality PATO:0002070 affinity A molecular quality that arises from the molecular attraction exerted between two atoms or compounds. PATOC:GVG An affinity which is relatively high. George Gkoutos 2009-09-18T01:29:42Z quality PATO:0002071 increased affinity An affinity which is relatively high. PATOC:GVG An affinity which is relatively low. George Gkoutos 2009-09-18T01:30:11Z quality PATO:0002072 decreased affinity An affinity which is relatively low. PATOC:GVG A molecular quality that arises from the synergistic strength of bond affinities between multiple bond interactions. George Gkoutos 2009-09-18T01:41:44Z quality PATO:0002073 avidity A molecular quality that arises from the synergistic strength of bond affinities between multiple bond interactions. Wikipedia:Wikipedia An avidity which is relatively high. George Gkoutos 2009-09-18T01:45:56Z quality PATO:0002074 increased avidity An avidity which is relatively high. PATOC:GVG An avidity which is relatively low. George Gkoutos 2009-09-18T01:45:59Z quality PATO:0002075 decreased avidity An avidity which is relatively low. PATOC:GVG A behavioral quality inhering in a bearer by virtue of the bearer's movement. George Gkoutos 2009-09-18T02:04:48Z movement behavioural quality quality PATO:0002076 movement behavioral quality A behavioral quality inhering in a bearer by virtue of the bearer's movement. PATOC:GVG A spatial quality inhering in a bearer by virtue of the bearer's being positioned with multiple entities of the same type above and below. George Gkoutos 2009-09-18T02:11:35Z quality PATO:0002077 stacked A spatial quality inhering in a bearer by virtue of the bearer's being positioned with multiple entities of the same type above and below. PATOC:CJM A quality inhering in a bearer by virtue of the bearer's having an empty space or cavity within. George Gkoutos 2009-09-18T02:19:20Z quality PATO:0002078 hollow A quality inhering in a bearer by virtue of the bearer's having an empty space or cavity within. url:http://www.merriam-webster.com/dictionary/hollow true A broken quality inhering in a bearer by virtue of the bearer's being separated into two contiguous wholes. George Gkoutos 2009-09-21T10:18:11Z quality PATO:0002080 broken into two pieces A broken quality inhering in a bearer by virtue of the bearer's being separated into two contiguous wholes. PATOC:CJM A broken quality inhering in a bearer by virtue of the bearer's being broken into multiple contiguous wholes. George Gkoutos 2009-09-21T10:18:51Z quality PATO:0002081 shattered A broken quality inhering in a bearer by virtue of the bearer's being broken into multiple contiguous wholes. PATOC:GJM A broken quality inhering in a bearer by virtue of the bearer's being still one contiguous whole but structurally damaged such that in danger of become two or more. George Gkoutos 2009-09-21T10:20:06Z quality PATO:0002082 partially broken A broken quality inhering in a bearer by virtue of the bearer's being still one contiguous whole but structurally damaged such that in danger of become two or more. PATOC:CJM Having extra or fewer parts. George Gkoutos 2009-09-21T10:41:58Z quality PATO:0002083 altered number of Having extra or fewer parts. PATOC:GVG The period after death of the organism. George Gkoutos 2009-09-25T11:29:21Z quality PATO:0002084 Terms were requested by the OBI consortium but it was later decided that the term was not reflecting a quality rather what it might be refered to as a "conferred quality". obsolete post-mortem true The period after death of the organism. thefreedictionary:thefreedictionary The period before death of the organism. George Gkoutos 2009-09-25T11:31:13Z quality PATO:0002085 Terms were requested by the OBI consortium but it was later decided that the term was not reflecting a quality rather what it might be refered to as a "conferred quality". obsolete pre-mortem true The period before death of the organism. merriam-webster:merriam-webster true A quality inhering in a bearer by virtue of the bearer's being short and wide and tapered distally. George Gkoutos 2009-09-30T09:53:43Z quality PATO:0002087 bullet-shaped A quality inhering in a bearer by virtue of the bearer's being short and wide and tapered distally. PATOC:GVG A structure quality inhering in a bearer by virtue of the bearer's body containing one cyst - a formation of a sac-like closed membranous structure not associated with neoplasia. George Gkoutos 2009-10-01T03:00:20Z quality PATO:0002088 monocystic A structure quality inhering in a bearer by virtue of the bearer's body containing one cyst - a formation of a sac-like closed membranous structure not associated with neoplasia. mondofacto:mondofacto A structure quality inhering in a bearer by virtue of the bearer's body containing more than one cyst - formations of sac-like closed membranous structures not associated with neoplasia. George Gkoutos 2009-10-01T03:02:54Z multicystic quality PATO:0002089 polycystic A structure quality inhering in a bearer by virtue of the bearer's body containing more than one cyst - formations of sac-like closed membranous structures not associated with neoplasia. PATOC:GVG A morphology quality inhering in a tumour by virtue of the bearer's exhibiting the morphological characteristics of a glandular epithelial cell. george 2009-10-05T11:25:52Z quality PATO:0002090 adenomatous A morphology quality inhering in a tumour by virtue of the bearer's exhibiting the morphological characteristics of a glandular epithelial cell. PATOC:GVG A quality of a single process inhering in a bearer by virtue of the bearer's having an onset and time course between acute and chronic. george 2009-10-05T11:31:35Z quality PATO:0002091 subacute A quality of a single process inhering in a bearer by virtue of the bearer's having an onset and time course between acute and chronic. PATOC:GVG A morphology quality inhering in a neoplastic cell by virtue of the bearer's exhibiting breakdown of cell-cell interaction maintaining tissue architecture, proliferative dysregulation and bizarre modification to nucleus size and shape. george 2009-10-05T11:45:53Z quality PATO:0002092 anaplastic A morphology quality inhering in a neoplastic cell by virtue of the bearer's exhibiting breakdown of cell-cell interaction maintaining tissue architecture, proliferative dysregulation and bizarre modification to nucleus size and shape. PATOC:GVG A volume quality inhering in a degenerating cell by virtue of the bearer's exhibiting an increase in volume associated with cytoplasmic abnormalities. george 2009-10-05T12:01:13Z quality PATO:0002093 ballooning A volume quality inhering in a degenerating cell by virtue of the bearer's exhibiting an increase in volume associated with cytoplasmic abnormalities. PATOC:GVG An affinity inhering in a tissue constituent by virtue of the bearer exhibiting a molecular interaction for basic dyes under specific pH conditions. george 2009-10-05T12:05:23Z quality PATO:0002094 basophilic An affinity inhering in a tissue constituent by virtue of the bearer exhibiting a molecular interaction for basic dyes under specific pH conditions. PATOC:GVG A disposition inhering in a tumour to progress or fail to progress during it's life time. george 2009-10-05T12:15:02Z quality PATO:0002095 obsolete neoplasm disposition true A disposition inhering in a tumour to progress or fail to progress during it's life time. PATOC:GVG A disposition inhering in a tumour by virtue of the bearer's disposition not to progress, invade surrounding tissues or metastasize. george 2009-10-05T12:47:14Z quality benign PATO:0002096 neoplastic, non-malignant A disposition inhering in a tumour by virtue of the bearer's disposition not to progress, invade surrounding tissues or metastasize. PATOC:GVG A disposition inhering in a tumour by virtue of the bearer's disposition to progress, invade surrounding tissues or metastasize. george 2009-10-05T12:50:22Z quality PATO:0002097 neoplastic, malignant A disposition inhering in a tumour by virtue of the bearer's disposition to progress, invade surrounding tissues or metastasize. PATOC:GVG A disposition inhering in a tumour by virtue of the bearer's disposition to spread and invade distant tissues. george 2009-10-05T12:54:48Z quality PATO:0002098 neoplastic, metastatic A disposition inhering in a tumour by virtue of the bearer's disposition to spread and invade distant tissues. PATOC:GVG A cellular quality inhering in a bearer by virtue of its stable specialization to a particular cell type. george 2009-10-05T12:58:54Z quality PATO:0002099 differentiated A cellular quality inhering in a bearer by virtue of its stable specialization to a particular cell type. PATOC:GVG A cellular quality inhering in a bearer by virtue of having not yet acquired a special structure of function. george 2009-10-05T12:59:21Z quality PATO:0002100 undifferentiated A cellular quality inhering in a bearer by virtue of having not yet acquired a special structure of function. PATOC:GVG A cellular quality inhering in a bearer by virtue of having changed from one fully differentiated state into another. george 2009-10-05T01:09:09Z quality trans-differentiated PATO:0002101 metaplastic A cellular quality inhering in a bearer by virtue of having changed from one fully differentiated state into another. PATOC:GVG A cellular quality inhering in a cell that arises by virtue of whether the bearer exhibits the ability to grow and proliferate in number through cell division. george 2009-10-05T01:16:31Z quality PATO:0002102 proliferative A cellular quality inhering in a cell that arises by virtue of whether the bearer exhibits the ability to grow and proliferate in number through cell division. PATOC:GVG A structural quality inhering in a bearer by virtue of the bearer's penetrating or permeating another substance or area. george 2009-10-05T01:27:56Z infiltrating quality PATO:0002103 infiltrative A structural quality inhering in a bearer by virtue of the bearer's penetrating or permeating another substance or area. PATOC:GVG A compositional quality inhering in an bearer by virtue of the bearer's infiltration by leukocytes, local edema and accumulation of plasma proteins. george 2009-10-05T01:37:35Z quality PATO:0002104 inflamed A compositional quality inhering in an bearer by virtue of the bearer's infiltration by leukocytes, local edema and accumulation of plasma proteins. PATOC:GVG A structural quality inhering in a bearer by virtue of the bearer's exhibiting excessive discharge of blood from the blood vessels. george 2009-10-05T01:55:53Z quality PATO:0002105 hemorrhagic A structural quality inhering in a bearer by virtue of the bearer's exhibiting excessive discharge of blood from the blood vessels. PATOC:GVG A cellular quality inhering in a bearer by virtue of its lacking most of the cellular characteristics which would allow it to be fully differentiated. george 2009-10-05T02:53:43Z quality PATO:0002106 poorly differentiated A cellular quality inhering in a bearer by virtue of its lacking most of the cellular characteristics which would allow it to be fully differentiated. PATOC:GVG A positional quality inhering in a bearer by virtue of the bearer's being at the edge or boundary of a related entity. george 2009-10-05T02:58:16Z quality PATO:0002107 peripheral A positional quality inhering in a bearer by virtue of the bearer's being at the edge or boundary of a related entity. PATOC:GVG A quality inhering in a bearer by virtue of the bearer's resembling small nipple like projection. george 2009-10-05T03:04:52Z quality PATO:0002108 papillary A quality inhering in a bearer by virtue of the bearer's resembling small nipple like projection. PATO:GVG A structural quality inhering in a bearer by virtue of the bearer's resembling cheese. george 2009-10-05T03:09:27Z cheese-like quality PATO:0002109 caseous A structural quality inhering in a bearer by virtue of the bearer's resembling cheese. answers.com:answers.com A cellular quality inhering in a bearer by virtue of its having most of the cellular characteristics of the tissue of origin. george 2009-10-05T03:26:29Z quality PATO:0002110 well differentiated A cellular quality inhering in a bearer by virtue of its having most of the cellular characteristics of the tissue of origin. PATOC:GVG A cellular quality inhering in a bearer by virtue of its lacking few of the cellular characteristics which would allow it to be fully differentiated. george 2009-10-05T03:29:42Z quality PATO:0002111 moderately well differentiated A cellular quality inhering in a bearer by virtue of its lacking few of the cellular characteristics which would allow it to be fully differentiated. PATOC:GVG A structural quality inhering in a bearer by virtue of the bearer's having a hole or holes, especially a row or array of small holes. george 2009-10-05T03:37:05Z PATO:0000649 quality permeable pierced PATO:0002112 perforate A structural quality inhering in a bearer by virtue of the bearer's having a hole or holes, especially a row or array of small holes. answers.com:answers.com Perforated like a sieve. george 2009-10-05T03:38:22Z quality PATO:0002113 cribriform Perforated like a sieve. merriam-webster:merriam-webster A composition quality inhering in a bearer by virtue of the bearer's containing excess lipid. george 2009-10-05T03:47:15Z quality PATO:0002114 fatty A composition quality inhering in a bearer by virtue of the bearer's containing excess lipid. PATOC:GVG A composition quality inhering in a bearer by virtue of the bearer's containing fibrin. george 2009-10-05T04:01:01Z quality PATO:0002115 fibrinoid A composition quality inhering in a bearer by virtue of the bearer's containing fibrin. PATOC:GVG A composition quality inhering in exudate by virtue of the bearer's containing fibrin. george 2009-10-05T04:03:03Z quality PATO:0002116 fibrinopurulent A composition quality inhering in exudate by virtue of the bearer's containing fibrin. PATOC:GVG A morphology quality inhering in a bearer by virtue of the bearer's exhbiting the morphological characteristics of a gland. george 2009-10-05T04:11:30Z quality PATO:0002117 glandular A morphology quality inhering in a bearer by virtue of the bearer's exhbiting the morphological characteristics of a gland. PATOC:GVG A quality inhering in a bearer by virtue of the bearer's being present in more than two copies. george 2009-10-06T03:28:38Z quality PATO:0002118 multiple A quality inhering in a bearer by virtue of the bearer's being present in more than two copies. PATOC:GVG A structural quality which is held by a bearer when the latter exhibits an excessive accumulation of intracellular fluid. george 2009-10-06T03:45:58Z quality PATO:0002119 hydropic A structural quality which is held by a bearer when the latter exhibits an excessive accumulation of intracellular fluid. PATOC:GVG A quality inhering a bearer by virtue of the bearer's ability to generate pus. george 2009-10-06T03:56:00Z quality purulent PATO:0002120 suppurative A quality inhering a bearer by virtue of the bearer's ability to generate pus. PATOC:GVG A spatial pattern inhering in a bearer by virtue of the bearer's structure resembling an irregular meshwork with cross-linking struts. george 2009-10-06T03:57:55Z quality PATO:0002121 trabecular A spatial pattern inhering in a bearer by virtue of the bearer's structure resembling an irregular meshwork with cross-linking struts. PATOC:GVG A composition quality inhering in a bearer by virtue of the bearer's being composed of more than one identifiable entities. george 2009-10-06T04:29:17Z quality PATO:0002122 mixed A composition quality inhering in a bearer by virtue of the bearer's being composed of more than one identifiable entities. PATOC:GVG Being smallest in amount, extent or degree. george 2009-10-06T04:33:48Z quality PATO:0002123 minimal Being smallest in amount, extent or degree. PATOC:GVG A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer. george 2009-10-06T04:37:14Z quality PATO:0002124 laminar A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer. PATOC:GVG A quality inhering in a bearer by virtue of the bearer's consisting a knot-like mass. george 2009-10-06T04:40:06Z quality PATO:0002125 nodular A quality inhering in a bearer by virtue of the bearer's consisting a knot-like mass. PATOC:GVG A quality inhering in a bearer by virtue of the bearer's containing bone. george 2009-10-06T04:42:11Z bony quality PATO:0002126 osseous A quality inhering in a bearer by virtue of the bearer's containing bone. PATOC:GVG A hardness quality of being rigid and resistant to pressure and fibrous. george 2009-10-06T04:49:30Z quality PATO:0002127 scirrhous A hardness quality of being rigid and resistant to pressure and fibrous. PATOC:GVG A quality inhering a bearer by virtue of the bearer's containing or resembling serum. george 2009-10-06T04:51:16Z quality PATO:0002128 serous A quality inhering a bearer by virtue of the bearer's containing or resembling serum. PATOC:GVG A disposition inhering in a tumour by virtue of the bearer's disposition to invade surrounding tissues. george 2009-10-06T05:02:45Z quality PATO:0002129 neoplastic, invasive A disposition inhering in a tumour by virtue of the bearer's disposition to invade surrounding tissues. PATOC:GVG A disposition inhering in a tumour by virtue of the bearer's disposition to invade surrounding tissues to a large extend. george 2009-10-06T05:03:13Z quality PATO:0002130 neoplastic, deeply invasive A disposition inhering in a tumour by virtue of the bearer's disposition to invade surrounding tissues to a large extend. PATOC:GVG A displaced angular placement quality inhering in a body part by virtue of the bearer's movement away from the medial plane of the body. george 2009-10-13T06:38:53Z quality PATO:0002131 abduction A displaced angular placement quality inhering in a body part by virtue of the bearer's movement away from the medial plane of the body. wikipedia:wikipedia A disposition inhering in a tumour by virtue of the bearer's disposition not to invade surrounding tissues. george 2009-10-06T05:04:18Z quality PATO:0002132 neoplastic, non-invasive A disposition inhering in a tumour by virtue of the bearer's disposition not to invade surrounding tissues. PATOC:GVG A displaced angular placement quality inhering in a body part by virtue of the bearer's movement closer the medial plane of the body. george 2009-10-13T06:41:39Z quality PATO:0002133 This term is also used in reference to the operation of the muscle in anatomy or musculature. adduction A displaced angular placement quality inhering in a body part by virtue of the bearer's movement closer the medial plane of the body. wikipedia:wikipedia A composition quaity inhering in a bearer by virtue of the bearer's containing of or pertaining to fibrils, or nanoscale fibers. george 2009-10-26T12:53:47Z fibrillate quality PATO:0002134 fibrillary A composition quaity inhering in a bearer by virtue of the bearer's containing of or pertaining to fibrils, or nanoscale fibers. wikipedia:wikipedia A duration quality of a process inhering in a bearer by virtue of the bearer's delay to complete the closure of the opening of an anatomical entity. george 2009-10-26T01:03:17Z quality PATO:0002135 delayed closure A duration quality of a process inhering in a bearer by virtue of the bearer's delay to complete the closure of the opening of an anatomical entity. PATOC:GVG A quality inhering in a bearer by virtue of the bearer's relative inability of electromagnetism to pass through a particular material, particularly X-rays. george 2009-10-26T01:14:38Z quality PATO:0002136 radiopacity A quality inhering in a bearer by virtue of the bearer's relative inability of electromagnetism to pass through a particular material, particularly X-rays. Wikipedia:Wikipedia A radiopacity quality inhering in a bearer by virtue of the bearer's prevention of the passage of electromagnetic radiation. george 2009-10-26T01:16:08Z quality PATO:0002137 radiopaque A radiopacity quality inhering in a bearer by virtue of the bearer's prevention of the passage of electromagnetic radiation. Wikipedia:Wikipedia A physical quality inhering in a bearer by virtue of the bearer's disposition to being fit to be eaten. george 2009-10-26T01:20:24Z edibleness quality PATO:0002138 edibility A physical quality inhering in a bearer by virtue of the bearer's disposition to being fit to be eaten. PATOC:VO A physical quality inhering in a bearer by virtue of the bearer being suitable for use as food. george 2009-10-26T01:21:34Z quality PATO:0002139 edible A physical quality inhering in a bearer by virtue of the bearer being suitable for use as food. PATOC:VO A physical quality inhering in a bearer by virtue of the bearer not being suitable for use as food. george 2009-10-26T01:22:27Z quality PATO:0002140 inedible A physical quality inhering in a bearer by virtue of the bearer not being suitable for use as food. PATOC:VO A density quality which lacks pattern. george 2009-10-28T01:57:53Z quality PATO:0002141 irregular density A density quality which lacks pattern. PATOC:GVG george 2009-10-28T03:14:54Z quality PATO:0002142 bracket george 2009-10-30T02:18:39Z quality PATO:0002143 sloped downward A radiopacity that is relatively high. george 2009-10-30T03:30:39Z quality PATO:0002144 increased radiopacity A radiopacity that is relatively high. PATOC:GVG A radiopacity that is relatively low. george 2009-10-30T03:31:31Z quality PATO:0002145 decreased radiopacity A radiopacity that is relatively low. PATOC:GVG A quality inhering in a bearer by virtue of the severity of infectious disease caused by the bearer in a target organism. george 2009-10-30T05:04:06Z quality PATO:0002146 virulence A quality inhering in a bearer by virtue of the severity of infectious disease caused by the bearer in a target organism. https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0001-8941-3984 A virulence that is relatively low. george 2009-10-30T05:05:02Z attenuated quality PATO:0002147 reduced virulence A virulence that is relatively low. PATOC:GVG A virulence that is relatively high. george 2009-10-30T05:13:10Z quality PATO:0002148 increased virulence A virulence that is relatively high. PATOC:GVG A quality inhering in a bearer by virtue of the bearer exhibiting increased density resulting in exhibiting increased degree of radiopacity (in X-rays). george 2009-11-03T02:59:08Z quality PATO:0002149 ivory A quality inhering in a bearer by virtue of the bearer exhibiting increased density resulting in exhibiting increased degree of radiopacity (in X-rays). PATOC:GVG A curvature quality inhering in a bearer by virtue of the bearer's being curved outwards from the part of the body from which the tail arises. george 2009-11-06T01:13:10Z splayed inferior (human torso) splayed posterior quality PATO:0002150 splayed caudal A curvature quality inhering in a bearer by virtue of the bearer's being curved outwards from the part of the body from which the tail arises. PATOC:GVG A curvature quality inhering in a bearer by virtue of the bearer's being curved outwards from the back or upper surface of an organism. george 2009-11-06T01:14:09Z quality splayed posterior (human torso) PATO:0002151 splayed dorsal A curvature quality inhering in a bearer by virtue of the bearer's being curved outwards from the back or upper surface of an organism. PATOC:GVG A curvature quality inhering in a bearer by virtue of the bearer's being curved outwards from the side. george 2009-11-06T01:14:22Z quality PATO:0002152 splayed lateral A curvature quality inhering in a bearer by virtue of the bearer's being curved outwards from the side. PATOC:GVG A curvature quality inhering in a bearer by virtue of the bearer's being curved outwards the front of an organism. george 2009-11-06T01:14:31Z splayed anterior splayed superior (human torso) quality PATO:0002153 splayed rostral A curvature quality inhering in a bearer by virtue of the bearer's being curved outwards the front of an organism. PATOC:GVG A curvature quality inhering in a bearer by virtue of the bearer's being curved outwards the abdomen of an organism. george 2009-11-06T01:14:42Z splayed anterior (human torso) splayed inferior (human head) quality PATO:0002154 splayed ventral A curvature quality inhering in a bearer by virtue of the bearer's being curved outwards the abdomen of an organism. PATOC:GVG A rotation quality inhering in a bearer by virtue of being rotated towards the middle of an organism. george 2009-11-06T02:23:28Z internally rotated quality PATO:0002155 medially rotated A rotation quality inhering in a bearer by virtue of being rotated towards the middle of an organism. PATOC:GVG A rotation quality inhering in a bearer by virtue of being rotated towards the side of an organism. george 2009-11-06T02:25:10Z externally rotated quality PATO:0002156 laterally rotated A rotation quality inhering in a bearer by virtue of being rotated towards the side of an organism. PATOC:GVG A positional quality inhering in a bearer by virtue of the bearer's being slightly out of its usual or proper place, or position. george 2009-11-06T03:34:15Z PATO:0002160 partial dislocated towards subluxation suluxated towards quality PATO:0002157 partially dislocated A positional quality inhering in a bearer by virtue of the bearer's being slightly out of its usual or proper place, or position. PATOC:GVG true true true Having two horns or horn-shaped branches. george 2009-11-11T02:37:52Z quality PATO:0002161 bicornuate Having two horns or horn-shaped branches. mondofacto:mondofacto A concave quality inhering in a bearer by virtue of the bearer's forming or resembling an arch of an increased apical height. george 2009-11-26T02:34:06Z quality PATO:0002162 high-arched A concave quality inhering in a bearer by virtue of the bearer's forming or resembling an arch of an increased apical height. PATOC:GVG A quality inhering in a bearer by virtue of the bearer's bodily structure that has protruded through an abnormal opening in the wall that contains it into the surface or boundary of another entity. george 2009-11-26T04:50:43Z quality PATO:0002163 herniated into A quality inhering in a bearer by virtue of the bearer's bodily structure that has protruded through an abnormal opening in the wall that contains it into the surface or boundary of another entity. PATOC:GVG A curvature quality inhering in a bearer by virtue of the bearer's being curved towards the middle. george 2009-12-02T10:06:21Z quality PATO:0002164 curved medial A curvature quality inhering in a bearer by virtue of the bearer's being curved towards the middle. PATOC:GVG To bent or hang downwards. george 2009-12-02T03:32:55Z sagging quality PATO:0002165 drooping To bent or hang downwards. thefreedictionary.:thefreedictionary. A duration quality of a process inhering in a bearer by virtue of the bearer's premature completion of the closure of the opening of an anatomical entity. george 2009-12-02T04:10:10Z quality PATO:0002166 premature closure A duration quality of a process inhering in a bearer by virtue of the bearer's premature completion of the closure of the opening of an anatomical entity. PATOC:GVG A protruding quality inhering in a bearer by virtue of the bearer's bodily structure that has protruded out of the surface or boundary of another entity. george 2009-12-02T05:19:32Z quality PATO:0002167 herniated out of A protruding quality inhering in a bearer by virtue of the bearer's bodily structure that has protruded out of the surface or boundary of another entity. PATOC:GVG An angular placement quality inhering in a bearer by virtue of the bearer being changed in position in relation to another entity. george 2010-01-14T04:45:18Z quality mislocalised to PATO:0002168 displaced to An angular placement quality inhering in a bearer by virtue of the bearer being changed in position in relation to another entity. PATOC:GVG A shape quality inhering in a bearer by virtue of the bearer's being split along the median axis. george 2010-02-03T04:37:15Z quality PATO:0002169 split medially A shape quality inhering in a bearer by virtue of the bearer's being split along the median axis. PATOC:GVG A shape quality inhering in a bearer by virtue of the bearer's being split asymmetrically on one side. george 2010-02-03T04:37:40Z quality PATO:0002170 split laterally A shape quality inhering in a bearer by virtue of the bearer's being split asymmetrically on one side. PATOC:GVG A shape quality inhering in a bearer by virtue of the bearer's being split on two side. george 2010-02-03T04:37:53Z quality PATO:0002171 split bilaterally A shape quality inhering in a bearer by virtue of the bearer's being split on two side. PATOC:GVG A shape quality inhering in a bearer by virtue of the bearer's being split along the radial axis. george 2010-02-03T04:42:35Z quality PATO:0002172 split radially A shape quality inhering in a bearer by virtue of the bearer's being split along the radial axis. PATOC:GVG An alignment quality inhering in a bearer by virtue of the bearer's being in a improper spatial positioning towards an additional entity. George Gkoutos 2010-02-22T03:18:17Z quality PATO:0002173 misaligned towards An alignment quality inhering in a bearer by virtue of the bearer's being in a improper spatial positioning towards an additional entity. PATOC:GVG An alignment quality inhering in a bearer by virtue of the bearer's being in a improper spatial positioning away from an additional entity. George Gkoutos 2010-02-22T03:18:48Z quality PATO:0002174 misaligned away from An alignment quality inhering in a bearer by virtue of the bearer's being in a improper spatial positioning away from an additional entity. PATOC:GVG A spatial quality inhering in a bearer by virtue of the bearer's changed direction of position towards another entity. George Gkoutos 2010-02-25T09:14:42Z quality PATO:0002175 deviation A spatial quality inhering in a bearer by virtue of the bearer's changed direction of position towards another entity. PATO:GVG A deviation quality inhering in a bearer by virtue of the bearer's changed direction of position towards the side. George Gkoutos 2010-02-25T09:16:04Z quality PATO:0002176 deviation towards the lateral side A deviation quality inhering in a bearer by virtue of the bearer's changed direction of position towards the side. PATOC:GVG A deviation quality inhering in a bearer by virtue of the bearer's changed direction of position towards the middle. George Gkoutos 2010-02-25T09:16:56Z quality PATO:0002177 deviation towards the medial side A deviation quality inhering in a bearer by virtue of the bearer's changed direction of position towards the middle. PATOC:GVG A positional quality inhering in a bearer by virtue of the bearer's being out of its usual or proper place, or position around a central point or axis. George Gkoutos 2010-02-25T11:24:58Z quality PATO:0002178 mislocalised radially A positional quality inhering in a bearer by virtue of the bearer's being out of its usual or proper place, or position around a central point or axis. PATOC:GVG A positional quality inhering in a bearer by virtue of the bearer's being positioned towards to point of attachment or origin. George Gkoutos 2010-02-25T12:34:48Z quality PATO:0002179 mislocalised proximally A positional quality inhering in a bearer by virtue of the bearer's being positioned towards to point of attachment or origin. PATOC:GVG A shape quality inhering in a bearer by virtue of the bearer's being free of curves, bends, or angles. George Gkoutos 2010-02-28T08:54:59Z quality PATO:0002180 straight A shape quality inhering in a bearer by virtue of the bearer's being free of curves, bends, or angles. merriam-webster:merriam-webster A positional quality inhering in a bearer by virtue the bearer's being changed in position. George Gkoutos 2010-03-01T02:56:33Z quality PATO:0002181 displaced A positional quality inhering in a bearer by virtue the bearer's being changed in position. PATOC:GVG A quality which inheres in a molecular entity, a single molecule, atom, ion, radical etc. George Gkoutos 2010-03-10T03:18:15Z PATO:0002061 relational molecular quality quality PATO:0002182 molecular quality A quality which inheres in a molecular entity, a single molecule, atom, ion, radical etc. PATOC:GVG A molecular quality that inheres in a molecular entity by virtue of whether that there is a presence of cycles in the connection of the atoms within the molecular entity. George Gkoutos 2010-03-10T03:19:46Z quality PATO:0002183 cyclicity A molecular quality that inheres in a molecular entity by virtue of whether that there is a presence of cycles in the connection of the atoms within the molecular entity. PATOC:JH Cyclic cyclicity inheres in a molecule when the atoms of the molecule do contain at least one cycle in the atom-atom connection paths (through bonds). George Gkoutos 2010-03-10T03:20:54Z quality PATO:0002184 cyclic cyclicity Cyclic cyclicity inheres in a molecule when the atoms of the molecule do contain at least one cycle in the atom-atom connection paths (through bonds). PATOC:JH Acyclic cyclicity inheres in a molecule when the atoms within the molecule do not contain at least one cycle in the atom-atom connection paths (through the bonds). George Gkoutos 2010-03-10T03:21:39Z quality PATO:0002185 acyclic cyclicity Acyclic cyclicity inheres in a molecule when the atoms within the molecule do not contain at least one cycle in the atom-atom connection paths (through the bonds). PATOC:JH A molecular quality that inheres in a molecular entity by virtue of whether or not the molecular entity has a separation of electric charge which leads to the molecule having an electric dipole. George Gkoutos 2010-03-10T03:22:04Z quality PATO:0002186 polarity A molecular quality that inheres in a molecular entity by virtue of whether or not the molecular entity has a separation of electric charge which leads to the molecule having an electric dipole. PATOC:JH Polar polarity is a quality that inheres in a molecular entity when the molecular entity is polar, i.e. does possess an electric dipole. George Gkoutos 2010-03-10T03:22:49Z quality PATO:0002187 polar polarity Polar polarity is a quality that inheres in a molecular entity when the molecular entity is polar, i.e. does possess an electric dipole. PATOC:JH A molecular quality which inheres in a molecular entity when the molecular entity does not possess an electrical dipole. George Gkoutos 2010-03-10T03:24:01Z quality PATO:0002188 nonpolar polarity A molecular quality which inheres in a molecular entity when the molecular entity does not possess an electrical dipole. PATOC:JH The ease of distortion of the electron cloud of a molecular entity by an electric field. George Gkoutos 2010-03-10T03:24:47Z quality PATO:0002189 electric polarizability The ease of distortion of the electron cloud of a molecular entity by an electric field. PATOC:JH A molecular quality that inheres in a molecular entity by virtue of the presence of a conjugated ring of unsaturated bonds, lone pairs, or empty orbitals that exhibit a stabilization stronger than would be expected by the stabilization of conjugation alone. George Gkoutos 2010-03-10T03:25:27Z quality PATO:0002190 aromaticity A molecular quality that inheres in a molecular entity by virtue of the presence of a conjugated ring of unsaturated bonds, lone pairs, or empty orbitals that exhibit a stabilization stronger than would be expected by the stabilization of conjugation alone. PATOC:JH A molecular quality that inheres in a molecular entity when it possesses at least one ring that is aromatic, i.e. A conjugated ring of unsaturated bonds, lone pairs, or empty orbitals that exhibit a stabilization stronger than would be expected by the stabilization of conjugation alone. George Gkoutos 2010-03-10T03:25:59Z quality PATO:0002191 aromatic A molecular quality that inheres in a molecular entity when it possesses at least one ring that is aromatic, i.e. A conjugated ring of unsaturated bonds, lone pairs, or empty orbitals that exhibit a stabilization stronger than would be expected by the stabilization of conjugation alone. PATOC:JH A quality that inheres in a molecular entity by virtue of the molecule possessing no rings that are aromatic. George Gkoutos 2010-03-10T03:26:41Z quality PATO:0002192 non-aromatic A quality that inheres in a molecular entity by virtue of the molecule possessing no rings that are aromatic. PATOC:JH A molecular quality that inheres in a molecular entity by virtue of the overall electric charge of the molecule, which is due to a comparison between the total number of electrons and the total number of protons. George Gkoutos 2010-03-10T03:28:54Z quality PATO:0002193 electric charge A molecular quality that inheres in a molecular entity by virtue of the overall electric charge of the molecule, which is due to a comparison between the total number of electrons and the total number of protons. PATOC:JH A quality which inheres in a molecular entity by virtue of the molecular entity possessing the same amount of electrons overall as protons, thus having an overall neutral charge. George Gkoutos 2010-03-10T03:29:37Z quality PATO:0002194 neutral charge A quality which inheres in a molecular entity by virtue of the molecular entity possessing the same amount of electrons overall as protons, thus having an overall neutral charge. PATOC:JH A quality which inheres in a molecular entity by virtue of the molecular entity possessing more protons overall than electrons, thus having an overall positive charge. George Gkoutos 2010-03-10T03:30:06Z quality PATO:0002195 positive charge A quality which inheres in a molecular entity by virtue of the molecular entity possessing more protons overall than electrons, thus having an overall positive charge. PATOC:JH A quality which inheres in a molecular entity by virtue of the molecular entity possessing more electrons overall than protons, thus having an overall negative charge. George Gkoutos 2010-03-10T03:30:39Z quality PATO:0002196 negative charge A quality which inheres in a molecular entity by virtue of the molecular entity possessing more electrons overall than protons, thus having an overall negative charge. PATOC:JH A quality that describes the power of an atom to attract electrons to itself . George Gkoutos 2010-03-10T03:31:15Z quality PATO:0002197 electronegativity A quality that describes the power of an atom to attract electrons to itself . PATOC:JH A quality inhering in a bearer by virtue of its constitution. George Gkoutos 2010-03-15T04:35:27Z quality PATO:0002198 quality of a substance A quality inhering in a bearer by virtue of its constitution. PATOC:GVG A quality which inheres in a substance by virtue of the ease with which the substance can be changed from a solid to a liquid state especially by the application of heat. George Gkoutos 2010-03-15T04:36:57Z quality PATO:0002199 meltability A quality which inheres in a substance by virtue of the ease with which the substance can be changed from a solid to a liquid state especially by the application of heat. PATOC:JH A quality which inheres in a substance by virtue of the ease with which the substance can be changed into a gaseous state. George Gkoutos 2010-03-15T04:38:02Z quality PATO:0002200 vaporizability A quality which inheres in a substance by virtue of the ease with which the substance can be changed into a gaseous state. PATOC:JH A behavioral quality inhering ina bearer by virtue of the bearer's unequal distribution of fine motor skill between its left and right hands or feet. haendel 2010-03-22T05:48:33Z quality PATO:0002201 Adapted from Wikipedia and the birnlex term that is dbxref'd. Added on behalf of OBI at March 2010 workshop. handedness A behavioral quality inhering ina bearer by virtue of the bearer's unequal distribution of fine motor skill between its left and right hands or feet. birnlex:2178 Handedness where the organism preferentially uses the left hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot. haendel 2010-03-22T05:49:06Z quality PATO:0002202 left handedness Handedness where the organism preferentially uses the left hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot. birnlex:2038 Handedness where the organism preferentially uses the right hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot. haendel 2010-03-22T05:49:19Z quality PATO:0002203 right handedness Handedness where the organism preferentially uses the right hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot. birnlex:2184 Handedness where the organism exhibits no overall dominance in the use of right or left hand or foot in the performance of tasks that require one hand or foot or a dominant hand or foot. haendel 2010-03-22T05:49:30Z quality PATO:0002204 ambidextrous handedness Handedness where the organism exhibits no overall dominance in the use of right or left hand or foot in the performance of tasks that require one hand or foot or a dominant hand or foot. birnlex:2042 A quality inhering in a bearer by virtue of the bearer's ability to hold an electrical charge. George Gkoutos 2010-03-25T09:42:51Z quality PATO:0002205 Capacitance is also a measure of the amount of electrical energy stored (or separated) for a given electric potential. capacitance A quality inhering in a bearer by virtue of the bearer's ability to hold an electrical charge. Wikipedia:Wikipedia A maturity quality inhering to a bearer by virtue of the bearer's being at the point or short after birth. George Gkoutos 2010-05-07T12:11:47Z quality PATO:0002206 neonatal A maturity quality inhering to a bearer by virtue of the bearer's being at the point or short after birth. PATOC:GVG A quality that is the distance between the end of the inserted object and the surface of the object into which it penetrates. George Gkoutos 2010-05-14T11:40:24Z quality PATO:0002207 insertion depth A quality that is the distance between the end of the inserted object and the surface of the object into which it penetrates. PATOC:GVG A concave 3-D shape quality inhering in a bearer by virtue of the bearer's being shaped in the form of a spoon. george 2010-07-08T12:13:12Z quality PATO:0002208 spoon-shaped A concave 3-D shape quality inhering in a bearer by virtue of the bearer's being shaped in the form of a spoon. thefreedictionary:http://www.thefreedictionary.com/spoon-shaped A shape quality inhering in a bearer by virtue of the bearer's having the shape of an incisor tooth. george 2010-07-08T12:16:04Z quality PATO:0002209 incisiform A shape quality inhering in a bearer by virtue of the bearer's having the shape of an incisor tooth. thefreedictionary:http://www.thefreedictionary.com/incisiform A convex 3-D shape quality inhering in a bearer by virtue of the bearer's resembling a teardrop. george 2010-07-08T12:19:08Z bulb-shaped bulblike quality swollen PATO:0002210 bulbous A convex 3-D shape quality inhering in a bearer by virtue of the bearer's resembling a teardrop. PATOC:GVG A curvature quality inhering in a bearer by virtue of the bearer's being curved backward or inward. george 2010-07-08T12:26:45Z quality PATO:0002211 recurved A curvature quality inhering in a bearer by virtue of the bearer's being curved backward or inward. merriam-webster:http://www.merriam-webster.com/dictionary/recurved A shape quality inhering in a bearer by virtue of the bearer's being small or narrow in circumference or width in proportion to length or height. george 2010-07-08T01:32:26Z quality gracile PATO:0002212 slender A shape quality inhering in a bearer by virtue of the bearer's being small or narrow in circumference or width in proportion to length or height. merriam-webster:http://www.merriam-webster.com/dictionary/slender A concave 3-D shape quality inhering in a bearer by virtue of the bearer's shape being inversely clavate. george 2010-07-08T01:47:09Z quality PATO:0002213 obclavate A concave 3-D shape quality inhering in a bearer by virtue of the bearer's shape being inversely clavate. PATOC:GVG A lobed quality inhering in a bearer by virtue of the bearer's being divided into or having two lobes. george 2010-07-08T01:54:08Z quality PATO:0002214 bilobed A lobed quality inhering in a bearer by virtue of the bearer's being divided into or having two lobes. thefreedictionary:http://www.thefreedictionary.com/bilobed A shape quality inhering in a bearer by virtue of the bearer's having the shape of a scythe or sickle. george 2010-07-08T01:57:46Z falcate hooked scythe-shaped sickle-shaped unciform uncinate quality PATO:0002215 falciform A shape quality inhering in a bearer by virtue of the bearer's having the shape of a scythe or sickle. merriam-webster:http://www.merriam-webster.com/dictionary/falciform A molecular quality that pertains to the post-translational modification of a protein by the covalent attachment of one or more ubiquitin monomer. george 2010-07-08T02:00:37Z quality Ubiquitylation PATO:0002216 ubiquinated A molecular quality that pertains to the post-translational modification of a protein by the covalent attachment of one or more ubiquitin monomer. neurolex:http://neurolex.org/ A molecular quality inhering in a bearer by virtue of the bearer's being combined, or impregnated, with nitric acid, or some of its compounds. george 2010-07-08T02:04:03Z quality PATO:0002217 nitrated A molecular quality inhering in a bearer by virtue of the bearer's being combined, or impregnated, with nitric acid, or some of its compounds. neurolex:http://neurolex.org/wiki/Category:Nitrated_Molecular_Quality A quality inhering in a bearer by virtue of the bearer's loss of myelin sheath. george 2010-07-08T02:08:06Z quality PATO:0002218 For example loss of myelin sheath from a normally myelinated axon or dendrite. demyelinated A quality inhering in a bearer by virtue of the bearer's loss of myelin sheath. thefreedictionary:http://www.thefreedictionary.com/demyelinated A quality inhering in a bearer that is shaped in the form of a fan. george 2010-07-09T01:43:42Z fan-like quality PATO:0002219 fan-shaped A quality inhering in a bearer that is shaped in the form of a fan. thefreedictionary:http://www.thefreedictionary.com/fan-shaped A quality inhering in a protein or a molecule by virtue of the bearer's having a phosphate (PO4) group. george 2010-07-09T01:50:14Z quality PATO:0002220 phosphorylated A quality inhering in a protein or a molecule by virtue of the bearer's having a phosphate (PO4) group. wikipedia:en.wikipedia.org/wiki/Phosphorylated A quality inhering in a bearer by virtue of the bearer's being phosphorylated to a more than normal extent, or fully saturated with phosphate groups. george 2010-07-09T01:51:52Z hyperphosphorylated quality PATO:0002221 increased phosphorylation A quality inhering in a bearer by virtue of the bearer's being phosphorylated to a more than normal extent, or fully saturated with phosphate groups. Wikipedia:http://en.wiktionary.org/wiki/hyperphosphorylated A quality inhering in a bearer by virtue of the bearer's being phosphorylated to a lesser than normal extent, or less than fully. george 2010-07-09T01:54:22Z hypophosporylated quality PATO:0002222 decreased phosphorylation A quality inhering in a bearer by virtue of the bearer's being phosphorylated to a lesser than normal extent, or less than fully. Wikipedia:http://en.wiktionary.org/wiki/hypophosphorylated A quality inhering in a bearer by virtue of the bearer's having reacted with oxygen, or been modified by oxidation (the reaction in which the atoms of an element lose electrons and the valence of the element increases). george 2010-07-09T01:59:35Z quality PATO:0002223 oxidized A quality inhering in a bearer by virtue of the bearer's having reacted with oxygen, or been modified by oxidation (the reaction in which the atoms of an element lose electrons and the valence of the element increases). Wikipedia:http://en.wiktionary.org/wiki/oxidized An angular shape quality inhering in a bearer by virtue of the bearer's having a single angle in its length giving the bearer the form of the letter V. george 2010-07-13T04:12:13Z quality PATO:0002224 V-shaped An angular shape quality inhering in a bearer by virtue of the bearer's having a single angle in its length giving the bearer the form of the letter V. PATOC:JE An angular shape quality inhering in a bearer by virtue of the bearer's having a single angle in its length giving the bearer the form of the letter L. george 2010-07-13T04:14:59Z quality PATO:0002225 L-shaped An angular shape quality inhering in a bearer by virtue of the bearer's having a single angle in its length giving the bearer the form of the letter L. PATOC:JE A cylindrical shape quality inhering in a bearer by virtue of the bearer's being imperfectly cylindrical or approximately cylindrical. george 2010-07-13T04:22:30Z quality PATO:0002226 subcylindrical A cylindrical shape quality inhering in a bearer by virtue of the bearer's being imperfectly cylindrical or approximately cylindrical. url:http://www.thefreedictionary.com/Subcylindrical A concave 3-D shape quality inhering in a bearer by virtue of the bearer's shape form resembling the shape of a cup. george 2010-07-13T04:29:32Z cup-like quality PATO:0002227 cup-shaped A concave 3-D shape quality inhering in a bearer by virtue of the bearer's shape form resembling the shape of a cup. url:http://www.thefreedictionary.com/cup-shaped A tapered shape quality inhering in a bearer by virtue of the bearer's tapering gradually to a sharp point. george 2010-07-15T09:03:18Z quality PATO:0002228 acuminate A tapered shape quality inhering in a bearer by virtue of the bearer's tapering gradually to a sharp point. url:http://www.thefreedictionary.com/acuminate A quadrangular shape quality inhering in a bearer by virtue of the bearer's being approximately rectangular. george 2010-07-19T12:18:57Z quality PATO:0002229 subrectangular A quadrangular shape quality inhering in a bearer by virtue of the bearer's being approximately rectangular. url:http://dictionary.reference.com/browse/subrectangular?qsrc=2446&o=100074 A triangular shape quality inhering in a bearer by virtue of the bearer's being nearly, but not perfectly, triangular. george 2010-07-19T12:20:59Z quality PATO:0002230 subtriangular A triangular shape quality inhering in a bearer by virtue of the bearer's being nearly, but not perfectly, triangular. url:http://www.thefreedictionary.com/Subtriangular A split shape quality inhering in a bearer by virtue of the bearer's having or being divided into many lobes or similar segments. george 2010-07-19T12:23:02Z quality PATO:0002231 multifid A split shape quality inhering in a bearer by virtue of the bearer's having or being divided into many lobes or similar segments. url:http://www.thefreedictionary.com/multifid A 2-D shape quality inhering in a bearer by virtue of the bearer's having shape or form of half a circle. george 2010-07-19T01:02:27Z half circle semicircle quality PATO:0002232 semicircular A 2-D shape quality inhering in a bearer by virtue of the bearer's having shape or form of half a circle. url:http://www.thefreedictionary.com/semicircle A spatial quality inhering in a bearer by virtue of the bearer's being located far (not close to) in space in relation to another entity. george 2010-07-19T02:43:53Z distant from remote from quality PATO:0002233 far from A spatial quality inhering in a bearer by virtue of the bearer's being located far (not close to) in space in relation to another entity. PATOC:PM A notched shape quality inhering in a bearer by virtue of the bearer's having a notched tip or edge. george 2010-07-19T04:25:58Z quality PATO:0002234 emarginate A notched shape quality inhering in a bearer by virtue of the bearer's having a notched tip or edge. url:http://www.thefreedictionary.com/emarginate A tapered shape quality inhering in a bearer by virtue of the bearer's being flat, slender, and tapering to a point. george 2010-07-19T04:29:05Z blade-shaped ensiform sword-like sword-shaped quality PATO:0002235 blade-like A tapered shape quality inhering in a bearer by virtue of the bearer's being flat, slender, and tapering to a point. PATOC:JE Shape quality inhering in a bearer by virtue of the bearer's being shaped like a wing. george 2010-07-23T02:19:14Z wing-shaped quality PATO:0002236 aliform Shape quality inhering in a bearer by virtue of the bearer's being shaped like a wing. url:http://www.thefreedictionary.com/aliform A curvature quality inhering in a bearer by virtue of the bearer's being curved backward or downward. george 2010-07-23T02:22:09Z quality PATO:0002237 retrorse A curvature quality inhering in a bearer by virtue of the bearer's being curved backward or downward. url:http://www.thefreedictionary.com/retrorse A curvature quality inhering in a bearer by virtue of the bearer's being curved forward or upward. george 2010-07-23T02:22:56Z quality PATO:0002238 antrorse A curvature quality inhering in a bearer by virtue of the bearer's being curved forward or upward. url:http://www.thefreedictionary.com/antrorse A concave 3-D shape that inheres in the bearer by virtue of the bearer's nearly) symmetric shape wide at its ends and narrow in the middle, resembling the figure of number 8. george 2010-07-23T02:25:24Z figure 8 shaped quality PATO:0002239 hourglass-shaped A concave 3-D shape that inheres in the bearer by virtue of the bearer's nearly) symmetric shape wide at its ends and narrow in the middle, resembling the figure of number 8. url:http://en.wikipedia.org/wiki/Hourglass-shaped A convex 3-D shape quality inhering in a bearer by virtue of the bearer's shape resembling falling drop. george 2010-07-23T02:31:11Z drop shaped quality PATO:0002240 teardrop-shaped A convex 3-D shape quality inhering in a bearer by virtue of the bearer's shape resembling falling drop. url:wordnetweb.princeton.edu/perl/webwn A lobed quality inhering in a bearer by virtue of the bearer's being divided into or having three lobes. george 2010-07-28T12:57:46Z quality PATO:0002241 trilobed A lobed quality inhering in a bearer by virtue of the bearer's being divided into or having three lobes. url:http://www.thefreedictionary.com/trilobed A physical quality inhering in a bearer by virtue of the bearer's rate of change of the position. george 2010-07-28T02:52:48Z quality PATO:0002242 velocity A physical quality inhering in a bearer by virtue of the bearer's rate of change of the position. url:http://en.wikipedia.org/wiki/Velocity A physical quality inhering in a fluid (liquid or gas) by virtue of the amount of fluid which passes through a given surface per unit time. george 2010-07-28T03:00:20Z volume flow rate volumetric flow rate quality PATO:0002243 fluid flow rate A physical quality inhering in a fluid (liquid or gas) by virtue of the amount of fluid which passes through a given surface per unit time. url:http://en.wikipedia.org/wiki/Volumetric_flow_rate A flow rate quality inhering in a substance by virtue of the mass of substance which passes through a given surface per unit time. george 2010-07-28T03:02:03Z quality PATO:0002244 mass flow rate A flow rate quality inhering in a substance by virtue of the mass of substance which passes through a given surface per unit time. url:http://en.wikipedia.org/wiki/Mass_flow_rate A force which relative high. george 2010-08-04T11:12:20Z increased force amplitude quality PATO:0002245 increased force A force which relative high. PATOC:GVG A force which is relative low. george 2010-08-04T11:13:13Z decreased force amplitude quality PATO:0002246 decreased force A force which is relative low. PATOC:GVG A quality inhering in a bearer by virtue of the bearer's having or lacking of substances produced by living organisms that have a color resulting from selective color absorption. george 2010-08-09T04:14:00Z quality PATO:0002247 degree of pigmentation A quality inhering in a bearer by virtue of the bearer's having or lacking of substances produced by living organisms that have a color resulting from selective color absorption. url:http://en.wikipedia.org/wiki/Biological_pigment A degree of pigmentation quality inhering in a bearer by virtue of the bearer's having substances produced by living organisms that have a color resulting from selective color absorption. george 2010-08-09T04:16:49Z quality PATO:0002248 pigmented A degree of pigmentation quality inhering in a bearer by virtue of the bearer's having substances produced by living organisms that have a color resulting from selective color absorption. PATOC:GVG A degree of pigmentation quality inhering in a bearer by virtue of the bearer's lacking substances produced by living organisms that have a color resulting from selective color absorption. george 2010-08-09T04:17:04Z depigmented quality PATO:0002249 unpigmented A degree of pigmentation quality inhering in a bearer by virtue of the bearer's lacking substances produced by living organisms that have a color resulting from selective color absorption. PATOC:GVG A degree of pigmentation quality that is relatively high. george 2010-08-09T04:17:19Z hyperpigmented quality PATO:0002250 increased pigmentation A degree of pigmentation quality that is relatively high. PATOC:GVG A degree of pigmentation quality that is relative low. george 2010-08-09T04:17:37Z hypopigmented quality PATO:0002251 decreased pigmentation A degree of pigmentation quality that is relative low. PATOC:GVG A quality inhering in a bearer by virtue of the bearer's being flattened along the antero-posterior axis. george 2010-08-16T03:57:42Z antero-posteriorly compressed quality PATO:0002252 antero-posteriorly flattened A quality inhering in a bearer by virtue of the bearer's being flattened along the antero-posterior axis. PATOC:JC A quality inhering in a bearer by virtue of the bearer's being roundish, flattish shape, possibly with a slightly angled edge. george 2010-08-16T03:57:48Z plate-like quality PATO:0002253 platelike A quality inhering in a bearer by virtue of the bearer's being roundish, flattish shape, possibly with a slightly angled edge. PATOC:CVC A quality inhering in a bearer by virtue of the bearer's surface becoming more extended in a plane. george 2010-08-16T03:59:34Z quality compressed PATO:0002254 Becoming flat but not necessarily completely flat. flattened A quality inhering in a bearer by virtue of the bearer's surface becoming more extended in a plane. PATOC:CVS Texture quality inhering in a bearer by virtue of the bearer's being marked with one or more channels. george 2010-09-01T10:27:48Z quality channeled creased PATO:0002255 grooved Texture quality inhering in a bearer by virtue of the bearer's being marked with one or more channels. PATOC:JE A cuscpidate quality inhering in a bearer by virtue of the bearer possessing three cusps. george 2010-09-08T02:21:50Z tricuspid quality PATO:0002256 tricuspidate A cuscpidate quality inhering in a bearer by virtue of the bearer possessing three cusps. PATOC:WD A cuscpidate quality inhering in a bearer by virtue of the bearer possessing more than one cusp. george 2010-09-08T02:23:22Z quality PATO:0002257 multicuspidate A cuscpidate quality inhering in a bearer by virtue of the bearer possessing more than one cusp. PATOC:WD A shape quality inhering in a bearer by virtue of the bearer's having a point. george 2010-09-08T03:15:16Z quality PATO:0002258 pointed A shape quality inhering in a bearer by virtue of the bearer's having a point. PATOC:http://www.merriam-webster.com/dictionary/pointed A spatial quality inhering in a bearer by virtue of the bearer's being located near in space in relation to another entity. george 2010-09-08T03:20:06Z PATO:0001771 approaches close to near to vicinity of quality PATO:0002259 adjacent to A spatial quality inhering in a bearer by virtue of the bearer's being located near in space in relation to another entity. PATOC:GVG A quality inhering in a bearer by virtue of the bearer's being partially upright in position or posture. george 2010-09-08T03:27:21Z semi upright quality PATO:0002260 semi erect A quality inhering in a bearer by virtue of the bearer's being partially upright in position or posture. PATOC:GVG A spatial quality inhering in a bearer by virtue of the bearer's location within another entity. george 2010-09-09T09:36:56Z quality PATO:0002261 located in A spatial quality inhering in a bearer by virtue of the bearer's location within another entity. PATOC:WD A quality inhering in a protein or a molecule by virtue of the addition of a phosphate (PO4) group to the bearer. george 2010-09-16T08:57:56Z quality PATO:0002262 phosphorylation A quality inhering in a protein or a molecule by virtue of the addition of a phosphate (PO4) group to the bearer. url:http://en.wikipedia.org/wiki/Phosphorylation A quality inhering in a protein or a molecule by virtue of the bearer's lacking a phosphate (PO4) group. george 2010-09-16T09:04:21Z quality PATO:0002263 dephosphorylated A quality inhering in a protein or a molecule by virtue of the bearer's lacking a phosphate (PO4) group. url:http://en.wikipedia.org/wiki/Dephosphorylation A structural quality inhering in a bearer by virtue of the bearer's being arranged in a systematic fashion. george 2010-09-16T10:22:52Z quality PATO:0002264 organization quality A structural quality inhering in a bearer by virtue of the bearer's being arranged in a systematic fashion. PATOC:GVG A behavioral quality of a process inhering in a bearer by virtue of the bearer's disposition to exhibit marked activity. george 2010-09-21T06:56:58Z quality PATO:0002265 behavioural activity A behavioral quality of a process inhering in a bearer by virtue of the bearer's disposition to exhibit marked activity. PATOC:GVG A shape that inheres in a 3 dimensional entity. george 2010-10-05T12:31:16Z quality PATO:0002266 3-D shape A shape that inheres in a 3 dimensional entity. PATOC:OREGON george 2010-10-05T12:34:31Z quality PATO:0002267 edge shape A positional quality inhering in a bearer by virtue of the bearer's being located in a position equidistant from edges. george 2010-10-05T01:09:32Z quality PATO:0002268 centered A positional quality inhering in a bearer by virtue of the bearer's being located in a position equidistant from edges. PATOC:OREGON A structural quality of the collection or massing of one physical object within another physical object. george 2010-10-26T01:57:02Z quality pooled PATO:0002269 accumulation A structural quality of the collection or massing of one physical object within another physical object. PATOC:CVC An increased number of physical objects that are accumulated within another physical object usually as a result of a failure to break down or remove objects in a timely manner. george 2010-10-26T02:00:20Z accumulated quality PATO:0002270 increased accumulation An increased number of physical objects that are accumulated within another physical object usually as a result of a failure to break down or remove objects in a timely manner. PATOC:GVG An accumulation which is relative low. george 2010-10-26T02:04:45Z quality PATO:0002271 decreased accumulation An accumulation which is relative low. PATOC:GVG A spatial quality inhering in a bearer by virtue of the bearer's being located at the same continuous distance relative to another object. george 2010-10-26T02:07:42Z quality PATO:0002272 parallel to A spatial quality inhering in a bearer by virtue of the bearer's being located at the same continuous distance relative to another object. PATOC:WD Multicolored quality inhering in a bearer by virtue of the bearer's being colored with a variegated pattern resembling marble,. george 2010-11-16T11:17:32Z quality PATO:0002273 marbled Multicolored quality inhering in a bearer by virtue of the bearer's being colored with a variegated pattern resembling marble,. url:http://www.oed.com/ Multicolored quality inhering in a bearer by virtue of the bearer's being dappled with spots, patches, or blotches of different colors. george 2010-11-16T11:22:57Z quality PATO:0002274 mottled Multicolored quality inhering in a bearer by virtue of the bearer's being dappled with spots, patches, or blotches of different colors. url:http://www.oed.com/ A color pattern quality inhering in a bearer by virtue of the bearer's color pattern in which light and dark colors (for example white and black) are codistributed to create a visual impression. george 2010-11-16T11:24:15Z quality PATO:0002275 high contrast color pattern A color pattern quality inhering in a bearer by virtue of the bearer's color pattern in which light and dark colors (for example white and black) are codistributed to create a visual impression. PATOC:WD A color pattern inhering in a bearer by virtue of bearer's exhibiting vertical bars of one hue or degree of saturation crossing another. george 2010-11-16T11:30:40Z quality PATO:0002276 barred A color pattern inhering in a bearer by virtue of bearer's exhibiting vertical bars of one hue or degree of saturation crossing another. PATOC:WD A quality of certain surfaces which appear to change colour as the angle of view changes. george 2010-12-12T12:37:41Z quality PATO:0002277 iridescent A quality of certain surfaces which appear to change colour as the angle of view changes. url:http://en.wikipedia.org/wiki/Iridescence A structural quality inhering in a bearer by virtue of the bearer's participating in a joint with another entity. george 2011-01-20T05:39:18Z quality PATO:0002278 articulated with A structural quality inhering in a bearer by virtue of the bearer's participating in a joint with another entity. PATOC:WD A structural quality inhering in a bearer by virtue of the bearer's being strongly articulated with another entity. george 2011-01-20T05:39:59Z quality PATO:0002279 tightly articulated with A structural quality inhering in a bearer by virtue of the bearer's being strongly articulated with another entity. PATOC:WD A structural quality inhering in a bearer by virtue of the bearer's possessing a broad surface in articulation with another entity. george 2011-01-20T05:40:29Z quality PATO:0002280 broadly articulated with A structural quality inhering in a bearer by virtue of the bearer's possessing a broad surface in articulation with another entity. PATOC:WD A cuscpidate quality inhering in a bearer by virtue of the bearer possessing two cusps. george 2011-02-07T03:13:18Z bicuspid quality PATO:0002281 biscupidate A cuscpidate quality inhering in a bearer by virtue of the bearer possessing two cusps. PATOC:GVG A mobility which is relative high. george 2011-03-09T09:16:03Z quality PATO:0002282 increased mobility A mobility which is relative high. PATO:GVG A mobility which is relative low. george 2011-03-09T09:16:47Z quality PATO:0002283 decreased mobility A mobility which is relative low. PATOC:GVG A physical quality that pertains by virtue of a pulling force that is directed away from the bearer and attempts to stretch or elongate the bearer. george 2011-03-10T08:41:21Z quality PATO:0002284 tension A physical quality that pertains by virtue of a pulling force that is directed away from the bearer and attempts to stretch or elongate the bearer. PATOC:GVG Branchiness quality inhering in a bearer by virtue of increasing the degree to which there are subdivisions or offshoots in a bearer entity. george 2011-03-10T09:07:57Z quality PATO:0002285 increased branchiness Branchiness quality inhering in a bearer by virtue of increasing the degree to which there are subdivisions or offshoots in a bearer entity. PATOC:CVS Branchiness quality inhering in a bearer by virtue of decreasing the degree to which there are subdivisions or offshoots in a bearer entity. george 2011-03-10T09:08:37Z quality PATO:0002286 decreased branchiness Branchiness quality inhering in a bearer by virtue of decreasing the degree to which there are subdivisions or offshoots in a bearer entity. PATOC:CVS An elasticity which is relatively high. George Gkoutos 2011-03-30T11:50:21Z quality PATO:0002287 increased elasticity An elasticity which is relatively high. PATOC:GVG An elasticity which is relatively low. George Gkoutos 2011-03-30T11:50:39Z quality PATO:0002288 decreased elasticity An elasticity which is relatively low. PATOC:GVG A hairy quality inhering in a bearer by virtue of the bearer's being covered with setae. George Gkoutos 2011-04-04T08:44:10Z quality PATO:0002289 Setose as a label is used extensively to describe insect phenotypes that have hairy-like appearances (i.e., they are covered in setae, not the hairs of mammals). A bristle is a type of seta. setose A hairy quality inhering in a bearer by virtue of the bearer's being covered with setae. ISBN:0913424137 George Gkoutos 2011-04-18T05:11:33Z quality PATO:0002290 aplastic/hypoplastic Absence of a tissue or organ due to failure to develop. George Gkoutos 2011-04-18T05:17:34Z quality PATO:0002291 agenesis Absence of a tissue or organ due to failure to develop. PATO:GVG A structural quality inhering in a bearer by virtue of the bearer's underlying structure being capable of change. George Gkoutos 2011-05-03T03:01:59Z transient structure quality PATO:0002292 For example, structures undergoing endochondral ossification change in composition from cartilaginous to ossified. transient A structural quality inhering in a bearer by virtue of the bearer's underlying structure being capable of change. PATOC:WD A structural quality inhering in a bearer by virtue of the bearer's underlying structure not changing over time. George Gkoutos 2011-05-03T03:03:50Z permanent structure quality PATO:0002293 permanent A structural quality inhering in a bearer by virtue of the bearer's underlying structure not changing over time. PATOC:WD A texture that is uniformly covered in short, oblong, or trench-like depressions. George Gkoutos 2011-05-03T03:12:47Z quality PATO:0002294 scrobiculate A texture that is uniformly covered in short, oblong, or trench-like depressions. Book:Book A surface feature shape inhering in a surface by virtue of the bearer's being divided by ridge-like structures into a number of small, irregular spaces. George Gkoutos 2011-05-17T07:57:45Z quality PATO:0002295 areolate A surface feature shape inhering in a surface by virtue of the bearer's being divided by ridge-like structures into a number of small, irregular spaces. Book:Book A texture quality inhering in a surface by virtue of the bearer's being marked by the presence of small, shallow, regular depressions called fovae. George Gkoutos 2011-05-17T07:59:30Z quality foveolate pitted PATO:0002296 foveate A texture quality inhering in a surface by virtue of the bearer's being marked by the presence of small, shallow, regular depressions called fovae. Book:Book A cellular motility which is lower relative to the normal or average. quality PATO:0002297 decreased cellular motility A cellular motility which is lower relative to the normal or average. PATOC:GVG A cellular motility which is higher relative to the normal or average. quality PATO:0002298 increased cellular motility A cellular motility which is higher relative to the normal or average. PATOC:GVG A cylindrical shape that is hollow. George Gkoutos 2011-06-08T06:33:50Z tube like tube-shaped tubulate quality PATO:0002299 tubular A cylindrical shape that is hollow. PATOC:GVG A quality that has a value that is increased compared to normal or average. George Gkoutos 2011-06-16T06:39:43Z quality PATO:0002300 increased quality A quality that has a value that is increased compared to normal or average. PATOC:GVG A quality that has a value that is decreased compared to normal or average. George Gkoutos 2011-06-16T06:40:15Z quality PATO:0002301 decreased quality A quality that has a value that is decreased compared to normal or average. PATOC:GVG A quality of a process that has a value that is decreased compared to normal or average. George Gkoutos 2011-06-16T06:50:59Z quality PATO:0002302 decreased process quality A quality of a process that has a value that is decreased compared to normal or average. PATOC:GVG A quality of an object that has a value that is decreased compared to normal or average. George Gkoutos 2011-06-16T06:51:54Z quality PATO:0002303 decreased object quality A quality of an object that has a value that is decreased compared to normal or average. PATOC:GVG A quality of a process that has a value that is increased compared to normal or average. George Gkoutos 2011-06-16T06:53:08Z quality PATO:0002304 increased process quality A quality of a process that has a value that is increased compared to normal or average. PATOC:GVG A quality of an object that has a value that is increased compared to normal or average. George Gkoutos 2011-06-16T06:54:01Z quality PATO:0002305 increased object quality A quality of an object that has a value that is increased compared to normal or average. PATOC:GVG A triangular quality inhering in a bearer by virtue of the bearer's having all sides of the same length. George Gkoutos 2011-06-27T11:22:50Z quality PATO:0002306 equilateral triangular A triangular quality inhering in a bearer by virtue of the bearer's having all sides of the same length. PATOC:JB A triangular quality inhering in a bearer by virtue of the bearer's having two sides have the same length. George Gkoutos 2011-06-27T11:23:52Z quality PATO:0002307 isosceles triangular A triangular quality inhering in a bearer by virtue of the bearer's having two sides have the same length. PATOC:JB A triangular quality inhering in a bearer by virtue of the bearer's having all sides of unequal length. George Gkoutos 2011-06-27T11:24:24Z quality PATO:0002308 scalene triangular A triangular quality inhering in a bearer by virtue of the bearer's having all sides of unequal length. PATOC:JB A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a by virtue of the bearer's exhibiting a consistently sized and approximately round cross-section along its length, which is many times larger than its diameter. George Gkoutos 2011-09-09T04:50:10Z quality PATO:0002309 Note that a fiber shaped object may take any circuitous or straight path through space (think of a length of string or rope). fiber shaped A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a by virtue of the bearer's exhibiting a consistently sized and approximately round cross-section along its length, which is many times larger than its diameter. PATOC:DC A quality inhering in a bearer by virtue of the bearer's being strong, thick or sturdy. George Gkoutos 2011-09-20T06:23:31Z quality PATO:0002310 robust A quality inhering in a bearer by virtue of the bearer's being strong, thick or sturdy. PATOC:BF Having a fringe or border of hairlike or fingerlike projections. George Gkoutos 2011-09-22T03:52:11Z quality PATO:0002311 fimbriated Having a fringe or border of hairlike or fingerlike projections. PATO:WS Consisting of segments or similar parts arranged in a longitudinal series. George Gkoutos 2011-10-03T03:42:23Z quality PATO:0002312 segmented Consisting of segments or similar parts arranged in a longitudinal series. OED: Having or resembling the shape of a telescope. George Gkoutos 2011-10-03T03:49:26Z quality PATO:0002313 telescopic Having or resembling the shape of a telescope. PATOC:BF Having the nature or characteristic of, a ligament; composed of the tissue proper to ligaments. George Gkoutos 2011-10-03T03:57:39Z quality PATO:0002314 ligamentous Having the nature or characteristic of, a ligament; composed of the tissue proper to ligaments. PATOC:BF A shape quality inhering in a bearer by virtue of the bearer's resembling the end of a brush with a multitude of bristles. George Gkoutos 2011-10-03T03:59:59Z quality PATO:0002315 brush-like shape A shape quality inhering in a bearer by virtue of the bearer's resembling the end of a brush with a multitude of bristles. PATOC:BF Being separate or discrete from other skeletal elements. George Gkoutos 2011-10-03T04:17:08Z quality free PATO:0002316 autogenous Being separate or discrete from other skeletal elements. PATOC:WD A convex quadrilateral is a parallelogram if and only if any one of the following statements are true: 1. Each diagonal divides the quadrilateral into two congruent triangles with the same orientation. 2. The opposite sides are congruent in pairs. 3. The diagonals bisect each other. 4. The opposite angles are congruent in pairs. 5. The sum of the squares of the sides equals the sum of the squares of the diagonals. (This is the parallelogram law) 6.It possesses rotational symmetry. 7.One pair of opposite sides are parallel and congruent. 8.Two pairs of adjacent angles are supplementary. George Gkoutos 2011-10-12T12:33:07Z quality PATO:0002317 parallelogram A convex quadrilateral is a parallelogram if and only if any one of the following statements are true: 1. Each diagonal divides the quadrilateral into two congruent triangles with the same orientation. 2. The opposite sides are congruent in pairs. 3. The diagonals bisect each other. 4. The opposite angles are congruent in pairs. 5. The sum of the squares of the sides equals the sum of the squares of the diagonals. (This is the parallelogram law) 6.It possesses rotational symmetry. 7.One pair of opposite sides are parallel and congruent. 8.Two pairs of adjacent angles are supplementary. wikipedia:Parallelogram A shape constituting a transition between a rectangle and a circle; a closed curve, of which the circle and ellipse are special cases, whose parametric equation is x = a.cos2/rt, y = b.cos2/rt George Gkoutos 2011-10-12T12:45:16Z Lamé curve quality PATO:0002318 superelliptic A shape constituting a transition between a rectangle and a circle; a closed curve, of which the circle and ellipse are special cases, whose parametric equation is x = a.cos2/rt, y = b.cos2/rt wiktionary:superellipse A shape with properties between those of a square and those of a circle. George Gkoutos 2011-10-12T12:47:48Z quality PATO:0002319 squircle A shape with properties between those of a square and those of a circle. wikipedia:Squircle A superelliptic shape inhering in a bearer by virtue of the bearer's shape resembling a diamond. George Gkoutos 2011-10-12T12:49:06Z quality PATO:0002320 diamond shaped A superelliptic shape inhering in a bearer by virtue of the bearer's shape resembling a diamond. PATO:WC George Gkoutos 2011-10-12T12:50:59Z quality PATO:0002321 hypoelliptic George Gkoutos 2011-10-12T12:51:19Z quality PATO:0002322 hyperelliptic A temporal distribution pattern of process occurrences within a regulation/reference process. George Gkoutos 2011-11-22T01:12:28Z quality PATO:0002323 temporal distribution quality A temporal distribution pattern of process occurrences within a regulation/reference process. PATOC:LC The temporal relation between the end of the process with respect to a reference process. George Gkoutos 2011-11-23T11:46:00Z quality completeness extent PATO:0002324 offset quality The temporal relation between the end of the process with respect to a reference process. PATOC:LC completeness GOC:CJM extent GOC:CJM The temporal relation between the start of the process with respect to a reference process. George Gkoutos 2011-11-23T11:47:34Z quality initiation PATO:0002325 onset quality The temporal relation between the start of the process with respect to a reference process. PATOC:LC An orientation inhering in a bearer by virtue of the bearer's placement at an angle. George Gkoutos 2011-11-23T12:06:09Z quality PATO:0002326 angle An orientation inhering in a bearer by virtue of the bearer's placement at an angle. PATOC:GVG An angle which is relatively high. George Gkoutos 2011-11-23T12:06:38Z quality PATO:0002327 increased angle to An angle which is relatively high. PATOC:GVG An angle which is relatively low. George Gkoutos 2011-11-23T12:06:54Z quality PATO:0002328 decreased angle to An angle which is relatively low. PATOC:GVG A shape quality inhering in a bearer by virtue of the bearer's exhibiting a upward bending of its leaves or other plant parts. gkoutos 2012-01-31T11:40:23Z quality PATO:0002329 hyponastic A shape quality inhering in a bearer by virtue of the bearer's exhibiting a upward bending of its leaves or other plant parts. PATOC:DS A quality inhering in a bearer by virtue of the bearer's being extended along a straight line, and is shaped like a reversed lance-point, with the tapering point attached to the leafstalk. gkoutos 2012-01-31T11:57:54Z quality PATO:0002330 oblanceolate A quality inhering in a bearer by virtue of the bearer's being extended along a straight line, and is shaped like a reversed lance-point, with the tapering point attached to the leafstalk. PATOC:PG A physical quality inhering in a bearer by virtue of the bearer exhibiting molecular attraction to another entity in contact. gkoutos 2012-01-31T12:28:16Z quality resinous PATO:0002331 adhesive A physical quality inhering in a bearer by virtue of the bearer exhibiting molecular attraction to another entity in contact. PATOC:GVG A physical quality inhering in a bearer by virtue of the bearer not exhibiting molecular attraction to another entity in contact. gkoutos 2012-01-31T12:28:57Z quality non-resinous PATO:0002332 non-adhesive A physical quality inhering in a bearer by virtue of the bearer not exhibiting molecular attraction to another entity in contact. PATOC:GVG A adhesivity which is relatively high. gkoutos 2012-01-31T12:32:43Z quality PATO:0002333 increased adhesivity A adhesivity which is relatively high. PATOC:GVG A adhesivity which is relatively low. gkoutos 2012-01-31T12:42:22Z quality PATO:0002334 decreased adhesivity A adhesivity which is relatively low. PATOC:GVG A shape quality inhering in a bearer by virtue of the bearer's being dome-shaped. gkoutos 2012-01-31T02:32:14Z quality PATO:0002335 tholiform A shape quality inhering in a bearer by virtue of the bearer's being dome-shaped. PATOC:dd A shape quality inhering in a bearer by virtue of the bearer's having triangular faces that meet at a common point and containing a polygonal shaped base. gkoutos 2012-01-31T02:35:02Z quality PATO:0002336 pyramidal A shape quality inhering in a bearer by virtue of the bearer's having triangular faces that meet at a common point and containing a polygonal shaped base. PATOC:DD A spheroid quality inhering in a bearer by virtue of the bearer's exhibiting a continuous convex surface with an axis of symmetry and one axis longer than the other; characterized with an egg-shaped form crossed with a lance-head shaped form. gkoutos 2012-01-31T02:43:15Z quality PATO:0002337 lance-ovate A spheroid quality inhering in a bearer by virtue of the bearer's exhibiting a continuous convex surface with an axis of symmetry and one axis longer than the other; characterized with an egg-shaped form crossed with a lance-head shaped form. PATOC:DD A shape quality inhering in a bearer by virtue of the bearer's being shaped like a lance-head, considerably longer than wide, tapering towards the tip from below the middle together forming three angles; attached at the broad end. gkoutos 2012-01-31T02:46:43Z quality PATO:0002338 lanceolate-triangular A shape quality inhering in a bearer by virtue of the bearer's being shaped like a lance-head, considerably longer than wide, tapering towards the tip from below the middle together forming three angles; attached at the broad end. PATOC:DD A quality of being covered with stiff or rough hairs. gkoutos 2012-01-31T02:51:37Z quality PATO:0002339 hispid A quality of being covered with stiff or rough hairs. PATOC:GVG A quality of being minutely hispid. gkoutos 2012-01-31T02:53:21Z quality PATO:0002340 hispidulous A quality of being minutely hispid. PATOC:DD A quality of being covered with short, dense, matted hairs. gkoutos 2012-01-31T02:55:56Z quality PATO:0002341 tomentose A quality of being covered with short, dense, matted hairs. thefreedictionary:www.thefreedictionary.com A quality inhering in a bearer by virtue of the bearer's being a cupule, with a structure similar to a cup that also encloses the ovule in partiality. gkoutos 2012-01-31T02:59:07Z quality PATO:0002342 cupulate A quality inhering in a bearer by virtue of the bearer's being a cupule, with a structure similar to a cup that also encloses the ovule in partiality. PATOC:DD A positional quality inhering in a bearer by virtue of the bearer's lying or growing on the ground but with erect or rising tips. gkoutos 2012-01-31T03:13:12Z quality PATO:0002343 decumbent A positional quality inhering in a bearer by virtue of the bearer's lying or growing on the ground but with erect or rising tips. thefreedictionary:www.thefreedictionary.com A quality inhering in a bearer by virtue of the bearer's being characterized by fine, entangled hairs giving the appearance of cobweb. gkoutos 2012-01-31T03:49:00Z quality PATO:0002344 arachnose A quality inhering in a bearer by virtue of the bearer's being characterized by fine, entangled hairs giving the appearance of cobweb. PATOC:DD A convex 3-D shape quality inhering in a bearer by virtue of the bearer's having a quadric surface in three dimensions obtained by rotating less than half of a circular arc about an axis passing through the endpoints of the arc gkoutos 2012-01-31T03:55:16Z quality PATO:0002345 lemon-shaped A convex 3-D shape quality inhering in a bearer by virtue of the bearer's having a quadric surface in three dimensions obtained by rotating less than half of a circular arc about an axis passing through the endpoints of the arc PATOC:MH A concave 3-D shape quality inhering in a bearer by virtue of the bearer's having two connected parts, roughly spherical, of different sizes. gkoutos 2012-01-31T03:58:10Z quality PATO:0002346 snowman-shaped A concave 3-D shape quality inhering in a bearer by virtue of the bearer's having two connected parts, roughly spherical, of different sizes. PATOC:MH A conical quality inhering in a bearer by virtue of the bearer's resembling a cone, with the pointed end attached to an organism. gkoutos 2012-01-31T04:05:28Z quality PATO:0002347 obconical A conical quality inhering in a bearer by virtue of the bearer's resembling a cone, with the pointed end attached to an organism. wiktionary:http://en.wiktionary.org/wiki/obconical A structural quality inhering in a bearer by virtue of the bearer resembling wood. gkoutos 2012-01-31T04:06:50Z quality PATO:0002348 ligneous A structural quality inhering in a bearer by virtue of the bearer resembling wood. merriam-webster:http://www.merriam-webster.com/dictionary/ligneous A spatial quality inhering in a bearer by virtue of the bearer's being located toward the base of an organism relative to another entity. gkoutos 2012-01-31T04:12:25Z quality PATO:0002349 basal to A spatial quality inhering in a bearer by virtue of the bearer's being located toward the base of an organism relative to another entity. merriam-webster:http://www.merriam-webster.com/dictionary/basal A spatial quality inhering in a bearer by virtue of the bearer's being located toward the stalk of an organism relative to another entity. gkoutos 2012-01-31T04:13:06Z quality PATO:0002350 cauline to A spatial quality inhering in a bearer by virtue of the bearer's being located toward the stalk of an organism relative to another entity. merriam-webster:http://www.merriam-webster.com/dictionary/cauline A structural quality inhering in a bearer by virtue of the bearer resembling or containing flesh. gkoutos 2012-01-31T04:15:30Z quality PATO:0002351 fleshy A structural quality inhering in a bearer by virtue of the bearer resembling or containing flesh. wiktionary:http://en.wiktionary.org/wiki/fleshy A quality inhering in a bearer by virtue of the bearer's upper parts die back to the rootstock at the end of the growing season. gkoutos 2012-01-31T04:29:36Z quality PATO:0002352 herbaceous A quality inhering in a bearer by virtue of the bearer's upper parts die back to the rootstock at the end of the growing season. PATOC:PG A quality that inheres in a bearer in virtue of its realizing one of its functions. gkoutos 2012-01-31T04:51:42Z quality PATO:0002353 activation quality A quality that inheres in a bearer in virtue of its realizing one of its functions. PATOC:RH A quality of an physical object that is currently realizing one of its functions. gkoutos 2012-01-31T04:52:04Z quality PATO:0002354 active A quality of an physical object that is currently realizing one of its functions. PATOC:RH A quality of a physical object that is currently realizing none of its functions. gkoutos 2012-01-31T04:52:14Z quality PATO:0002355 inactive A quality of a physical object that is currently realizing none of its functions. PATOC:RH A quality of a physical object that has been constantly realizing some of its functions. gkoutos 2012-01-31T04:52:24Z quality PATO:0002356 constitutively active A quality of a physical object that has been constantly realizing some of its functions. PATOC:RH A shape quality inhering in a bearer by virtue of the bearer's having a strait side and an arched side giving the bearer the form of the letter D. gkoutos 2012-02-21T11:46:51Z quality PATO:0002357 D-shaped A shape quality inhering in a bearer by virtue of the bearer's having a strait side and an arched side giving the bearer the form of the letter D. PATOC:AE An elongated raised margin or border. gkoutos 2012-02-21T12:27:39Z ridge-like quality PATO:0002358 ridged An elongated raised margin or border. PATOC:GVG A quality inhering in a bearer by virtue of the bearer's width being notably higher than its length. gkoutos 2012-03-13T06:04:00Z quality PATO:0002359 broad A quality inhering in a bearer by virtue of the bearer's width being notably higher than its length. PATOC:GVG A disposition that can be compared on a linear scale - that is that it can be increased or decreased. gkoutos 2012-03-16T06:31:50Z quality PATO:0002360 tendency A disposition that can be compared on a linear scale - that is that it can be increased or decreased. PATOC:RH A tendency which is relatively high. gkoutos 2012-03-16T06:31:57Z quality PATO:0002361 increased tendency A tendency which is relatively high. PATOC:GVG A tendency which is relatively low. gkoutos 2012-03-16T06:32:57Z quality PATO:0002362 decreased tendency A tendency which is relatively low. PATOC:GVG A medium brown color with a metallic sheen, resembles the actual alloy bronze. gkoutos 2012-05-03T11:08:18Z quality PATO:0002363 bronze A medium brown color with a metallic sheen, resembles the actual alloy bronze. PATO:LC A quality inhering in a bearer by virtue of the bearer's length being notably lower than its width. gkoutos 2012-04-18T06:31:29Z quality PATO:0002364 shortened A quality inhering in a bearer by virtue of the bearer's length being notably lower than its width. PATOC:GVG Female quality of having complete, unaltered reproductive organs gkoutos 2012-05-03T11:18:41Z quality PATO:0002365 intact female Female quality of having complete, unaltered reproductive organs PATOC:MF Male quality of having complete, unaltered reproductive organs. gkoutos 2012-05-03T11:19:06Z quality PATO:0002366 intact male Male quality of having complete, unaltered reproductive organs. PATOC:MF Male quality of being incapable to reproduce because of functional loss of the testicles from surgical removal or chemical means. gkoutos 2012-05-03T11:22:29Z quality PATO:0002367 castrated male Male quality of being incapable to reproduce because of functional loss of the testicles from surgical removal or chemical means. PATOC:MF A viviparous organism having never given birth. gkoutos 2012-05-03T11:25:25Z quality PATO:0002368 nulliparous A viviparous organism having never given birth. PATOC:mf A viviparous organism that has given birth two or more times. gkoutos 2012-05-03T11:26:34Z quality PATO:0002369 multiparous A viviparous organism that has given birth two or more times. wiki:http://en.wikipedia.org/wiki/Parity_(biology) The number of time that a viviparous organism has given birth. gkoutos 2012-05-03T11:27:56Z quality PATO:0002370 parity The number of time that a viviparous organism has given birth. wiki:http://en.wikipedia.org/wiki/Parity_(biology) A viviparous organism having given birth one time. gkoutos 2012-05-03T11:29:38Z quality PATO:0002371 primiparous A viviparous organism having given birth one time. wiki:http://en.wikipedia.org/wiki/Parity_(biology) A viviparous organism that has given birth five or more times. gkoutos 2012-05-03T11:30:28Z quality PATO:0002372 grand multiparous A viviparous organism that has given birth five or more times. wiki:http://en.wikipedia.org/wiki/Parity_(biology) A positional quality inhering in a bearer by virtue of the bearer's location of features or characteristics along the mediolateral axis. gkoutos 2012-07-05T01:49:04Z quality PATO:0002373 mediolateral polarity A positional quality inhering in a bearer by virtue of the bearer's location of features or characteristics along the mediolateral axis. PATOC:DS Recurrent and often more or less cyclic alteration. gkoutos 2012-07-05T01:52:36Z quality PATO:0002374 fluctuating Recurrent and often more or less cyclic alteration. PATOC:DS A concave 3-D shape quality inhering in a bearer by virtue of the bearer's shape form resembling the shape of a trumpet. gkoutos 2012-07-05T02:45:17Z quality PATO:0002375 trumpet-shaped A concave 3-D shape quality inhering in a bearer by virtue of the bearer's shape form resembling the shape of a trumpet. PATOC:DS A structure quality inhering in a bearer by virtue of the bearer's being filled with air. gkoutos 2012-07-05T02:55:10Z air-filled quality PATO:0002376 inflated A structure quality inhering in a bearer by virtue of the bearer's being filled with air. PATOC:CVS A structure quality inhering in a bearer by virtue of the bearer's being not filed with air. gkoutos 2012-07-05T02:56:07Z quality PATO:0002377 uninflated A structure quality inhering in a bearer by virtue of the bearer's being not filed with air. PATOC:CVS Having a shape that resembles a many-lobed "berry," such as a raspberry. gkoutos 2012-07-05T02:58:05Z quality PATO:0002378 acinus Having a shape that resembles a many-lobed "berry," such as a raspberry. wikipedia:https://en.wikipedia.org/wiki/Acinus A female fertility quality inhering in a female by virtue of the bearer's not being capable of reproducing because of surgical removal of ovaries and uterus. gkoutos 2012-07-05T03:04:28Z quality PATO:0002379 ovariohysterectomized female A female fertility quality inhering in a female by virtue of the bearer's not being capable of reproducing because of surgical removal of ovaries and uterus. PATOC:MF A female fertility quality inhering in a female by virtue of the bearer's not being capable of reproducing because of surgical removal of ovaries. gkoutos 2012-07-05T03:06:12Z quality PATO:0002380 ovariectomized female A female fertility quality inhering in a female by virtue of the bearer's not being capable of reproducing because of surgical removal of ovaries. PATOC:MF A composition quality inhering in an bearer by virtue of the presence of long chain aliphatic lipids on the surface of an organism. gkoutos 2012-07-05T03:17:00Z quality PATO:0002381 waxiness A composition quality inhering in an bearer by virtue of the presence of long chain aliphatic lipids on the surface of an organism. PATOC:lm A waxiness which is relatively high. gkoutos 2012-07-05T03:18:03Z quality PATO:0002382 increased waxiness A waxiness which is relatively high. PATOC:GVG A waxiness which is relatively low. gkoutos 2012-07-05T03:18:14Z quality PATO:0002383 decreased waxiness Presence of long chain aliphatic lipids on the surface of an organism. gkoutos 2012-07-05T03:18:21Z quality PATO:0002384 waxy Presence of long chain aliphatic lipids on the surface of an organism. PATOC:lm A shape quality inhering in a bearer by virtue of the bearer's being marked by narrow lines, usually parallel, with at least one salient angle on the margin gkoutos 2012-07-05T05:17:07Z quality PATO:0002385 striate-angular A shape quality inhering in a bearer by virtue of the bearer's being marked by narrow lines, usually parallel, with at least one salient angle on the margin FNA:FNA A concave 3-D shape that inheres in the bearer by virtue of the bearer's shape that is wider at one end and narrow in the middle. gkoutos 2012-07-23T03:13:41Z anvil shaped quality PATO:0002386 anvil A concave 3-D shape that inheres in the bearer by virtue of the bearer's shape that is wider at one end and narrow in the middle. PATOC:AD Extremely acute and aggressive onset of a pathological process. gkoutos 2012-09-15T02:57:46Z per-acute quality PATO:0002387 peracute Extremely acute and aggressive onset of a pathological process. PATOC:PNS Being supported by a peduncle or stalk. gkoutos 2012-10-12T01:10:41Z quality PATO:0002388 pedunculate Being supported by a peduncle or stalk. PATOC:GV Growing horizontal to the ground without setting roots. gkoutos 2012-10-12T01:33:50Z quality PATO:0002389 procumbent Growing horizontal to the ground without setting roots. PATO:PG A length quality which is equal to the length of any straight line segment that passes from the center of a circle to any endpoint on the circular boundary. The radius is half of the diameter. gkoutos 2012-11-15T05:17:15Z quality PATO:0002390 radius A length quality which is equal to the length of any straight line segment that passes from the center of a circle to any endpoint on the circular boundary. The radius is half of the diameter. PATO:DS A shape quality inhering in a bearer by virtue of the bearer's having three rays or radiating branches. gkoutos 2012-11-15T05:19:32Z quality PATO:0002391 triradiate A shape quality inhering in a bearer by virtue of the bearer's having three rays or radiating branches. merriam-webster:merriam-webster A spatial quality inhering in a bearer by virtue of the bearer's being located on a sloping line joining two nonconsecutive points of an entity relative to another entity. gkoutos 2012-11-15T05:21:51Z quality PATO:0002392 diagonal to A spatial quality inhering in a bearer by virtue of the bearer's being located on a sloping line joining two nonconsecutive points of an entity relative to another entity. PATOC:GVG A tolerance quality inhering in a bearer by virtue of the bearer's increased ability to endure a stimulus. gkoutos 2012-11-15T05:32:07Z quality PATO:0002393 increased tolerance to A tolerance quality inhering in a bearer by virtue of the bearer's increased ability to endure a stimulus. PATOC:LC A tolerance quality inhering in a bearer by virtue of the bearer's decreased ability to endure a stimulus. gkoutos 2012-11-15T05:33:05Z quality PATO:0002394 decreased tolerance to A tolerance quality inhering in a bearer by virtue of the bearer's decreased ability to endure a stimulus. PATOC:LC A positional quality inhering in a bearer by virtue of the bearer's being positioned away from the axis of an organism. gkoutos 2012-11-20T04:13:32Z quality PATO:0002395 mislocalized abaxially A positional quality inhering in a bearer by virtue of the bearer's being positioned away from the axis of an organism. PATOC:EH A positional quality inhering in a bearer by virtue of the bearer's being positioned towards the axis of an organism. gkoutos 2012-11-20T04:15:12Z quality PATO:0002396 mislocalized adaxially A positional quality inhering in a bearer by virtue of the bearer's being positioned towards the axis of an organism. PATOC:EH A circular shape quality inhering in a bearer by virtue of the bearer's being nearly, but not perfectly, circular. gkoutos 2012-12-07T05:32:18Z quality round rounded PATO:0002397 subcircular A circular shape quality inhering in a bearer by virtue of the bearer's being nearly, but not perfectly, circular. PATOC:AD gkoutos 2012-12-07T05:34:16Z quality PATO:0002398 obsolete <new term> true A rotation quality inhering in a bearer by virtue of being rotated towards the front and the middle of an organism. gkoutos 2012-12-07T05:41:01Z quality PATO:0002399 anteromedially rotated A rotation quality inhering in a bearer by virtue of being rotated towards the front and the middle of an organism. PATOC:JI Having a spindle-like shape that is wide in the middle and tapers at both ends. gkoutos 2012-12-07T05:43:25Z quality PATO:0002400 fusiform Having a spindle-like shape that is wide in the middle and tapers at both ends. wikipedia:wikipedia characterised by an unidentifiable pattern. gkoutos 2012-12-17T10:37:55Z quality PATO:0002401 random pattern characterised by an unidentifiable pattern. PATOC:MPATH Multiple lesions some interconnecting with each other. gkoutos 2012-12-17T10:40:18Z quality PATO:0002402 multifocal to coalescing Multiple lesions some interconnecting with each other. PATOC:MPATH Affecting all regions without specificity of distribution. gkoutos 2012-12-17T10:41:37Z generalised quality PATO:0002403 generalized Affecting all regions without specificity of distribution. PATOC:MPTH Affecting a segment or segments. gkoutos 2012-12-17T10:43:13Z quality PATO:0002404 segmental Affecting a segment or segments. PATOC:MPATH A structural quality inhering in a bearer by virtue of the bearer's disposition to be reduced to smaller pieces with little effort. gkoutos 2012-12-17T10:47:16Z quality PATO:0002405 friability A structural quality inhering in a bearer by virtue of the bearer's disposition to be reduced to smaller pieces with little effort. Wikipedia:https://en.wikipedia.org/wiki/Friability Easily reduced to powder or easily fragmentable or crumbly. gkoutos 2012-12-17T10:48:30Z quality PATO:0002406 friable Easily reduced to powder or easily fragmentable or crumbly. PATOC:MPATH Having become firm or hard especially by increase of fibrous elements. gkoutos 2012-12-17T10:49:11Z quality PATO:0002407 indurated Having become firm or hard especially by increase of fibrous elements. mw:http://www.merriam-webster.com/dictionary/indurated Having the consistency of water. gkoutos 2012-12-17T10:51:32Z quality PATO:0002408 watery Having the consistency of water. PATOC:MPATH Bounded structure filled with fluid. gkoutos 2012-12-17T10:53:18Z quality PATO:0002409 fluid-filled Bounded structure filled with fluid. PATOC:MPATH A colour that is very pale yellowish brown. gkoutos 2012-12-17T10:54:55Z quality PATO:0002410 beige A colour that is very pale yellowish brown. PATOC:MPATH A color consisting of yellow and brown hue. gkoutos 2012-12-17T10:55:51Z quality PATO:0002411 yellow brown A color consisting of yellow and brown hue. PATOC:GVG A color consisting of yellow and brown hue and low brightness. gkoutos 2012-12-17T10:56:22Z quality PATO:0002412 dark yellow brown A color consisting of yellow and brown hue and low brightness. PATOC:GVG A color consisting of yellow and brown hue and high brightness. gkoutos 2012-12-17T10:57:27Z quality PATO:0002413 light yellow brown A color consisting of yellow and brown hue and high brightness. PATOC:GVG A quality of duration having progressive course of indefinite duration with active, acute-like elements. gkoutos 2012-12-17T10:59:58Z quality PATO:0002414 chronic-active A quality of duration having progressive course of indefinite duration with active, acute-like elements. PATOC:MPATH Single lesion with expansion into surrounding tissue. gkoutos 2012-12-17T11:01:31Z quality PATO:0002415 focally extensive Single lesion with expansion into surrounding tissue. PATOC:MPATH Flattened from above downward; below the normal level or the level of the surrounding parts. gkoutos 2012-12-17T12:06:55Z quality PATO:0002416 sunken Flattened from above downward; below the normal level or the level of the surrounding parts. PATOC:MPATH Extending through or affecting the entire thickness of the wall of an organ or cavity or boundary. gkoutos 2012-12-17T02:16:18Z quality PATO:0002417 transmural Extending through or affecting the entire thickness of the wall of an organ or cavity or boundary. PATOC:MPATH An affinity inhering in a tissue constituent by virtue of the bearer exhibiting a molecular interaction for acidic dyes under specific pH conditions. gkoutos 2012-12-17T03:01:19Z quality PATO:0002418 acidophilic An affinity inhering in a tissue constituent by virtue of the bearer exhibiting a molecular interaction for acidic dyes under specific pH conditions. PATOC:GVG An affinity inhering in a tissue constituent by virtue of the bearer exhibiting a molecular interaction for eosin dye. gkoutos 2012-12-17T03:02:09Z quality PATO:0002419 eosinophilic An affinity inhering in a tissue constituent by virtue of the bearer exhibiting a molecular interaction for eosin dye. PATOC:GVG Having both hydrophilic and hydrophobic (or lipophilic) groups. gkoutos 2012-12-17T03:04:39Z quality PATO:0002420 amphiphilic Having both hydrophilic and hydrophobic (or lipophilic) groups. wikipedia:http://en.wiktionary.org/wiki/amphiphilic Having or resembling the characteristic of a cicatrix - a scar resulting from formation and contraction of fibrous tissue. gkoutos 2012-12-17T03:08:09Z quality PATO:0002421 cicatricial Having or resembling the characteristic of a cicatrix - a scar resulting from formation and contraction of fibrous tissue. mw:http://www.merriam-webster.com/dictionary/cicatricial Pertaining to the individual parts making up an aggregate fruit like a many-lobed "berry," such as a raspberry. gkoutos 2012-12-17T03:11:10Z quality PATO:0002422 Acinus is Latin for berry. acinar Pertaining to the individual parts making up an aggregate fruit like a many-lobed "berry," such as a raspberry. wikipedia:https://en.wikipedia.org/wiki/Acinus A round or lobulated protruding form resembling a nipple. gkoutos 2012-12-17T03:13:44Z quality PATO:0002423 papillomatous A round or lobulated protruding form resembling a nipple. PATOC:MPATH A positional quality inhering in a bearer by virtue of the bearer's having two or more entities that extend from a common point in different directions. gkoutos 2012-12-20T11:43:47Z quality PATO:0002424 divergent from A positional quality inhering in a bearer by virtue of the bearer's having two or more entities that extend from a common point in different directions. PATOC:AD Open to view or not covered by another entity. gkoutos 2012-12-20T11:47:16Z quality PATO:0002425 exposed Open to view or not covered by another entity. PATOC:WD A shape quality inhering in a bearer by virtue of the bearer's being shaped like a boat. gkoutos 2013-01-29T09:12:03Z quality PATO:0002426 scaphoid A shape quality inhering in a bearer by virtue of the bearer's being shaped like a boat. wordnetweb:wordnetweb A surface feature shape having numerous very small circular rounded projections or protuberances. gkoutos 2013-01-29T09:15:53Z quality PATO:0002427 knobbled A surface feature shape having numerous very small circular rounded projections or protuberances. thefreedictionary.com:thefreedictionary.com A 3-D shape with three supports or legs. gkoutos 2013-01-29T09:18:44Z quality PATO:0002428 tripodal A 3-D shape with three supports or legs. PATOC:WC A shape quality inhering in a bearer by virtue of the bearer's being shaped in the form of the letter X. gkoutos 2013-01-29T09:19:53Z quality PATO:0002429 x-shaped A shape quality inhering in a bearer by virtue of the bearer's being shaped in the form of the letter X. PATOC:WC A shape quality in which the bearer is shaped like a narrow band; ligulate. gkoutos 2013-01-29T09:21:17Z quality PATO:0002430 strap-shaped A shape quality in which the bearer is shaped like a narrow band; ligulate. thefreedictionary:thefreedictionary A shape quality in which the bearer possesses a gradual, yet distinct, thinning from a wide starting point. gkoutos 2013-01-29T09:24:46Z quality PATO:0002431 waisted A shape quality in which the bearer possesses a gradual, yet distinct, thinning from a wide starting point. PATOC:WC A shape that is in the form of a spade. gkoutos 2013-01-29T09:26:49Z quality PATO:0002432 spade-shaped A shape that is in the form of a spade. PATOC:WC A surface feature shape marked by large amounts of relief, often with multiple ridges and grooves in close association. Topographically complex. gkoutos 2013-01-29T09:27:55Z quality PATO:0002433 sculpted surface A surface feature shape marked by large amounts of relief, often with multiple ridges and grooves in close association. Topographically complex. PATOC:AD A spatial quality inhering in a bearer by virtue of the bearer's being located at a right angle relative to another entity. gkoutos 2013-01-29T09:29:55Z quality PATO:0002434 perpendicular to A spatial quality inhering in a bearer by virtue of the bearer's being located at a right angle relative to another entity. PATOC:WC A positional quality inhering in a bearer by virtue of the bearer touching another entity along a border or with a projecting part. gkoutos 2013-01-29T09:31:12Z abut quality PATO:0002435 abutting A positional quality inhering in a bearer by virtue of the bearer touching another entity along a border or with a projecting part. merriam-webster:merriam-webster A positional quality inhering in a bearer by virtue of the bearer's position being displaced from a reference point. gkoutos 2013-01-29T09:32:22Z quality PATO:0002436 offset A positional quality inhering in a bearer by virtue of the bearer's position being displaced from a reference point. PATOC:AD A structural quality inhering in a bearer by virtue of the bearer's being locked together or interconnected to another entity. gkoutos 2013-01-29T09:37:13Z quality PATO:0002437 interlocked with A structural quality inhering in a bearer by virtue of the bearer's being locked together or interconnected to another entity. merriam-webster:merriam-webster A structural quality inhering in a bearer by virtue of the bearer's being located or placed beneath the skin. gkoutos 2013-01-29T09:41:50Z subcutaneous quality PATO:0002438 subdermal A structural quality inhering in a bearer by virtue of the bearer's being located or placed beneath the skin. thefreedictionary:thefreedictionary An angular shape quality inhering in a bearer by virtue of the bearer's having two angles in its length giving the bearer the form of the letter W. gkoutos 2013-01-29T09:45:54Z quality PATO:0002439 w-shaped An angular shape quality inhering in a bearer by virtue of the bearer's having two angles in its length giving the bearer the form of the letter W. PATOC:WC A surface feature shape quality inhering in a bearer by virtue of the degree of the bearer's highly topographical with ridges, pits, rugosity or other surface structures. gkoutos 2013-01-29T10:57:42Z quality PATO:0002440 ornamentation A surface feature shape quality inhering in a bearer by virtue of the degree of the bearer's highly topographical with ridges, pits, rugosity or other surface structures. PATOC:GVG A surface feature shape in which the bearer's surface is highly topographical with ridges, pits, rugosity or other surface structures. gkoutos 2013-01-29T10:59:42Z quality PATO:0002441 ornamented A surface feature shape in which the bearer's surface is highly topographical with ridges, pits, rugosity or other surface structures. PATOC:AD A surface feature shape in which the bearer's surface is lacking ridges, pits, rugosity or other surface structures. gkoutos 2013-01-29T11:00:20Z quality PATO:0002442 unornamented A surface feature shape in which the bearer's surface is lacking ridges, pits, rugosity or other surface structures. PATOC:AD A positional quality inhering in a bearer by virtue of the bearer's being located at the same level as another entity. gkoutos 2013-01-29T11:01:46Z quality PATO:0002443 level with A positional quality inhering in a bearer by virtue of the bearer's being located at the same level as another entity. PATOC:NI A composition quality inhering in a bearer by virtue of the bearer's being composed of or possessing inorganic material. gkoutos 2013-01-29T11:03:49Z quality PATO:0002444 mineralized A composition quality inhering in a bearer by virtue of the bearer's being composed of or possessing inorganic material. PATOC:WC A shape quality inhering in a bearer by virtue of the bearer's being twisted or turned. gkoutos 2013-01-29T11:05:26Z twisted quality PATO:0002445 The word "torsion" has multiple different meanings in different context (e.g. the act of twisting or the morphology of the digestive tract in gastropods). This term refers purely to the resulting shape and is not to be used in the engineering and mechanics sense of torsion. Note: kinked PATO:0001798(synonym twisted) is similar to 'torsioned', but it is different in that something that is kinked has sharp twists or turns. torsioned A shape quality inhering in a bearer by virtue of the bearer's being twisted or turned. freedictionary:freedictionary A shape quality inhering in a bearer by virtue of the bearer's having a shape resembling an anchor. gkoutos 2013-01-29T11:07:17Z quality PATO:0002446 anchor-shaped A shape quality inhering in a bearer by virtue of the bearer's having a shape resembling an anchor. PATOC:WC A shape quality inhering in a bearer by virtue of the bearer being divided into four parts. gkoutos 2013-01-29T11:08:28Z quality PATO:0002447 quadripartite A shape quality inhering in a bearer by virtue of the bearer being divided into four parts. PATOC:WC A quality inhering in a bearer by virtue of the bearer's being aligned or positioned towards another entity. gkoutos 2013-02-16T02:57:06Z quality PATO:0002448 oriented towards A quality inhering in a bearer by virtue of the bearer's being aligned or positioned towards another entity. PATOC:WD A spatial quality inhering in a bearer by virtue of the bearer's being located toward the rear and mid-line surface of an organism relative to another entity. gkoutos 2013-02-16T03:00:46Z quality PATO:0002449 posteromedial to A spatial quality inhering in a bearer by virtue of the bearer's being located toward the rear and mid-line surface of an organism relative to another entity. PATOC:WC A hardness quality of giving significant resistance to pressure. gkoutos 2013-02-26T02:02:38Z quality PATO:0002450 firm A hardness quality of giving significant resistance to pressure. PATOC:CM A quality inhering in a bearer by virtue of the bearer's exhibiting a phenotypic difference between males and females of the same species. gkoutos 2013-03-11T09:22:04Z quality PATO:0002451 sexually dimorphic A quality inhering in a bearer by virtue of the bearer's exhibiting a phenotypic difference between males and females of the same species. PATOC:WC A structural quality inhering in a bearer by virtue of the bearer being thinner or more loosely packed. gkoutos 2013-04-08T08:43:31Z quality PATO:0002452 decondensed A structural quality inhering in a bearer by virtue of the bearer being thinner or more loosely packed. PATOC:JL A structural quality inhering in a bearer by virtue of the bearer bring gradually worn away. gkoutos 2013-04-08T08:45:08Z quality PATO:0002453 eroding A structural quality inhering in a bearer by virtue of the bearer bring gradually worn away. PATOC:JL A quality inhering in a bearer by virtue of the bearer's similarity to the appearance of a carpel. gkoutos 2013-04-09T06:00:28Z quality PATO:0002454 carpel-like A quality inhering in a bearer by virtue of the bearer's similarity to the appearance of a carpel. PATO:JL A quality inhering in a bearer by virtue of the bearer's architecture bearing resemblence to a corymb type of inflorescence. gkoutos 2013-04-09T06:01:02Z quality PATO:0002455 corymb-like A quality inhering in a bearer by virtue of the bearer's architecture bearing resemblence to a corymb type of inflorescence. PATOC:JL A quality inhering in a bearer by virtue of the bearer's similarity to the appearance of an inflorescence. gkoutos 2013-04-09T06:02:05Z quality PATO:0002456 inflorescence-like A quality inhering in a bearer by virtue of the bearer's similarity to the appearance of an inflorescence. PATOC:JL A structural quality inhering in a bearer by virtue of the bearer's similarity to the appearance of a leaf. gkoutos 2013-04-09T06:02:58Z quality PATO:0002457 leaf-like A structural quality inhering in a bearer by virtue of the bearer's similarity to the appearance of a leaf. PATOC:JL A quality inhering in a bearer by virtue of the bearer being thin and lacking outgrowths. gkoutos 2013-04-09T06:03:56Z quality PATO:0002458 pin-like A quality inhering in a bearer by virtue of the bearer being thin and lacking outgrowths. PATOC:JL A structural quality inhering in a bearer by virtue of the bearer's similarity to the appearance of a sepal, gkoutos 2013-04-09T06:04:36Z quality PATO:0002459 sepal-like A structural quality inhering in a bearer by virtue of the bearer's similarity to the appearance of a sepal, PATOC:JL A structural quality inhering in a bearer by virtue of the bearer being smaller and contracted, especially due to loss of moisture. gkoutos 2013-04-09T06:05:18Z quality PATO:0002460 shriveled A structural quality inhering in a bearer by virtue of the bearer being smaller and contracted, especially due to loss of moisture. PATOC:JL To bend or hang downwards due to loss of water gkoutos 2013-04-09T06:06:14Z quality PATO:0002461 wilty A composition quality inhering in an bearer by virtue of the bearer's consisting of collagen. gkoutos 2013-09-15T11:34:15Z quality PATO:0002462 collagenous A composition quality inhering in an bearer by virtue of the bearer's consisting of collagen. PATOC:WD A positional quality inhering in a bearer by virtue of some aspect of the bearer extending to the position of another entity. gkoutos 2013-09-15T11:41:00Z quality PATO:0002463 extends to A positional quality inhering in a bearer by virtue of some aspect of the bearer extending to the position of another entity. PATOC:WD A positional quality inhering in a bearer by virtue of some aspect of the bearer extending past the position of another entity. gkoutos 2013-09-15T11:42:15Z quality PATO:0002464 extends beyond A positional quality inhering in a bearer by virtue of some aspect of the bearer extending past the position of another entity. PATOC:WD A quality inhering in a bearer by virtue of the bearer's resembling a prism. gkoutos 2013-09-15T11:44:03Z quality tent shaped PATO:0002465 prism shaped A shape quality inhering in a bearer by virtue of the bearer resembling a keyhole. gkoutos 2013-09-15T11:45:53Z quality PATO:0002466 keyhole shaped A shape quality inhering in a bearer by virtue of the bearer resembling a keyhole. PATOC:WD A shape quality inhering in a bearer by virtue of the bearer resembling a thin narrow strip. gkoutos 2013-09-15T11:47:11Z quality PATO:0002467 lathlike A shape quality inhering in a bearer by virtue of the bearer resembling a thin narrow strip. PATOC:WD A structure quality inhering in a bearer by virtue of the bearer's being capable of swelling or stretching. gkoutos 2013-09-15T11:48:26Z quality PATO:0002468 distensible A structure quality inhering in a bearer by virtue of the bearer's being capable of swelling or stretching. PATOC:WD Structural quality inhering in a bearer in which a joint has apposed bony surfaces united by fibrous tissue, permitting no movement; found only between bones. gkoutos 2013-09-15T11:55:50Z quality PATO:0002469 sutured to Structural quality inhering in a bearer in which a joint has apposed bony surfaces united by fibrous tissue, permitting no movement; found only between bones. PATOC:WD A morphological quality between two bearers inhering that one bearer is subject to change the nature, function, or condition of itself to become the other. gkoutos 2013-09-15T12:01:57Z quality PATO:0002470 transformed to A morphological quality between two bearers inhering that one bearer is subject to change the nature, function, or condition of itself to become the other. PATOC:LC A physical quality inhering in a bearer by virtue of the bearer's increased rate of change of the position. gkoutos 2013-09-15T12:03:45Z quality PATO:0002471 increased velocity A physical quality inhering in a bearer by virtue of the bearer's increased rate of change of the position. PATOC:NV A physical quality inhering in a bearer by virtue of the bearer's decreased rate of change of the position. gkoutos 2013-09-15T12:05:06Z quality PATO:0002472 decreased velocity A physical quality inhering in a bearer by virtue of the bearer's decreased rate of change of the position. PATOC:NV A disposition inhering in a tumour by virtue of the bearer's disposition to spontaneously arise. gkoutos 2013-09-15T12:07:08Z quality PATO:0002473 neoplastic, spontaneous A disposition inhering in a tumour by virtue of the bearer's disposition to spontaneously arise. PATOC:NV A flavor quality inhering in a bearer by virtue of the bearer's having an acrid, sharp, or disagreeable flavor. gkoutos 2013-09-15T12:09:15Z quality PATO:0002474 bitter A flavor quality inhering in a bearer by virtue of the bearer's having an acrid, sharp, or disagreeable flavor. PATOC:LC A position quality inhering in a bearer by virtue of the bearer's existing near the end of another entity. gkoutos 2013-09-15T12:17:41Z quality PATO:0002475 subterminal A position quality inhering in a bearer by virtue of the bearer's existing near the end of another entity. PATOC:WD A position quality inhering in a bearer by virtue of the bearer's forming the end of another entity. gkoutos 2013-09-15T12:18:08Z quality PATO:0002476 terminal A position quality inhering in a bearer by virtue of the bearer's forming the end of another entity. PATOC:WD A structural quality inhering in a bearer by virtue of the bearer's disposition to breaks without significant deformation (strain) when subjected to stress. gkoutos 2013-09-15T12:25:03Z quality PATO:0002477 brittle A structural quality inhering in a bearer by virtue of the bearer's disposition to breaks without significant deformation (strain) when subjected to stress. wikipedia:http://en.wikipedia.org/wiki/Brittleness A shape quality inhering in a bearer by virtue of the bearer's being marked by narrow lines or grooves, usually parallel, that are oriented transversely relative to the long axis of the bearer. gkoutos 2013-09-15T12:29:15Z quality PATO:0002478 transversely striated A shape quality inhering in a bearer by virtue of the bearer's being marked by narrow lines or grooves, usually parallel, that are oriented transversely relative to the long axis of the bearer. PATOC:DS A shape quality inhering in a bearer by virtue of the bearer's being marked by narrow lines or grooves, usually parallel, that are oriented obliquely relative to the long axis of the bearer. gkoutos 2013-09-15T12:29:42Z quality PATO:0002479 obliquely striated A shape quality inhering in a bearer by virtue of the bearer's being marked by narrow lines or grooves, usually parallel, that are oriented obliquely relative to the long axis of the bearer. PATOC:DS A quality inhering in an bearer by virtue of the bearer's possessing only minor levels of ossification. gkoutos 2013-09-30T05:47:07Z quality PATO:0002480 poorly ossified A quality inhering in an bearer by virtue of the bearer's possessing only minor levels of ossification. PATOC:AD An orientation quality inhering in a bearer by virtue of the bearer having a slanting direction or position : neither perpendicular nor parallel. gkoutos 2013-09-30T05:49:50Z quality PATO:0002481 oblique orientation An orientation quality inhering in a bearer by virtue of the bearer having a slanting direction or position : neither perpendicular nor parallel. merriam-wester:http://www.merriam-webster.com/dictionary/oblique Shape quality inhering in a bearer by virtue of the bearer exhibiting a narrow and elongate opening. gkoutos 2013-09-30T05:51:39Z quality PATO:0002482 slit-like Shape quality inhering in a bearer by virtue of the bearer exhibiting a narrow and elongate opening. PATOC:WD Positional quality in which an entity is located outside of another entity. gkoutos 2013-09-30T06:06:27Z quality PATO:0002483 external to Positional quality in which an entity is located outside of another entity. PATOC:WD An angular shape quality inhering in a bearer by virtue of the bearer's having a single angle in its length giving the bearer the form of an inverted letter V. gkoutos 2013-10-10T03:55:44Z chevron shaped quality PATO:0002484 inverted-V shaped An angular shape quality inhering in a bearer by virtue of the bearer's having a single angle in its length giving the bearer the form of an inverted letter V. PATOC:WD A shape quality inhering in a bearer by virtue of the bearer's possessing two sides that are at the same continuous distance relative to each other. gkoutos 2013-10-10T03:58:37Z quality PATO:0002485 parallel-sided A shape quality inhering in a bearer by virtue of the bearer's possessing two sides that are at the same continuous distance relative to each other. PATOC:WD A quality inhering in a process by virtue of that process having two or more organisms as participants. gkoutos 2013-10-10T04:08:44Z quality PATO:0002486 multi-organismal process quality A quality inhering in a process by virtue of that process having two or more organisms as participants. PATOC:DS A quality inhering in a process by virtue of that process having exactly one organism as a participant. gkoutos 2013-10-10T04:09:51Z quality PATO:0002487 single organismal process quality A quality inhering in a process by virtue of that process having exactly one organism as a participant. PATOC:DS Overlap with quality inhering in a bearer by virtue of the bearer's being positioned over another entity so as to cover some portion of it. gkoutos 2013-10-10T04:12:22Z quality PATO:0002488 overlapping Overlap with quality inhering in a bearer by virtue of the bearer's being positioned over another entity so as to cover some portion of it. PATOC:WD Overlap with quality inhering in a bearer by virtue of the bearer's being positioned under another entity so as to be covered by some portion of it. gkoutos 2013-10-10T04:13:04Z quality PATO:0002489 overlapped by Overlap with quality inhering in a bearer by virtue of the bearer's being positioned under another entity so as to be covered by some portion of it. PATOC:WD An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed anteriorly. gkoutos 2013-10-10T05:11:26Z anteriorly directly quality PATO:0002490 anterior orientation An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed anteriorly. PATOC:WD An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed anterodorsally. gkoutos 2013-10-10T05:12:15Z anterodorsally directed quality PATO:0002491 anterodorsal orientation An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed anterodorsally. PATOC:WD An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed anterolaterally. gkoutos 2013-10-10T05:13:17Z anterolaterally directed quality PATO:0002492 anterolateral orientation An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed anterolaterally. PATOC:WD An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed anteroventrally. gkoutos 2013-10-10T05:13:55Z anteroventrally directed quality PATO:0002493 anteroventral orientation An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed anteroventrally. PATOC:WD An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed distally. gkoutos 2013-10-10T05:14:37Z distally directed quality PATO:0002494 distal orientation An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed distally. PATOC:WD An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed dorsally. gkoutos 2013-10-10T05:15:24Z dorsally directed quality PATO:0002495 dorsal orientation An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed dorsally. PATOC:WD An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed dorsolaterally. gkoutos 2013-10-10T05:16:04Z dorsolaterally directed quality PATO:0002496 dorsolateral orientation An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed dorsolaterally. PATOC:WD An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed laterally. gkoutos 2013-10-10T05:16:45Z laterally directed quality PATO:0002497 lateral orientation An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed laterally. PATOC:WD An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed medially. gkoutos 2013-10-10T05:17:30Z medially directed quality PATO:0002498 medial orientation An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed medially. PATOC:WD An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed posteriorly. gkoutos 2013-10-10T05:18:21Z posteriorly directed quality PATO:0002499 posterior orientation An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed posteriorly. PATOC:WD An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed ventrolaterally. gkoutos 2013-10-10T05:19:16Z ventrolaterally directed quality PATO:0002500 ventrolaterally orientation An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed ventrolaterally. PATOC:WD An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed ventrally. gkoutos 2013-10-10T05:19:22Z ventrally directed quality PATO:0002501 ventral orientation An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed ventrally. PATOC:WD An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed transversely. gkoutos 2013-10-10T05:19:25Z transversely oriented quality PATO:0002502 transverse orientation An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed transversely. PATOC:WD An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed posterolaterally. gkoutos 2013-10-10T05:19:28Z posterolaterally directed quality PATO:0002503 posterolateral orientation An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed posterolaterally. PATOC:WD An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed posterodorsally. gkoutos 2013-10-10T05:19:36Z posterodorsally directed quality PATO:0002504 posterodorsal orientation An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed posterodorsally. PATOC:WD A nucleate quality inhering in a bearer by virtue of the bearer's having one or more nucleus. gkoutos 2013-10-21T05:44:34Z quality PATO:0002505 nucleated A nucleate quality inhering in a bearer by virtue of the bearer's having one or more nucleus. PATOC:GVG A surface feature shape quality inhering in a bearer by virtue of the bearer's not having undulating edges forming lobes. gkoutos 2013-10-25T04:42:40Z quality PATO:0002506 alobate A surface feature shape quality inhering in a bearer by virtue of the bearer's not having undulating edges forming lobes. PATOC:DOS A composition quality inhering in a bearer by virtue of the bearer's consisting of keratin. segerdel 2014-02-04T12:38:14Z quality PATO:0002507 keratinous A composition quality inhering in a bearer by virtue of the bearer's consisting of keratin. PATOC:EJS A positional quality inhering in a bearer by virtue of the bearer being hidden from view. segerdel 2014-02-04T01:30:21Z quality PATO:0002508 concealed A positional quality inhering in a bearer by virtue of the bearer being hidden from view. PATOC:EJS A 2-D shape quality inhering in a bearer by virtue of the bearer's having six angles and six sides. segerdel 2014-02-04T01:50:05Z quality PATO:0002509 hexagonal A 2-D shape quality inhering in a bearer by virtue of the bearer's having six angles and six sides. Merriam-Webster:hexagonal A concave 3-D shape quality inhering in a bearer by virtue of the bearer being divided into multiple parts. segerdel 2014-02-06T01:15:28Z quality PATO:0002510 multipartite A concave 3-D shape quality inhering in a bearer by virtue of the bearer being divided into multiple parts. PATOC:EJS A shape quality inhering in a bearer by virtue of the bearer's similarity to the appearance of a cane. segerdel 2014-02-06T02:04:35Z quality cane-shaped PATO:0002511 cane-like A shape quality inhering in a bearer by virtue of the bearer's similarity to the appearance of a cane. PATOC:EJS A positional quality inhering in a bearer by virtue of the bearer flowing or coming together with another entity. segerdel 2014-02-06T02:28:39Z quality PATO:0002512 confluent with A positional quality inhering in a bearer by virtue of the bearer flowing or coming together with another entity. Merriam-Webster:confluent A positional quality inhering in a bearer by virtue of the bearer's having a slanting direction (neither perpendicular nor parallel) relative to another entity. segerdel 2014-02-06T02:54:16Z quality PATO:0002513 oblique to A positional quality inhering in a bearer by virtue of the bearer's having a slanting direction (neither perpendicular nor parallel) relative to another entity. PATOC:EJS An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed anteromedially. segerdel 2014-02-07T12:59:10Z medioanterior orientation quality PATO:0002514 anteromedial orientation An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed anteromedially. PATOC:EJS An elevation quality inhering in a bearer by virtue the bearer's being in a high position relative to another entity. segerdel 2014-02-07T01:12:48Z quality PATO:0002515 increased elevation relative to An elevation quality inhering in a bearer by virtue the bearer's being in a high position relative to another entity. PATOC:EJS A positional quality inhering in a bearer by virtue of the bearer being hidden from view or covered by another entity. segerdel 2014-02-10T01:13:53Z quality PATO:0002516 concealed by A positional quality inhering in a bearer by virtue of the bearer being hidden from view or covered by another entity. PATOC:EJS A shape quality inhering in a bearer by virtue of the bearer's similarity to the appearance of a saddle. segerdel 2014-02-10T01:23:13Z quality PATO:0002517 saddle-shaped A shape quality inhering in a bearer by virtue of the bearer's similarity to the appearance of a saddle. PATOC:EJS A positional quality inhering in a bearer by virtue of the bearer being level or even with another surface. segerdel 2014-02-10T01:26:50Z quality PATO:0002518 flush A positional quality inhering in a bearer by virtue of the bearer being level or even with another surface. WordReference:flush A structural quality inhering in a bearer by virtue of the bearer's having an open, latticed, or porous structure; used especially of bone. segerdel 2014-02-10T01:33:14Z quality PATO:0002519 cancellous A structural quality inhering in a bearer by virtue of the bearer's having an open, latticed, or porous structure; used especially of bone. TheFreeDictionary:cancellous A shape quality inhering in a bearer by virtue of the bearer being shaped like a scute or an osteoderm. segerdel 2014-02-10T01:37:47Z quality PATO:0002520 scute-like A shape quality inhering in a bearer by virtue of the bearer being shaped like a scute or an osteoderm. PATOC:EJS A shape quality inhering in a bearer by virtue of the bearer's similarity to the appearance of a funnel. segerdel 2014-02-10T01:40:05Z quality PATO:0002521 funnel-shaped A shape quality inhering in a bearer by virtue of the bearer's similarity to the appearance of a funnel. PATOC:EJS A shape quality inhering in a bearer by virtue of the bearer having an elongate structure, similar to a ridge, that extends longitudinally along an anatomical entity. segerdel 2014-02-10T01:46:38Z quality PATO:0002522 keel-shaped A shape quality inhering in a bearer by virtue of the bearer having an elongate structure, similar to a ridge, that extends longitudinally along an anatomical entity. PATOC:EJS A positional quality inhering in a bearer by virtue of the bearer's being located at a right angle relative to another entity and to the horizon. segerdel 2014-02-10T02:25:42Z quality PATO:0002523 vertical to A positional quality inhering in a bearer by virtue of the bearer's being located at a right angle relative to another entity and to the horizon. PATOC:EJS An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed mesiolaterally. segerdel 2014-02-10T02:37:42Z quality PATO:0002524 mesiolateral orientation An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed mesiolaterally. PATOC:EJS A structural quality inhering in a bearer by virtue of the bearer being in a position that produces a separation in, or acting to separate, another entity. segerdel 2014-02-10T02:48:15Z quality PATO:0002525 separating A structural quality inhering in a bearer by virtue of the bearer being in a position that produces a separation in, or acting to separate, another entity. PATOC:EJS An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed anterodistally. segerdel 2014-03-11T11:28:39Z antero-distal orientation quality PATO:0002526 anterodistal orientation An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed anterodistally. PATOC:EJS An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed posterodistally. segerdel 2014-03-11T11:29:22Z postero-distal orientation quality PATO:0002527 posterodistal orientation An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed posterodistally. PATOC:EJS PATO:0002628 quality PATO:0002528 obsoleted because the ID was accidentally reused obsolete borderline intensity true PATO:0002629 quality PATO:0002529 obsoleted because the ID was accidentally reused obsolete profound intensity true PATO:0002630 quality PATO:0002530 obsoleted because the ID was accidentally reused obsolete episodic true PATO:0002631 quality PATO:0002531 obsoleted because the ID was accidentally reused obsolete refractory true PATO:0002632 quality PATO:0002532 obsoleted because the ID was accidentally reused obsolete secondary true A multipartite quality inhering in a bearer by virtue of the bearer being divided into two parts. wasila.dahdul 2014-08-12T11:12:13Z quality PATO:0002533 bipartite A multipartite quality inhering in a bearer by virtue of the bearer being divided into two parts. PATOC:WD A shape quality inhering in a bearer by virtue of the bearer's being shaped like a plowshare. wasila.dahdul 2014-08-12T11:23:12Z Image:http://2.bp.blogspot.com/_TbkIC-eqFNM/S66IJ3omNWI/AAAAAAAAFSk/pzThLJPvYZw/s1600/ard-detail.gif plow-share shaped quality PATO:0002534 plowshare shaped A shape quality inhering in a bearer by virtue of the bearer's being shaped like a plowshare. PATOC:WD A shape quality inhering in a bearer by virtue of the bearer's having a short and stout cylindrical shape. wasila.dahdul 2014-08-12T11:30:08Z quality PATO:0002535 peg-like A shape quality inhering in a bearer by virtue of the bearer's having a short and stout cylindrical shape. PATOC:WD A shape quality inhering in a bearer by virtue of the bearer's having a shape like a boomerang, with two arms connected at an angle. wasila.dahdul 2014-08-12T11:32:16Z quality PATO:0002536 boomerang shaped A shape quality inhering in a bearer by virtue of the bearer's having a shape like a boomerang, with two arms connected at an angle. PATOC:WD A spheroid quality inhering in a bearer by virtue of the bearer's exhibiting a shape not quite ovoid. approximately ovoid. wasila.dahdul 2014-08-12T11:51:38Z quality PATO:0002537 subovoid A spheroid quality inhering in a bearer by virtue of the bearer's exhibiting a shape not quite ovoid. approximately ovoid. merriam-webster:http://www.merriam-webster.com/dictionary/subovoid A shape quality that obtains by virtue of the bearer being concave on one side and convex on the other. wasila.dahdul 2014-08-12T11:56:13Z concavoconvex quality PATO:0002538 concavo-convex A shape quality that obtains by virtue of the bearer being concave on one side and convex on the other. merriam-webster:http://www.merriam-webster.com/dictionary/concavo-convex A shape quality inhering in a bearer by virtue of the bearer's having a shape like a ring (a circular shape enclosing a space). wasila.dahdul 2014-08-12T12:01:56Z annular ring-shaped quality PATO:0002539 ring shaped A shape quality inhering in a bearer by virtue of the bearer's having a shape like a ring (a circular shape enclosing a space). PATOC:WD A shape quality inhering in a bearer by virtue of the bearer's possessing a small, spike-like shape. wasila.dahdul 2014-08-12T12:07:44Z quality PATO:0002540 spur shaped A shape quality inhering in a bearer by virtue of the bearer's possessing a small, spike-like shape. PATOC:WD Pertaining to the ability or tendency of an organism or cell to maintain internal equilibrium by adjusting its physiological processes. haendel 2014-12-01T16:07:28Z quality PATO:0002541 homeostatic Pertaining to the ability or tendency of an organism or cell to maintain internal equilibrium by adjusting its physiological processes. GO:0042592 An intensity which is borderline in it its effect or force as compared to baseline or normal. haendel 2014-05-26T06:42:21Z quality PATO:0002628 borderline intensity An intensity which is characterized by being very severe. haendel 2014-05-26T06:44:11Z quality PATO:0002629 profound intensity An intensity which is characterized by being very severe. PATO:MAH An occurrence quality inhering in a bearer by virtue of the bearer's having a course that occurs occasionally. haendel 2014-05-26T06:50:16Z quality PATO:0002630 episodic An occurrence quality inhering in a bearer by virtue of the bearer's having a course that occurs occasionally. PATO:MAH An occurrence of a process during which time there is an inability to change the course, extent, or repetition of the process. haendel 2014-05-26T13:09:29Z quality PATO:0002631 refractory An occurrence of a process during which time there is an inability to change the course, extent, or repetition of the process. PATO:MAH A quality in which the effect or outcome is not primary or the focus of the observation. haendel 2014-05-26T13:17:45Z quality PATO:0002632 secondary A quality in which the effect or outcome is not primary or the focus of the observation. PATO:MAH A 3-D shape that is half of a sphere. wasila.dahdul 2014-09-09T12:25:08Z quality PATO:0005000 hemispheroid A 3-D shape that is half of a sphere. PATOC:WD A variability quality inhering in the bearer by virtue of the bearer having a variable number or count of an entity. wasila.dahdul 2014-09-09T12:27:33Z quality variable number PATO:0005001 variability of count A variability quality inhering in the bearer by virtue of the bearer having a variable number or count of an entity. PATOC:WD Having the shape of a pear; tapering near the top and bulging toward the base or bottom. From thefreedictionary.com wasila.dahdul 2014-09-09T12:30:02Z quality PATO:0005002 pear shaped Having the shape of a pear; tapering near the top and bulging toward the base or bottom. From thefreedictionary.com PATOC:WD A quality inhering in a bearer by virtue of the bearer's resembling the form of a paddle. wasila.dahdul 2014-09-09T12:34:45Z quality PATO:0005003 paddle shaped A quality inhering in a bearer by virtue of the bearer's resembling the form of a paddle. PATOC:WD A shape that is almost an ellipse. wasila.dahdul 2014-09-09T12:36:15Z quality PATO:0005004 subelliptical A shape that is almost an ellipse. PATOC:WD Shape quality inhering in a bearer expanding outward, or having parts expanding outward, from a center point. wasila.dahdul 2014-09-09T12:37:27Z quality PATO:0005005 radiating Shape quality inhering in a bearer expanding outward, or having parts expanding outward, from a center point. PATOC:WD A morphology quality inhering in a bearer by virtue of the bearer's being morphologically distinguishable from another entity. wasila.dahdul 2014-09-09T12:40:57Z distinct from quality PATO:0005006 differentiated from A morphology quality inhering in a bearer by virtue of the bearer's being morphologically distinguishable from another entity. PATOC:WD A 3-D shape inhering in a bearer by virtue of the bearer's having dentition characterized by high-crowned teeth and enamel which extends far past the gum line, which provides extra material for wear and tear. wasila.dahdul 2014-09-09T12:58:01Z quality PATO:0005007 Need to include axiom: hypsodont inheres_in some ('tooth crown' and bearer_of 'increased height'). hypsodont A 3-D shape inhering in a bearer by virtue of the bearer's having dentition characterized by high-crowned teeth and enamel which extends far past the gum line, which provides extra material for wear and tear. DOI:10.1111/j.1469-185X.2011.00176.x A 3-D shape inhering in a bearer by virtue of the bearer's having dentition characterized by low-crowned teeth. Human teeth are brachydont. wasila.dahdul 2014-09-09T12:59:35Z quality PATO:0005008 Need to include axiom: brachydont inheres_in some ('tooth crown' and bearer_of 'decreased height'). brachydont A 3-D shape inhering in a bearer by virtue of the bearer's having dentition characterized by low-crowned teeth. Human teeth are brachydont. DOI:10.1111/j.1469-185X.2011.00176.x A 3-D shape inhering in a bearer by virtue of the bearer's having an entity in the form of a molar tooth. wasila.dahdul 2014-09-09T13:03:00Z quality PATO:0005009 molariform A 3-D shape inhering in a bearer by virtue of the bearer's having an entity in the form of a molar tooth. PATOC:WD A branched quality inhering in a bearer by virtue of the bearer's having many fine filaments or branches that give a feathery appearance: for example, resembling a feather. wasila.dahdul 2014-09-25T15:03:17Z quality PATO:0005010 plumose A branched quality inhering in a bearer by virtue of the bearer's having many fine filaments or branches that give a feathery appearance: for example, resembling a feather. www.oxforddictionaries.com:http://www.oxforddictionaries.com/us/definition/american_english/plumose A positional quality inhering in a bearer by virtue of the bearer possessing an uninterrupted or unbroken connection or spatial distribution relative to the position of another entity. wasila.dahdul 2014-09-25T15:07:34Z quality PATO:0005011 continuous with A positional quality inhering in a bearer by virtue of the bearer possessing an uninterrupted or unbroken connection or spatial distribution relative to the position of another entity. PATOC:WD A structural quality inhering in a bearer by virtue of the bearer being fully formed compared to entities lacking parts. wasila.dahdul 2014-09-25T15:11:47Z quality PATO:0005012 complete structure A structural quality inhering in a bearer by virtue of the bearer being fully formed compared to entities lacking parts. PATOC:WD A structural quality inhering in a bearer by virtue of the bearer's lacking parts or having a reduced form compared to fully formed entities. wasila.dahdul 2014-09-25T15:12:35Z quality PATO:0005013 incomplete structure A structural quality inhering in a bearer by virtue of the bearer's lacking parts or having a reduced form compared to fully formed entities. PATOC:WD A spheroid shape quality inhering in a bearer by virtue of the bearer's being nearly, but not perfectly, spherical. wasila.dahdul 2014-09-25T15:16:25Z quality PATO:0005014 subspherical A spheroid shape quality inhering in a bearer by virtue of the bearer's being nearly, but not perfectly, spherical. PATOC:WD A size quality inhering in an entity or set of entities in which size increases or decreases along the extent of the entity or set. wasila.dahdul 2014-09-25T15:17:51Z gradient of size quality PATO:0005015 tapered size A size quality inhering in an entity or set of entities in which size increases or decreases along the extent of the entity or set. PATOC:WD A positional quality inhering in a bearer by virtue of the bearer's being enclosed on all sides by another entity. wasila.dahdul 2014-09-25T15:20:55Z enclosed by quality PATO:0005016 surrounded by A positional quality inhering in a bearer by virtue of the bearer's being enclosed on all sides by another entity. PATOC:WD A quality inhering in a bearer by virtue of the bearer's being compressed from the side facing the lips to the side facing the tongue. wasila.dahdul 2014-10-02T11:52:09Z quality PATO:0005017 labiolingually compressed A quality inhering in a bearer by virtue of the bearer's being compressed from the side facing the lips to the side facing the tongue. PATOC:WD A quality inhering in a bearer by virtue of the bearer's being compressed from the side facing the midline of the jaw to the side opposite the midline. wasila.dahdul 2014-10-02T11:53:52Z quality PATO:0005018 mesiodistally compressed A quality inhering in a bearer by virtue of the bearer's being compressed from the side facing the midline of the jaw to the side opposite the midline. PATOC:WD A curvature quality inhering in a bearer by virtue of the bearer's being curved towards the tongue. wasila.dahdul 2014-10-02T12:01:16Z quality PATO:0005019 curved lingually A curvature quality inhering in a bearer by virtue of the bearer's being curved towards the tongue. PATOC:WD A shape quality inhering on a bearer by virtue of a bearer's shape lacking in pattern or uniformity; for example, it may have sides of different lengths, different curvatures, or unequal angles. wasila.dahdul 2014-10-03T10:23:17Z quality PATO:0005020 irregularly shaped A shape quality inhering on a bearer by virtue of a bearer's shape lacking in pattern or uniformity; for example, it may have sides of different lengths, different curvatures, or unequal angles. PATOC:WD Cuspidate quality inhering in a bearer by virtue of the bearer's possessing a single cusp. wasila.dahdul 2014-10-17T14:14:04Z quality PATO:0005021 unicuspidate Cuspidate quality inhering in a bearer by virtue of the bearer's possessing a single cusp. PATOC:WD A diameter that remains constant throughout the extent of an entity. wasila.dahdul 2014-10-17T14:15:59Z quality PATO:0005022 uniform diameter A diameter that remains constant throughout the extent of an entity. PATOC:WD An orientation quality inhering in a bearer by virtue of the bearer having a position that is in the parasagittal plane. wasila.dahdul 2014-10-17T14:21:30Z quality PATO:0005023 parasagittal orientation An orientation quality inhering in a bearer by virtue of the bearer having a position that is in the parasagittal plane. PATOC:WD An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed along the longitudinal or anterior-posterior axis. wasila.dahdul 2014-10-17T14:24:19Z quality PATO:0005024 longitudinal orientation An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed along the longitudinal or anterior-posterior axis. PATOC:WD A structural quality inhering in the bearer by virtue of the bearer consisting of a single, maximally connected structure. davidos 2014-12-12T08:41:11Z quality PATO:0010000 What counts as maximally connected may be relative to some specification of granularity. maximally connected A structural quality inhering in the bearer by virtue of the bearer consisting of a single, maximally connected structure. GOC:dos A structural quality inhering in the bearer by virtue of the bearer consisting of multiple structures lacking any physical connection to each other. davidos 2014-12-12T08:43:17Z quality PATO:0010001 disconnected A structural quality inhering in the bearer by virtue of the bearer consisting of multiple structures lacking any physical connection to each other. GOC:dos The velocity of spatial propagation of a process. Examples include the velocity of propagation of an action potential along an axon. dos 2019-07-18T18:24:15Z quality PATO:0010002 propagation velocity The velocity of spatial propagation of a process. Examples include the velocity of propagation of an action potential along an axon. orcid:0000-0002-7073-9172 A propagation velocity that is higher than normal. dos 2019-07-18T18:24:25Z quality PATO:0010003 increased propagation velocity A propagation velocity that is higher than normal. orcid:0000-0002-7073-9172 A propagation velocity that is lower than normal. dos 2019-07-18T18:24:36Z quality PATO:0010004 decreased propagation velocity A propagation velocity that is lower than normal. orcid:0000-0002-7073-9172 A physical quality of a process that is its spatial distribution. For example, bone mineralization follows stereotypical spatial distribution patterns during development, which may be altered in some phenotypes. dos 2019-07-18T18:49:08Z quality PATO:0010005 spatial distribution of a process A physical quality of a process that is its spatial distribution. For example, bone mineralization follows stereotypical spatial distribution patterns during development, which may be altered in some phenotypes. orcid:0000-0002-7073-9172 A quality of a single cell inhering in the bearer by virtue of the bearer's size or shape or structure. http://orcid.org/0000-0002-7073-9172 2021-01-23T11:31:53Z quality PATO:0010006 Use this term for morphologies that can *only* inhere in a cell, e.g. morphological qualities inhering in a cell by virtue of the presence, location or shape of one or more cell parts. cell morphology A quality of a single cell inhering in the bearer by virtue of the bearer's size or shape or structure. ORCID:0000-0002-7073-9172 Absence due to a degenerative process. cjm quality PATO:0015001 absence due to degeneration Absence due to a degenerative process. PATOC:PortlandMeetingFeb2015 The ability of a process to produce its output. cjm quality PATO:0015002 process efficacy The ability of a process to produce its output. PATOC:PortlandMeetingFeb2015 A decrease in the ability of a process to produce its output. cjm quality PATO:0015003 decreased efficacy A decrease in the ability of a process to produce its output. PATOC:PortlandMeetingFeb2015 A increase in the ability of a process to produce its output. cjm quality PATO:0015004 increased efficacy A increase in the ability of a process to produce its output. PATOC:PortlandMeetingFeb2015 Slender and spirally coiled. tendrilled quality tendril-like tendril-shaped PATO:0015005 tendrilous Slender and spirally coiled. https://en.wiktionary.org/wiki/tendril A quality inhering in a structure by virtue of it consisting of many of repeated, similar or identical subunits, arranged in some orderly array. quality PATO:0015006 A complete coverage of this domain would subclasses homopolymeric, copolymeric, crystalline. polymeric A quality inhering in a structure by virtue of it consisting of many of repeated, similar or identical subunits, arranged in some orderly array. GOC:DOS https://github.com/pato-ontology/pato/issues/78 A quality inhering in a bearer by virtue of the degree to which the bearers stands out or projects beyond a surface or line. quality PATO:0015007 prominence A quality inhering in a bearer by virtue of the degree to which the bearers stands out or projects beyond a surface or line. GOC:CJM A quality inhering in a bearer by virtue of the extent to which the bearer is capable of being stretched or swollen. quality PATO:0015008 distensibility A quality inhering in a bearer by virtue of the extent to which the bearer is capable of being stretched or swollen. GOC:CJM A quality inhering in air by virtue of the partial pressure exerted by the bearer's water vapour content. quality PATO:0015009 humidity A quality inhering in air by virtue of the partial pressure exerted by the bearer's water vapour content. https://github.com/pato-ontology/pato/issues/90 An increase in humidity. quality humid PATO:0015010 increased humidity An increase in humidity. https://github.com/pato-ontology/pato/issues/90 An decrease in humidity. quality PATO:0015011 decreased humidity An decrease in humidity. https://github.com/pato-ontology/pato/issues/90 A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity consisting of roughly equal proportions of positively and negatively charged particles, having neither a defined volume nor defined shape, having internal magnetic fields, and being electrically conductive. quality PATO:0015012 quality of a plasma A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity consisting of roughly equal proportions of positively and negatively charged particles, having neither a defined volume nor defined shape, having internal magnetic fields, and being electrically conductive. https://github.com/pato-ontology/pato/issues/88 The degree to which the bearer is exposed to visible light. quality PATO:0015013 degree of illumination The degree to which the bearer is exposed to visible light. https://github.com/pato-ontology/pato/issues/89 An increase in illumination. quality illuminated PATO:0015014 increased degree of illumination An increase in illumination. https://github.com/pato-ontology/pato/issues/89 An decrease in illumination. quality PATO:0015015 decreased degree of illumination An decrease in illumination. https://github.com/pato-ontology/pato/issues/89 Having a shape or form that resembles a step of a stairway (e.g., a ledge or offset margin). quality PATO:0015016 stepped Having a shape or form that resembles a step of a stairway (e.g., a ledge or offset margin). http://www.thefreedictionary.com/stepped https://github.com/pato-ontology/pato/issues/82 A physical quality inhering in an entity by virtue of a portion of the bearer's molecular or polymolecular constituents present in one phase being dispersed in a portion of the bearer's constituents present in another phase. quality PATO:0015017 quality of a colloid A physical quality inhering in an entity by virtue of a portion of the bearer's molecular or polymolecular constituents present in one phase being dispersed in a portion of the bearer's constituents present in another phase. ENVO:pb https://github.com/pato-ontology/pato/issues/91 https://goldbook.iupac.org/html/C/C01172.html A physical quality inhering in an entity by virtue of the bearer's solid or liquid constituents being suspended in a gas. quality PATO:0015018 quality of an aerosol A physical quality inhering in an entity by virtue of the bearer's solid or liquid constituents being suspended in a gas. ENVO:pb https://github.com/pato-ontology/pato/issues/91 A concave 3-D shape quality inhering in a bearer by virtue of the bearer's being shaped in the form of the letter C. quality PATO:0015019 C-shaped A concave 3-D shape quality inhering in a bearer by virtue of the bearer's being shaped in the form of the letter C. github:mah11 https://github.com/pato-ontology/pato/issues/96 A concave 3-D shape quality inhering in a bearer by virtue of the bearer's being shaped in the form of the letter J. quality PATO:0015020 J-shaped A concave 3-D shape quality inhering in a bearer by virtue of the bearer's being shaped in the form of the letter J. github:mah11 https://github.com/pato-ontology/pato/issues/96 The propensity of a material to undergo combustion. Combustion encompasses smouldering and flaming combustion. Combustibility is usually applied to solids. quality PATO:0015021 combustibility The propensity of a material to undergo combustion. Combustion encompasses smouldering and flaming combustion. Combustibility is usually applied to solids. https://en.wikipedia.org/wiki/Combustibility https://github.com/EnvironmentOntology/envo/issues/384 An increase in combustibility. combustible quality PATO:0015022 increased combustibility An decrease in combustibility. quality noncombustible PATO:0015023 decreased combustibility An increase in porosity. quality PATO:0015024 increased porosity An increase in porosity. https://github.com/pato-ontology/pato/issues/110 An decrease in porosity. quality PATO:0015025 decreased porosity An decrease in porosity. https://github.com/pato-ontology/pato/issues/110 quality, state, or degree of being stable. quality PATO:0015026 stability quality, state, or degree of being stable. https://github.com/pato-ontology/pato/issues/113 An increase in stability. quality PATO:0015027 increased stability An increase in stability. https://github.com/pato-ontology/pato/issues/113 A decrease in stability. quality PATO:0015028 decreased stability A decrease in stability. https://github.com/pato-ontology/pato/issues/113 A physical quality inhering in an entity by virtue of the bearer's solid or liquid constituents being transiently dispersed in a solid, liquid, or gas before settling due to gravity or centrifugal forces. quality PATO:0015029 quality of a suspension A physical quality inhering in an entity by virtue of the bearer's solid or liquid constituents being transiently dispersed in a solid, liquid, or gas before settling due to gravity or centrifugal forces. ENVO:pb https://github.com/pato-ontology/pato/issues/91 A shape that ineres in a bearer by virtue of the bearer's mass being distributed in a feather-like fashion. feather-shaped plumed quality PATO:0015030 plume-shaped A shape that ineres in a bearer by virtue of the bearer's mass being distributed in a feather-like fashion. https://github.com/pato-ontology/pato/issues/122 The presence of a constituent, impurity, or some other undesirable element that spoils, corrupts, infects, makes unfit, or makes inferior a material, physical body, natural environment, place of human occupancy, or other material entity. degree of contamination quality PATO:0015031 contamination The presence of a constituent, impurity, or some other undesirable element that spoils, corrupts, infects, makes unfit, or makes inferior a material, physical body, natural environment, place of human occupancy, or other material entity. https://en.wikipedia.org/wiki/Contamination https://github.com/pato-ontology/pato/issues/420 An increase in contamination. contaminated quality PATO:0015032 increased contamination An increase in contamination. https://en.wikipedia.org/wiki/Contamination https://github.com/pato-ontology/pato/issues/420 A decrease in contamination. uncontaminated quality PATO:0015033 decreased contamination A decrease in contamination. https://en.wikipedia.org/wiki/Contamination https://github.com/pato-ontology/pato/issues/420 A biological sex quality inhering in an individual based upon genotypic composition of sex chromosomes. mah quality PATO:0020000 Note that the chromosomal constitution of genotypic sex varies in different organisms. In human, we have XY, XX, though abnormal XXY, X0, XYY, and other combinations are possible. genotypic sex A biological sex quality inhering in an individual based upon genotypic composition of sex chromosomes. PATOC:MAH A biological sex quality inhering in an individual based upon genotypic composition that confers the capability for an organism to differentiate male gonads. mah quality PATO:0020001 Note that the chromosomal constitution of genotypic sex varies in different organisms. In human, this would be XY, though abnormal XXY and XYY would also result in a male phenotypic outcome. male genotypic sex A biological sex quality inhering in an individual based upon genotypic composition that confers the capability for an organism to differentiate male gonads. PATOC:MAH A biological sex quality inhering in an individual or a population based upon genotypic composition that confers the capability for an organism to differentiate female gonads. mah quality PATO:0020002 Note that the chromosomal constitution of genotypic sex varies in different organisms. In human, this would be XX, though abnormal X0 and XXX would also result in a female phenotypic outcome. female genotypic sex A biological sex quality inhering in an individual or a population based upon genotypic composition that confers the capability for an organism to differentiate female gonads. PATOC:MAH A physical quality inhering in a bearer by virtue of the bearer's disposition to being fit to be used as a safe means of hydration. pbuttigieg 2015-09-01T16:16:44Z drinkability quality PATO:0025000 potability A physical quality inhering in a bearer by virtue of the bearer's disposition to being fit to be used as a safe means of hydration. Wikipedia:https://en.wikipedia.org/wiki/Drinking_water A physical quality inhering in a bearer by virtue of the bearer not being suitable for use as a safe means of hydration. pbuttigieg 2015-09-01T16:18:57Z undrinkable quality PATO:0025001 non-potable A physical quality inhering in a bearer by virtue of the bearer not being suitable for use as a safe means of hydration. Wikipedia:https://en.wikipedia.org/wiki/Drinking_water A physical quality inhering in a bearer by virtue of the bearer being suitable for use as a safe means of hydration. pbuttigieg 2015-09-01T16:19:02Z drinkable quality PATO:0025002 potable A physical quality inhering in a bearer by virtue of the bearer being suitable for use as a safe means of hydration. Wikipedia:https://en.wikipedia.org/wiki/Drinking_water A malformed quality inhering in a bearer by virtue of the bearer's gross morphology containing what are normally anterior structures and missing some or all of what are normally posterior structures. segerdel quality PATO:0030000 anterioralized A malformed quality inhering in a bearer by virtue of the bearer's gross morphology containing what are normally anterior structures and missing some or all of what are normally posterior structures. PATOC:EJS A malformed quality inhering in a bearer by virtue of the bearer's gross morphology containing what are normally dorsal structures and missing some or all of what are normally ventral structures. segerdel quality PATO:0030001 dorsalized A malformed quality inhering in a bearer by virtue of the bearer's gross morphology containing what are normally dorsal structures and missing some or all of what are normally ventral structures. PATOC:EJS A malformed quality inhering in a bearer by virtue of the bearer's gross morphology containing what are normally posterior structures and missing some or all of what are normally anterior structures. segerdel quality PATO:0030002 posterioralized A malformed quality inhering in a bearer by virtue of the bearer's gross morphology containing what are normally posterior structures and missing some or all of what are normally anterior structures. PATOC:EJS A malformed quality inhering in a bearer by virtue of the bearer's gross morphology containing what are normally ventral structures and missing some or all of what are normally dorsal structures. segerdel quality PATO:0030003 ventralized A malformed quality inhering in a bearer by virtue of the bearer's gross morphology containing what are normally ventral structures and missing some or all of what are normally dorsal structures. PATOC:EJS An anterioralized quality inhering in a bearer by virtue of the bearer's gross morphology containing what are normally anterior structures and missing some but not all of what are normally posterior structures. segerdel quality PATO:0030004 partially anterioralized An anterioralized quality inhering in a bearer by virtue of the bearer's gross morphology containing what are normally anterior structures and missing some but not all of what are normally posterior structures. PATOC:EJS A dorsalized quality inhering in a bearer by virtue of the bearer's gross morphology containing what are normally dorsal structures and missing some but not all of what are normally ventral structures. segerdel quality PATO:0030005 partially dorsalized A dorsalized quality inhering in a bearer by virtue of the bearer's gross morphology containing what are normally dorsal structures and missing some but not all of what are normally ventral structures. PATOC:EJS A posterioralized quality inhering in a bearer by virtue of the bearer's gross morphology containing what are normally posterior structures and missing some but not all of what are normally anterior structures. segerdel quality PATO:0030006 partially posterioralized A posterioralized quality inhering in a bearer by virtue of the bearer's gross morphology containing what are normally posterior structures and missing some but not all of what are normally anterior structures. PATOC:EJS A ventralized quality inhering in a bearer by virtue of the bearer's gross morphology containing what are normally ventral structures and missing some but not all of what are normally dorsal structures. segerdel quality PATO:0030007 partially ventralized A ventralized quality inhering in a bearer by virtue of the bearer's gross morphology containing what are normally ventral structures and missing some but not all of what are normally dorsal structures. PATOC:EJS An oriented quality inhering in a bearer by virtue of the bearer's being abnormally placed or arranged. 2018-05-21T22:44:38Z http://orcid.org/0000-0001-5208-3432 quality PATO:0040000 heterotaxic An oriented quality inhering in a bearer by virtue of the bearer's being abnormally placed or arranged. http://medical-dictionary.thefreedictionary.com/heterotaxic PATO:0002539 quality PATO:0040001 obsolete ring-shaped true A positional quality inhering in a bearer by virtue of some aspect of that bearer beginning from a position on another entity. 2018-05-24T04:10:53Z http://orcid.org/0000-0001-5208-3432 quality PATO:0040002 Original label "originates from" changed to current label to differentiate that this term is a positional quality rather than one that connects between an entity and another entity it originates from. position originates from The ability of a pathogen to produce an infectious disease or disorder in an another organism. 2018-08-02T04:24:52Z http://orcid.org/0000-0001-5208-3432 quality PATO:0040003 pathogenicity The ability of a pathogen to produce an infectious disease or disorder in an another organism. https://orcid.org/0000-0001-8941-3984 A texture quality inhering in a bearer by virtue of the bearer's being covered or partially covered with hair that has increased thickness and softness. 2018-08-02T04:39:30Z http://orcid.org/0000-0001-5208-3432 quality PATO:0040004 plush A texture quality inhering in a bearer by virtue of the bearer's being covered or partially covered with hair that has increased thickness and softness. https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0003-4606-0597 An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed posteroventrally. 2018-11-12T22:54:16Z http://orcid.org/0000-0001-5208-3432 posteroventrally oriented quality PATO:0040005 posteroventral orientation An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed posteroventrally. https://orcid.org/0000-0003-3162-7490 A shape quality inhering in a bearer by virtue of the bearer's having a shape like a crown. 2018-11-12T18:09:59Z http://orcid.org/0000-0001-5208-3432 quality PATO:0040006 crown like A shape quality inhering in a bearer by virtue of the bearer's having a shape like a crown. https://orcid.org/0000-0003-3162-7490 A shape quality inhering in a bearer by virtue of the bearer's having a shape like a shell. 2018-11-12T18:12:47Z http://orcid.org/0000-0001-5208-3432 quality PATO:0040007 shell shaped A shape quality inhering in a bearer by virtue of the bearer's having a shape like a shell. https://orcid.org/0000-0003-3162-7490 A shape quality inhering in a bearer by virtue of the bearer's having an ornamental border consisting of short straight or twisted threads or strips hanging from cut or raveled edges or from a separate band. 2018-11-12T18:15:10Z http://orcid.org/0000-0001-5208-3432 quality PATO:0040008 fringed A shape quality inhering in a bearer by virtue of the bearer's having an ornamental border consisting of short straight or twisted threads or strips hanging from cut or raveled edges or from a separate band. https://orcid.org/0000-0003-3162-7490 https://www.merriam-webster.com/dictionary/fringe A concave 3-D shape quality inhering in a bearer by virtue of the bearer's being shaped in the form of a bowl. 2018-11-12T18:17:01Z http://orcid.org/0000-0001-5208-3432 quality PATO:0040009 bowl shaped A concave 3-D shape quality inhering in a bearer by virtue of the bearer's being shaped in the form of a bowl. https://orcid.org/0000-0003-3162-7490 Mobility relative to a second entity. 2018-11-12T18:20:08Z http://orcid.org/0000-0001-5208-3432 quality PATO:0040010 For example, distinct anteroposterior mobility of palatine relative to mesethmoid. mobile relative to Mobility relative to a second entity. https://orcid.org/0000-0003-3162-7490 Immobility relative to a second entity. 2018-11-12T18:21:07Z http://orcid.org/0000-0001-5208-3432 quality PATO:0040011 For example: distinct anteroposterior immobility of palatine relative to mesethmoid. immobile relative to Immobility relative to a second entity. https://orcid.org/0000-0003-3162-7490 A shape that is in the form of a plug, being tube-like and expanded on one end. 2018-11-12T18:24:41Z http://orcid.org/0000-0001-5208-3432 plug like quality PATO:0040012 plug shaped A shape that is in the form of a plug, being tube-like and expanded on one end. https://orcid.org/0000-0003-3162-7490 An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed dorsomedially. 2018-11-12T18:27:57Z http://orcid.org/0000-0001-5208-3432 dorsomedially directed quality PATO:0040013 dorsomedial orientation An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed dorsomedially. https://orcid.org/0000-0003-3162-7490 A shape that is in the form of a narrow strip encircling an object. 2018-11-12T18:31:51Z http://orcid.org/0000-0001-5208-3432 band like band-like strip like strip-like quality PATO:0040014 band shaped A shape that is in the form of a narrow strip encircling an object. https://orcid.org/0000-0003-3162-7490 https://www.merriam-webster.com/dictionary/band A concave 3-D shape quality inhering in a bearer by virtue of the bearer's shape resembling that of a trough, being narrow, long, and boxlike in shape. 2018-11-12T18:35:51Z http://orcid.org/0000-0001-5208-3432 trough like trough-like trough-shaped quality PATO:0040015 trough shaped A concave 3-D shape quality inhering in a bearer by virtue of the bearer's shape resembling that of a trough, being narrow, long, and boxlike in shape. http://www.dictionary.com/browse/trough https://orcid.org/0000-0003-3162-7490 A shape quality inhering in a bearer by virtue of the bearer's having five angles and five sides. 2018-11-12T18:39:48Z http://orcid.org/0000-0001-5208-3432 quality PATO:0040016 pentagonal A shape quality inhering in a bearer by virtue of the bearer's having five angles and five sides. https://orcid.org/0000-0003-3162-7490 https://www.merriam-webster.com/dictionary/pentagonal A growth quality of occurrent in which the growth of an organism, structure or group of organisms is abnormal. 2018-11-12T19:01:51Z http://orcid.org/0000-0001-5208-3432 dysgenesis quality PATO:0040017 dysplastic growth A growth quality of occurrent in which the growth of an organism, structure or group of organisms is abnormal. https://www.cancer.gov/publications/dictionaries/cancer-terms/def/dysplasia Fibrosis is the formation of excess fibrous connective tissue in an organ or tissue in a reparative or reactive process. 2018-11-12T23:16:17Z http://orcid.org/0000-0001-5208-3432 quality PATO:0040019 fibrotic Fibrosis is the formation of excess fibrous connective tissue in an organ or tissue in a reparative or reactive process. https://en.wikipedia.org/wiki/Fibrosis Female quality of being incapable to reproduce because of functional loss of the ovaries and/or uterus from surgical removal. 2018-11-16T22:52:49Z http://orcid.org/0000-0001-5208-3432 quality PATO:0040020 spayed female The bearer of this quality has_part n=1 of the indicated entity type, where n is bilaterally paired for a comparable organism.. http://orcid.org/0000-0001-5208-3432 quality PATO:0040021 unpaired The bearer of this quality has_part n=1 of the indicated entity type, where n is bilaterally paired for a comparable organism.. https://orcid.org/0000-0003-3162-7490 A shape quality inhering in a bearer by virtue of the bearer being expanded laterally and or opened outward in shape. 2018-11-19T21:49:07Z http://orcid.org/0000-0001-5208-3432 quality PATO:0040022 flared An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed distomedially, ie, pertaining to an inside aspect, but also farther away from the center of the body. 2018-11-19T21:54:33Z http://orcid.org/0000-0001-5208-3432 disto-medial orientation distomedial quality PATO:0040023 distomedial orientation An orientation quality inhering in a bearer by virtue of the bearer having a position that is directed distomedially, ie, pertaining to an inside aspect, but also farther away from the center of the body. https://en.wiktionary.org/wiki/distomedial The bearer of this quality has_part n=2 of the indicated entity type, where n is unpaired for a comparable organism. http://orcid.org/0000-0001-5208-3432 paired quality PATO:0040024 bilaterally paired The bearer of this quality has_part n=2 of the indicated entity type, where n is unpaired for a comparable organism. https://orcid.org/0000-0003-3162-7490 A structural quality which is held by a bearer where a localized pathological or traumatic structural change, damage, deformity, or discontinuity of tissue, organ, or body part is present. http://orcid.org/0000-0001-5208-3432 quality PATO:0040025 lesioned A structural quality which is held by a bearer where a localized pathological or traumatic structural change, damage, deformity, or discontinuity of tissue, organ, or body part is present. NCIT:C3824 A structural quality inhering in a bearer by virtue of the bearer's being marked by interruptions or gaps. http://orcid.org/0000-0001-5208-3432 structurally interrupted quality PATO:0040026 This term is intended for use for terms such as MP:0010461 discontinuous pulmonary artery and MP:0004157 interrupted aortic arch. structurally discontinuous A ploidy quality inhering in a bearer by virtue of the bearer's haploid cells undergo chromosome doubling. http://orcid.org/0000-0001-5208-3432 double haploid double-haploid quality PATO:0040027 doubled haploid A ploidy quality inhering in a bearer by virtue of the bearer's haploid cells undergo chromosome doubling. Wikipedia:https://en.wikipedia.org/wiki/Doubled_haploidy An organismal quality of having successfully reproduced. http://orcid.org/0000-0001-5208-3432 quality PATO:0040028 parous An organismal quality of having successfully reproduced. EFO:0002947 A physical quality inhering in a bearer by virtue of that bearer being shielded from visible light. http://orcid.org/0000-0001-5208-3432 quality PATO:0040029 Shaded does not refer to radiation more generally, as this would be more shielded than shaded. shaded A physical quality inhering in a bearer by virtue of that bearer being shielded from visible light. https://orcid.org/0000-0002-4366-3088 A width and length quality which is relatively small, where both width and length are decreased. http://orcid.org/0000-0001-5208-3432 quality PATO:0040030 decreased width and length A width and length quality that is relatively large, where both width and length are increased. http://orcid.org/0000-0001-5208-3432 quality PATO:0040031 increased width and length A distance traveled in a specific time that is relatively high. http://orcid.org/0000-0001-5208-3432 quality PATO:0040032 increased linear velocity A distance traveled in a specific time that is relatively high. https://orcid.org/0000-0002-2244-7917 A distance traveled in a specific time that is relatively low. http://orcid.org/0000-0001-5208-3432 quality PATO:0040033 decreased linear velocity A distance traveled in a specific time that is relatively low. https://orcid.org/0000-0002-2244-7917 A broken quality where an entity is cracked or broken, usually a bone. http://orcid.org/0000-0001-5208-3432 quality PATO:0040034 fractured A broken quality where an entity is cracked or broken, usually a bone. https://medlineplus.gov/fractures.html A fractured quality where the fracture traverses the bone perpendicular to the axis of the bone. http://orcid.org/0000-0001-5208-3432 fractured, transverse quality PATO:0040035 transversely fractured A fractured quality where the fracture traverses the bone perpendicular to the axis of the bone. https://radiopaedia.org/articles/transverse-fracture?lang=us A fractured quality in which one of the fragments is driven into another fragment. http://orcid.org/0000-0001-5208-3432 fractured, impacted impact fractured quality PATO:0040036 impact-fractured A fractured quality in which one of the fragments is driven into another fragment. https://www.dictionary.com/browse/impacted-fracture A fractured quality where the fracture runs parallel to the long axis of a bone. http://orcid.org/0000-0001-5208-3432 fractured, linear quality PATO:0040037 linearly fractured A fractured quality where the fracture runs parallel to the long axis of a bone. https://www.dictionary.com/browse/linear-fracture A fractured quality where the fracture occurs at a plane oblique to the long axis of the bone. http://orcid.org/0000-0001-5208-3432 fractured, oblique quality PATO:0040038 obliquely fractured A fractured quality where the fracture occurs at a plane oblique to the long axis of the bone. https://radiopaedia.org/articles/oblique-fracture?lang=us A fractured quality that occurs when torque (a rotating force) is applied along the axis of a bone. http://orcid.org/0000-0001-5208-3432 fractured, spiral fractured, torsion quality PATO:0040039 spirally fractured A fractured quality that occurs when torque (a rotating force) is applied along the axis of a bone. https://en.wikipedia.org/wiki/Spiral_fracture A fractured quality that is caused by a loss of bone mass (osteoporosis) that occurs as part of aging. http://orcid.org/0000-0001-5208-3432 compression fractured fractured, compression fractured, wedge wedge fractured quality PATO:0040040 compression-fractured A fractured quality that is caused by a loss of bone mass (osteoporosis) that occurs as part of aging. https://www.mayoclinic.org/diseases-conditions/osteoporosis/multimedia/compression-fractures/img-20008995 A fractured quality in which the fragment of bone tears away from the main mass of bone as a result of physical trauma. http://orcid.org/0000-0001-5208-3432 fractured, avulsion quality PATO:0040041 avulsion fractured A fractured quality in which the fragment of bone tears away from the main mass of bone as a result of physical trauma. https://en.wikipedia.org/wiki/Avulsion_fracture A proportionality quality inhering in a bearer by virtue of the bearer's decreased magnitude in respect to a related entity. http://orcid.org/0000-0001-5208-3432 decreased proportion decreased proportionality decreased quotient decreased ratio quality PATO:0040042 Example: decreased proportion of CD4 T cells relative to total T cells. decreased proportionality to A proportionality quality inhering in a bearer by virtue of the bearer's decreased magnitude in respect to a related entity. https://orcid.org/0000-0001-5208-3432 A proportionality quality inhering in a bearer by virtue of the bearer's increased magnitude in respect to a related entity. http://orcid.org/0000-0001-5208-3432 increased proportion increased proportionality increased quotient increased ratio quality PATO:0040043 Example: increased proportion of CD4 T cells relative to total T cells. increased proportionality to A proportionality quality inhering in a bearer by virtue of the bearer's increased magnitude in respect to a related entity. https://orcid.org/0000-0001-5208-3432 A structural quality inhering in a bearer by virtue of the bearer's components being torn, typically used for soft tissues or membranes. http://orcid.org/0000-0001-5208-3432 burst quality PATO:0040044 ruptured A structural quality inhering in a bearer by virtue of the bearer's components being torn, typically used for soft tissues or membranes. https://orcid.org/0000-0003-4606-0597 Existing or functioning as though broken into separate parts; disorganized; disunified. http://orcid.org/0000-0001-5208-3432 quality PATO:0040047 Moved to a child of wholeness because broken implies a trauma and fragmented could be caused by a developmental process. See HP:0100168 Fragmented epiphyses as an example. fragmented Existing or functioning as though broken into separate parts; disorganized; disunified. https://www.dictionary.com/browse/unfragmented Red due to increase blood circulation in a defined area. http://orcid.org/0000-0001-5208-3432 erythema skin redness quality PATO:0040048 erythematous Red due to increase blood circulation in a defined area. https://orcid.org/0000-0002-0736-9199 A phenotypic sex quality inhering in a plant organism or a population of plants in which the flowers have two stamens. http://orcid.org/0000-0001-5208-3432 quality PATO:0040050 diandrous A phenotypic sex quality inhering in a plant organism or a population of plants in which the flowers have two stamens. http://orcid.org/0000-0002-2908-3327 https://orcid.org/0000-0001-8815-0078 A phenotypic sex quality inhering in a plant organism or a population of plants in which the flowers have only one stamen. http://orcid.org/0000-0001-5208-3432 quality PATO:0040051 monandrous A phenotypic sex quality inhering in a plant organism or a population of plants in which the flowers have only one stamen. http://orcid.org/0000-0002-2908-3327 https://orcid.org/0000-0001-8815-0078 A sequential hermaphroditic quality whereby organisms start out as female and change to male at a later life stage. https://orcid.org/0000-0001-8815-0078 protogyny quality PATO:0040052 protogynous A sequential hermaphroditic quality whereby organisms start out as female and change to male at a later life stage. https://en.wikipedia.org/wiki/Sequential_hermaphroditism http://orcid.org/0000-0002-2908-3327 A sequential hermaphroditic quality whereby organisms start out as male and change to female at a later life stage. https://orcid.org/0000-0001-8815-0078 protandry quality PATO:0040053 protandrous A sequential hermaphroditic quality whereby organisms start out as male and change to female at a later life stage. http://orcid.org/0000-0002-2908-3327 https://en.wikipedia.org/wiki/Sequential_hermaphroditism A protogynous quality whereby organisms start out as female and change to hermaphrodite at a later life stage. https://orcid.org/0000-0001-8815-0078 protogynous hermaphrodite protogynous hermaphroditic quality PATO:0040054 protogynous hermaphroditism A protogynous quality whereby organisms start out as female and change to hermaphrodite at a later life stage. https://en.wikipedia.org/wiki/Sequential_hermaphroditism A protandrous quality whereby organisms start out as male and change to hermaphrodite at a later life stage. https://orcid.org/0000-0001-8815-0078 protandrous hermaphrodite protandrous hermaphroditic quality PATO:0040055 protandrous hermaphroditism A protandrous quality whereby organisms start out as male and change to hermaphrodite at a later life stage. https://en.wikipedia.org/wiki/Sequential_hermaphroditism A physical quality inhering in a bearer by virtue of the bearer's disposition to deform by heating. https://orcid.org/0000-0002-2996-719X https://orcid.org/0000-0002-8166-0486 https://orcid.org/0000-0003-1072-8081 http://orcid.org/0000-0001-5208-3432 quality PATO:0040070 thermoplastic A physical quality inhering in a bearer by virtue of the bearer's disposition to deform by heating. http://www.gesamp.org/publications/guidelines-for-the-monitoring-and-assessment-of-plastic-litter-in-the-ocean https://orcid.org/0000-0002-8166-0486 A rate which is relatively normal. quality PATO:0045000 normal rate A quality of an object that has a value that is normal or average. Luke Slater 2017-12-21T14:11:01Z quality PATO:0045001 normal object quality An acidity which is relatively normal. quality PATO:0045002 normal acidity A adhesivity which is relatively normal or average. Luke Slater 2017-12-22T14:16:43Z quality PATO:0045003 normal adhesivity An affinity which is relatively normal or average. Luke Slater 2017-12-22T14:16:43Z quality PATO:0045004 normal affinity An age which is relatively normal or average. Luke Slater 2017-12-22T14:16:43Z quality PATO:0045005 normal age An avidity which is relatively normal or average. Luke Slater 2017-12-22T14:16:43Z quality PATO:0045006 normal avidity A behavioural quality of a process inhering in a bearer by virtue of the bearer's exhibiting normal or average activity. Luke Slater 2017-12-22T14:16:43Z quality PATO:0045007 normal behavioural activity A cellular motility which is normal or average. Luke Slater 2017-12-22T14:16:43Z quality PATO:0045008 normal cellular motility A coiling which is normal or average. Luke Slater 2017-12-22T14:16:43Z quality PATO:0045009 normal coiling A concentration which is relatively normal or average. Luke Slater 2017-12-22T14:16:43Z quality PATO:0045010 normal concentration A contractility which is relatively normal or average. Luke Slater 2017-12-22T14:16:43Z quality PATO:0045011 normal contractility A coordination which is relatively normal or average. Luke Slater 2017-12-22T14:16:43Z quality PATO:0045012 normal coordination A curvature which is relatively normal or average. Luke Slater 2017-12-22T14:16:43Z quality PATO:0045013 normal curvature A distance which is relatively normal or average. Luke Slater 2017-12-22T14:16:43Z quality PATO:0045014 normal distance An efficiency which is relatively normal or average. Luke Slater 2017-12-22T14:16:43Z quality PATO:0045015 normal efficiency An elasticity which is relatively normal or average. Luke Slater 2017-12-22T14:16:43Z quality PATO:0045016 normal elasticity A fecundity which is relatively normal or average. Luke Slater 2017-12-22T14:16:43Z quality PATO:0045017 normal fecundity A female fertility which is relatively normal or average. Luke Slater 2017-12-22T14:16:43Z quality PATO:0045018 normal female fertility A female receptivity which is relatively normal or average. Luke Slater 2017-12-22T14:16:43Z quality PATO:0045019 normal female receptivity A fertility which is relatively normal or average. Luke Slater 2017-12-22T14:16:43Z quality PATO:0045020 normal fertility A flexibility which is relatively normal or average. Luke Slater 2017-12-22T14:16:43Z quality PATO:0045021 normal flexibility A fluid flow which is relatively normal or average. Luke Slater 2017-12-22T14:16:43Z quality PATO:0045022 normal fluid flow A fluorescence which is relatively normal or average. Luke Slater 2017-12-22T14:16:43Z quality PATO:0045023 normal fluorescence A force which is relatively normal or average. Luke Slater 2017-12-22T14:16:43Z quality PATO:0045024 normal force A fragility which is relatively normal or average. Luke Slater 2017-12-22T14:16:43Z quality PATO:0045025 normal fragility A life span which is relatively normal or average. Luke Slater 2017-12-22T14:16:43Z quality PATO:0045026 normal life span A magnetism which is relatively normal or average. Luke Slater 2017-12-22T14:16:43Z quality PATO:0045027 normal magnetism A male fertility which is relatively normal or average. Luke Slater 2017-12-22T14:16:43Z quality PATO:0045028 normal male fertility A male receptivity which is relatively normal or average. Luke Slater 2017-12-22T14:16:43Z quality PATO:0045029 normal male receptivity A mass which is relatively normal or average. Luke Slater 2017-12-22T14:16:43Z quality PATO:0045030 normal mass A density which is relatively normal or average. Luke Slater 2017-12-22T14:16:43Z quality PATO:0045031 normal mass density A mobility which is relatively normal or average. Luke Slater 2017-12-22T14:16:43Z quality PATO:0045032 normal mobility An odor quality of having relatively normal or average odor. Luke Slater 2017-12-22T14:16:43Z quality PATO:0045033 normal odor An osmolality which is relatively normal or average odor. Luke Slater 2017-12-22T14:16:43Z quality PATO:0045034 normal osmolality An osmolarity which is relatively normal or average odor. Luke Slater 2017-12-22T14:16:43Z quality PATO:0045035 normal osmolarity A permeability which is relatively normal or average. Luke Slater 2017-12-22T14:16:43Z quality PATO:0045036 normal permeability A quality inhering in a bearer by virtue of the bearer's being phosphorylated to a normal or average extent. Luke Slater 2017-12-22T14:16:43Z quality PATO:0045037 normal phosphorylation A photosensitivity which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality PATO:0045038 normal photosensitivity A degree of pigmentation quality which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality PATO:0045039 normal pigmentation A position which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality PATO:0045040 normal position An angle which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality PATO:0045041 normal angle to A distribution which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality PATO:0045042 normal distribution An elevation which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality PATO:0045043 normal elevation A pressure which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality PATO:0045044 normal pressure A radioactivity which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality PATO:0045045 normal radioactivity A radiopacity which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality PATO:0045046 normal radiopacity A resistance to a stimulus which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality PATO:0045047 normal resistance to A sensitivity to irradiation which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality PATO:0045048 normal sensitivity to irradiation A sensitivity toward an external stimulus which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality PATO:0045049 normal sensitivity toward A size quality which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality PATO:0045050 normal size An area which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality PATO:0045051 normal area A depth quality which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality PATO:0045052 normal depth A height which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality PATO:0045053 normal height A length quality which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality PATO:0045054 normal length A diameter which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality PATO:0045055 normal diameter An anterior-posterior diameter which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality PATO:0045056 normal anterior-posterior diameter A perimeter which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality PATO:0045057 normal perimeter A circumference which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality PATO:0045058 normal circumference A thickness which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality PATO:0045059 normal thickness A volume which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality PATO:0045060 normal volume A width which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality PATO:0045061 normal width A solubility which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality PATO:0045062 normal solubility A speed which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality PATO:0045063 normal speed A strength which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality PATO:0045064 normal strength A fatigability which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality PATO:0045065 normal fatigability A susceptibility toward an external stimulus which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality PATO:0045066 normal susceptibility toward A temperature which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality PATO:0045067 normal temperature A tendency which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality PATO:0045068 normal tendency A threshold which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality PATO:0045069 normal threshold A tolerance to an external stimulus which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality PATO:0045070 normal tolerance to A tonicity which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality PATO:0045071 normal tonicity A turgor which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality PATO:0045072 normal turgor A quality of a process that has a value that is normal or average. Luke Slater 2017-12-21T14:11:01Z quality PATO:0045073 normal process quality A variability which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality PATO:0045074 normal variability A variability of color which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality PATO:0045075 normal variability of color A variability of rate which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality PATO:0045076 normal variability of rate A variability of size which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality PATO:0045077 normal variability of size A variability of temperature which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality PATO:0045078 normal variability of temperature A velocity which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality PATO:0045079 normal velocity A virulence which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality PATO:0045080 normal virulence A viscosity which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality PATO:0045081 normal viscosity A waxiness which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality PATO:0045082 normal waxiness A wetness which is relatively normal or average Luke Slater 2017-12-22T14:16:43Z quality PATO:0045083 normal wetness A duration quality of a process which is relatively normal. quality PATO:0045084 normal duration A duration quality of temperature quality of a process which is relatively normal. quality PATO:0045085 normal duration of temperature An occurrence which is relatively normal. quality PATO:0045086 normal occurrence A frequency which is relatively normal. quality PATO:0045087 normal frequency A sensitivity of a process which is relatively normal. quality PATO:0045088 normal sensitivity of a process A sensitivity of occurrent to oxygen which is relatively normal. quality PATO:0045089 normal sensitivity of a process to oxygen The four cardinal directions or cardinal points are the directions north, east, south, and west, commonly denoted by their initials, N, E, S, W. East and west are at right angles to north and south, with east being in the clockwise direction of rotation from north and west being directly opposite east. Luke Slater 2017-12-22T14:16:43Z quality PATO:0045090 cardinal direction The four cardinal directions or cardinal points are the directions north, east, south, and west, commonly denoted by their initials, N, E, S, W. East and west are at right angles to north and south, with east being in the clockwise direction of rotation from north and west being directly opposite east. Wikipedia:http://en.wikipedia.org/wiki/Cardinal_direction North is one of the four compass points or cardinal directions. It is the opposite of south and is perpendicular to east and west. Luke Slater 2017-12-22T14:16:43Z quality PATO:0045091 north North is one of the four compass points or cardinal directions. It is the opposite of south and is perpendicular to east and west. Wikipedia:http://en.wikipedia.org/wiki/North East is one of the four cardinal directions or points of the compass. It is the opposite direction from west. Luke Slater 2017-12-22T14:16:43Z quality PATO:0045092 east East is one of the four cardinal directions or points of the compass. It is the opposite direction from west. Wikipedia:http://en.wikipedia.org/wiki/East South is one of the four cardinal directions or compass points. South is the polar opposite of north and is perpendicular to east and west. Luke Slater 2017-12-22T14:16:43Z quality PATO:0045093 south South is one of the four cardinal directions or compass points. South is the polar opposite of north and is perpendicular to east and west. Wikipedia:http://en.wikipedia.org/wiki/South West is one of the four cardinal directions or points of the compass. It is the opposite direction from east. Luke Slater 2017-12-22T14:16:43Z quality PATO:0045094 west West is one of the four cardinal directions or points of the compass. It is the opposite direction from east. Wikipedia:http://en.wikipedia.org/wiki/West The number of repeated events per unit time, occurring in a repeating series. (e.g. the number of heart beats occurring over 1 minute) quality PATO:0050000 rate of occurence The number of repeated events per unit time, occurring in a repeating series. (e.g. the number of heart beats occurring over 1 minute) https://orcid.org/0000-0002-9943-9018 The rate of output of a continuous process. Example include: growth rate, cell migration rate, enzyme reaction rate. quality PATO:0050001 rate of continuous process The rate of output of a continuous process. Example include: growth rate, cell migration rate, enzyme reaction rate. https://orcid.org/0000-0002-9943-9018 A spatial distribution of a process in which the process occupies a smaller length, area, or volume than the reference process. For example, heterochromatin may form over a shorter length of a chromosome in a mutant than in wild type. midori 2019-07-29T14:22:24Z quality PATO:0055001 decreased spatial extent of a process A spatial distribution of a process in which the process occupies a smaller length, area, or volume than the reference process. For example, heterochromatin may form over a shorter length of a chromosome in a mutant than in wild type. orcid:0000-0003-4148-4606 A spatial distribution of a process in which the process occupies a greater length, area, or volume than the reference process. For example, heterochromatin may form over a shorter length of a chromosome in a mutant than in wild type. midori 2019-07-29T14:23:31Z quality PATO:0055002 increased spatial extent of a process A spatial distribution of a process in which the process occupies a greater length, area, or volume than the reference process. For example, heterochromatin may form over a shorter length of a chromosome in a mutant than in wild type. https://orcid.org/0000-0003-4148-4606 A rate of occurrence that is relatively high. https://orcid.org/0000-0003-4148-4606 2020-08-19T09:23:19Z quality PATO:0055003 increased rate of occurrence A rate of occurrence that is relatively high. https://orcid.org/0000-0003-4148-4606 A rate of occurrence that is relatively low. https://orcid.org/0000-0003-4148-4606 2020-08-19T09:24:35Z quality PATO:0055004 decreased rate of occurrence A rate of occurrence that is relatively low. https://orcid.org/0000-0003-4148-4606 A rate of output of a continuous process that is relatively high. https://orcid.org/0000-0003-4148-4606 2020-08-19T09:24:56Z quality PATO:0055005 increased rate of continuous process A rate of output of a continuous process that is relatively high. https://orcid.org/0000-0003-4148-4606 A rate of output of a continuous process that is relatively low. https://orcid.org/0000-0003-4148-4606 2020-08-19T09:25:07Z quality PATO:0055006 decreased rate of continuous process A rate of output of a continuous process that is relatively low. https://orcid.org/0000-0003-4148-4606 A quality inhering in a bearer by virtue of the bearer's being present in one sex and absent from the other in members of the same species. http://orcid.org/0000-0002-1373-1705 2019-08-23T08:46:30Z quality PATO:0060001 sex-specific A quality inhering in a bearer by virtue of the bearer's being present in one sex and absent from the other in members of the same species. http://orcid.org/0000-0002-1373-1705 A quality inhering in a bearer by virtue of the bearer's being present in males and absent from females in members of the same species. http://orcid.org/0000-0002-1373-1705 2019-08-23T08:49:59Z quality PATO:0060002 male-specific A quality inhering in a bearer by virtue of the bearer's being present in males and absent from females in members of the same species. http://orcid.org/0000-0002-1373-1705 A quality inhering in a bearer by virtue of the bearer's being present in females and absent from males in members of the same species. http://orcid.org/0000-0002-1373-1705 2019-08-23T08:51:22Z quality PATO:0060003 female-specific A quality inhering in a bearer by virtue of the bearer's being present in females and absent from males in members of the same species. http://orcid.org/0000-0002-1373-1705 The breakdown, disintegration, destruction of an entity due to the breaking of cell membranes by any means. https://orcid.org/0000-0002-3528-5267 quality PATO:0065001 lysed The breakdown, disintegration, destruction of an entity due to the breaking of cell membranes by any means. https://en.wikipedia.org/wiki/Lysis A degree of pigmentation quality that is diversified with patches, or irregularity. https://orcid.org/0000-0002-3528-5267 quality PATO:0065002 patchy pigmentation A degree of pigmentation quality that is diversified with patches, or irregularity. https://medlineplus.gov/ency/article/003224.htm A hermaphroditic quality that inheres in a population or organism where an organism changes is a different sexes during different life stages. https://orcid.org/0000-0001-8815-0078 sequential hermaphroditic quality PATO:0070000 Sequential hermaphrodity is generally characterized by an organism producing female gametes and male gametes during different life stages. sequential hermaphrodite A hermaphroditic quality that inheres in a population or organism where an organism changes is a different sexes during different life stages. http://orcid.org/0000-0002-2908-3327 https://en.wikipedia.org/wiki/Sequential_hermaphroditism https://orcid.org/0000-0001-8815-0078 A cell morphology that inheres in neurons which have a small round soma, a large number of short, smooth, or slightly beaded primary dendrites that give rise to only a few secondary branches, and a branched axon that establishes a dense axonal mesh with thin shafts. http://orcid.org/0000-0001-7258-9596 ilxtr:NeurogliaformPhenotype quality PATO:0070001 neurogliaform morphology A cell morphology that inheres in neurons which have a small round soma, a large number of short, smooth, or slightly beaded primary dendrites that give rise to only a few secondary branches, and a branched axon that establishes a dense axonal mesh with thin shafts. PMID:17122314 A cell morphology that inheres in multipolar neurons with densely branched terminal axonal arborizations that form basket-like structures surrounding and synapsing to the somas of target cells. http://orcid.org/0000-0001-7258-9596 ILX:0101123 ilxtr:BasketPhenotype nifext:3 quality PATO:0070002 basket cell morphology A cell morphology that inheres in multipolar neurons with densely branched terminal axonal arborizations that form basket-like structures surrounding and synapsing to the somas of target cells. WikipediaVersioned:Basket_cell&oldid=951703880 doi:10.1016/b978-0-12-369497-3.10004-4 A basket cell morphology that inheres in neurons with axonal arbors composed of frequent, short, curvy axonal branches that tend to be near their somata and within the same layer. http://orcid.org/0000-0001-7258-9596 ilxtr:SmallBasketPhenotype quality PATO:0070003 small basket cell morphology A basket cell morphology that inheres in neurons with axonal arbors composed of frequent, short, curvy axonal branches that tend to be near their somata and within the same layer. PMID:11884355 A basket cell morphology that inheres in neurons that are large, and typically ascend to give rise to many long horizontally and vertically projecting axon collaterals that traverse neighboring columns and can extend through all cortical layers. http://orcid.org/0000-0001-7258-9596 ilxtr:LargeBasketPhenotype quality PATO:0070004 large basket cell morphology A basket cell morphology that inheres in neurons that are large, and typically ascend to give rise to many long horizontally and vertically projecting axon collaterals that traverse neighboring columns and can extend through all cortical layers. PMID:11884355 A basket cell morphology that inheres in neurons which have simpler dendritic arbors (compared to small or large basket cell morphology), and an axonal plexus of intermediate density, composed of a few long, smooth axonal branches. http://orcid.org/0000-0001-7258-9596 ilxtr:NestBasketPhenotype quality PATO:0070005 nest basket cell morphology A basket cell morphology that inheres in neurons which have simpler dendritic arbors (compared to small or large basket cell morphology), and an axonal plexus of intermediate density, composed of a few long, smooth axonal branches. PMID:11884355 A cell morphology that inheres in neurons which have two principal dendrites that emerge from the soma and begin to branch some distance from it, have few spines, and branch in narrow fields. This is in contrast to bitufted morphology where branching occurs close to the soma. http://orcid.org/0000-0001-7258-9596 ILX:0101312 ilxtr:BipolarPhenotype nifext:2 quality PATO:0070006 This is specific to cortical bipolar cells and are distinguished from retinal bipolar cell morphology which has an axon and dendrite emerging from opposite ends of the soma. cortical bipolar morphology A cell morphology that inheres in neurons which have two principal dendrites that emerge from the soma and begin to branch some distance from it, have few spines, and branch in narrow fields. This is in contrast to bitufted morphology where branching occurs close to the soma. PMID:18568015 doi:10.1016/b978-0-12-369497-3.10004-4 A cell morphology that inheres in neurons which are large and non-spiny, with dendrites radiating in a multipolar or bitufted pattern, often favouring the descending side, and axons that ascend directly from the superficial side of the soma, and travel upward without branching. http://orcid.org/0000-0001-7258-9596 ilxtr:MartinottiPhenotype quality PATO:0070007 Martinotti morphology A cell morphology that inheres in neurons which are large and non-spiny, with dendrites radiating in a multipolar or bitufted pattern, often favouring the descending side, and axons that ascend directly from the superficial side of the soma, and travel upward without branching. doi:10.1016/b978-0-12-369497-3.10004-4 A Martinotti cell morphology that inheres in neurons which have axons that form a horizontal ramification, making it T-shaped. http://orcid.org/0000-0001-7258-9596 'T-shaped' Martinotti morphology quality PATO:0070008 T Martinotti morphology A Martinotti cell morphology that inheres in neurons which have axons that form a horizontal ramification, making it T-shaped. doi:10.1016/b978-0-12-369497-3.10004-4 A Martinotti cell morphology that inheres in neurons which have axons that form a fan-like plexus. http://orcid.org/0000-0001-7258-9596 'fanning-out' Martinotti morphology quality PATO:0070009 fan Martinotti morphology A Martinotti cell morphology that inheres in neurons which have axons that form a fan-like plexus. doi:10.1016/b978-0-12-369497-3.10004-4 A cell morphology that inheres in neurons that have dendritic processes radiating from the cell body forming a star-like shape. http://orcid.org/0000-0001-7258-9596 ILX:0111036 SAO:9271919883 quality PATO:0070010 stellate morphology A cell morphology that inheres in neurons that have dendritic processes radiating from the cell body forming a star-like shape. ISBN:9780123973481 A cell morphology that inheres in neurons which are small and round, and make highly specialized synapses with the axon initial segments of pyramidal neurons, wrapping them with candle-shaped synaptic 'cartridges'. http://orcid.org/0000-0001-7258-9596 ILX:0102028 ilxtr:ChandelierPhenotype nifext:4 quality PATO:0070011 Chandelier cells can be bitufted or multipolar. chandelier cell morphology A cell morphology that inheres in neurons which are small and round, and make highly specialized synapses with the axon initial segments of pyramidal neurons, wrapping them with candle-shaped synaptic 'cartridges'. doi:10.1016/b978-0-12-369497-3.10004-4 Chandelier cells can be bitufted or multipolar. DOI:10.1016/B978-0-12-369497-3.10004-4 A cell morphology that inheres in neurons which have two clusters of primary dendrites that originate directly and extend from opposite ends of the soma, and axons that form a plexus which spreads widely. Compared to the narrow vertical axonal projection of bipolar morphology, and the 'horse-tail' axonal cluster of double boquet cells, bitufted morphology has wide horizontal axonal spans, and branching that occur close to the soma. Their vertical projection is also less extensive and crosses mostly to neighboring layers. http://orcid.org/0000-0001-7258-9596 ilxtr:BituftedPhenotype quality PATO:0070012 bitufted cell morphology A cell morphology that inheres in neurons which have two clusters of primary dendrites that originate directly and extend from opposite ends of the soma, and axons that form a plexus which spreads widely. Compared to the narrow vertical axonal projection of bipolar morphology, and the 'horse-tail' axonal cluster of double boquet cells, bitufted morphology has wide horizontal axonal spans, and branching that occur close to the soma. Their vertical projection is also less extensive and crosses mostly to neighboring layers. PMID:15378039 PMID:18568015 doi:10.1016/b978-0-12-369497-3.10004-4 A cell morphology that inheres in neurons which have spiny basal dendrites and resemble pyramidal cells but lose their apical dendrites as they mature. Their axons nearly always emerge from the descending side of the soma, but often recurve and ascend with arc-like collaterals. http://orcid.org/0000-0001-7258-9596 ilxtr:SpinyStellatePhenotype quality PATO:0070013 spiny stellate cell morphology A cell morphology that inheres in neurons which have spiny basal dendrites and resemble pyramidal cells but lose their apical dendrites as they mature. Their axons nearly always emerge from the descending side of the soma, but often recurve and ascend with arc-like collaterals. doi:10.1016/b978-0-12-369497-3.10004-4 A cell morphology that inheres in neurons which have a pyramidal shaped soma, a single axon, a large apical dendrite and multiple basal dendrites. http://orcid.org/0000-0001-7258-9596 ILX:0109553 SAO:1465673360 quality PATO:0070015 pyramidal family morphology A cell morphology that inheres in neurons which have a pyramidal shaped soma, a single axon, a large apical dendrite and multiple basal dendrites. doi:10.1016/b978-0-12-369497-3.10004-4 A pyramidal family morphology that inheres in neurons which have an apical tree which is oriented parallel to the pia. http://orcid.org/0000-0001-7258-9596 ilxtr:HorizontalPyramidalPhenotype quality PATO:0070016 horizontal pyramidal morphology A pyramidal family morphology that inheres in neurons which have an apical tree which is oriented parallel to the pia. PMID:30715238 A pyramidal family morphology that inheres in neurons which have a standard pyramidal shape with its apical dendrite aligned vertically. http://orcid.org/0000-0001-7258-9596 ilxtr:PyramidalPhenotype pyramidal cell morphology vertical pyramidal morphology quality PATO:0070017 standard pyramidal morphology A pyramidal family morphology that inheres in neurons which have a standard pyramidal shape with its apical dendrite aligned vertically. doi:10.1016/b978-0-12-369497-3.10004-4 A pyramidal cell morphology that inheres in neurons which have a distinct tuft formation, distal from the soma. http://orcid.org/0000-0001-7258-9596 ilxtr:TuftedPyramidalPhenotype quality PATO:0070018 tufted pyramidal morphology A pyramidal cell morphology that inheres in neurons which have a distinct tuft formation, distal from the soma. PMID:30715238 A pyramidal cell morphology that inheres in neurons which lack a clear tuft formation but extend to large radial distances. http://orcid.org/0000-0001-7258-9596 ilxtr:UntuftedPyramidalPhenotype quality PATO:0070019 untufted pyramidal morphology A pyramidal cell morphology that inheres in neurons which lack a clear tuft formation but extend to large radial distances. PMID:30715238 A pyramidal cell morphology that inheres in neurons which lack a tuft formation but extend to small radial distances forming a star-like shape. http://orcid.org/0000-0001-7258-9596 ilxtr:StarPyramidalPhenotype quality PATO:0070020 stellate pyramidal morphology A pyramidal cell morphology that inheres in neurons which lack a tuft formation but extend to small radial distances forming a star-like shape. PMID:30715238 A pyramidal cell morphology that inheres in neurons which have an apical tree which is oriented towards the white matter. http://orcid.org/0000-0001-7258-9596 ilxtr:InvertedPyramidalPhenotype quality PATO:0070021 inverted pyramidal morphology A pyramidal cell morphology that inheres in neurons which have an apical tree which is oriented towards the white matter. PMID:30715238 A cell morphology that inheres in neurons with only one process, a neurite, that extends from the cell body. The neurite then branches to form dendritic and axonal processes. http://orcid.org/0000-0001-7258-9596 quality PATO:0070025 unipolar neuron morphology A cell morphology that inheres in neurons with only one process, a neurite, that extends from the cell body. The neurite then branches to form dendritic and axonal processes. WikipediaVersioned:Unipolar_neuron&oldid=994458581 A cell morphology that inheres in neurons which possess a single axon and many dendrites and dendritic branches. http://orcid.org/0000-0001-7258-9596 ILX:0107196 NLX:378 quality PATO:0070026 multipolar neuron morphology A cell morphology that inheres in neurons which possess a single axon and many dendrites and dendritic branches. WikipediaVersioned:Multipolar_neuron&oldid=1022942606 A cell morphology that inheres in neurons with dendrites that are bidirectional, emerging from opposite ends of the soma, with the two arbors extending in radial or tangential directions. http://orcid.org/0000-0001-7258-9596 quality PATO:0070027 This morphology type is distinct from bitufted cell morphology in that it refers to bitufted dendrite morphology rather than bitufted cell morphology. bitufted dendrite cell morphology A cell morphology that inheres in neurons with dendrites that are bidirectional, emerging from opposite ends of the soma, with the two arbors extending in radial or tangential directions. PMID:18568015 A neuron projection quality that is a characteristic of neurons whose soma is located in the telencephalon and that project to structures outside the telencephalon http://orcid.org/0000-0001-7258-9596 ILX:0770101 ET projecting quality PATO:0070028 extratelencephalic projecting A neuron projection quality that is a characteristic of neurons whose soma is located in the telencephalon and that project to structures outside the telencephalon DOI:10.1101/2020.10.19.343129 A neuron projection quality that is a characteristic of neurons with soma in the cerebral cortex and projections to the thalamus. http://orcid.org/0000-0001-7258-9596 ILX:0770102 CT projecting quality PATO:0070029 corticothalamic projecting A neuron projection quality that is a characteristic of neurons with soma in the cerebral cortex and projections to the thalamus. DOI:10.1101/2020.10.19.343129 A neuron projection quality that is a characteristic of neurons with projections that terminate locally rather than distantly. http://orcid.org/0000-0001-7258-9596 ILX:0770103 NP quality PATO:0070030 near projecting A neuron projection quality that is a characteristic of neurons with projections that terminate locally rather than distantly. DOI:10.1101/2020.10.19.343129 A neuron projection quality that is a characteristic of neurons that project to the medulla oblongata from other brain regions. http://orcid.org/0000-0001-7258-9596 MY projecting quality PATO:0070031 corticomedulla projecting A neuron projection quality that is a characteristic of neurons that project to the medulla oblongata from other brain regions. DOI:10.1101/2020.10.19.343129 A physical quality inhering in a neuron by virtue of the relative location of its soma and the regions to which it projects and makes synaptic contacts in. http://orcid.org/0000-0001-7258-9596 quality PATO:0070033 neuron projection quality A physical quality inhering in a neuron by virtue of the relative location of its soma and the regions to which it projects and makes synaptic contacts in. DOI:10.1101/2020.10.19.343129 A neuron projection quality that is a characteristic of neurons with both soma and projections entirely within the telencephalon. http://orcid.org/0000-0001-7258-9596 ILX:0770100 IT projecting quality PATO:0070034 intratelencephalic projecting A neuron projection quality that is a characteristic of neurons with both soma and projections entirely within the telencephalon. DOI:10.1101/2020.10.19.343129 A quality inhering in a neuron's dendrites by virtue of the bearer's physical composition. http://orcid.org/0000-0001-7258-9596 ILX:0103022 quality PATO:0070036 dendrite quality A dendrite quality inhering in a neuron by virtue of the bearer's dendrite having spines. http://orcid.org/0000-0001-7258-9596 ILX:0110980 quality PATO:0070038 spiny dendrite quality A dendrite quality inhering in a neuron by virtue of the bearer's dendrite having a terminal tuft. http://orcid.org/0000-0001-7258-9596 ILX:0112065 SAO:754373097 quality PATO:0070039 tufted dendrite quality A dendrite quality inhering in a neuron by virtue of the bearer's dendrite having a terminal tuft. ILX:0112065 A dendrite quality inhering in a neuron by virtue of the bearer's dendrite having few or no recognizable dendritic spines. http://orcid.org/0000-0001-7258-9596 ILX:0100932 SAO:128827344 quality PATO:0070040 aspiny dendrite quality A dendrite quality inhering in a neuron by virtue of the bearer's dendrite having few or no recognizable dendritic spines. ILX:0100932 A dendrite quality inhering in a neuron by virtue of the bearer's dendrite having numerous swellings or varicosities along their length. http://orcid.org/0000-0001-7258-9596 ILX:0112263 SAO:1706854098 quality PATO:0070041 varicose dendrite quality A dendrite quality inhering in a neuron by virtue of the bearer's dendrite having numerous swellings or varicosities along their length. ILX:0112263 A cell morphology that inheres in retinal neurons which have two principal fibres, an axon and a dendrite, that emerge from opposite end the soma. http://orcid.org/0000-0001-7258-9596 quality PATO:0070042 This is distinct from cortical bipolar morphology which has two dendrites emerging from opposite ends of the soma, rather than one axon and one dendrite. retinal bipolar morphology A cell morphology that inheres in retinal neurons which have two principal fibres, an axon and a dendrite, that emerge from opposite end the soma. WikipediaVersioned:Retina_bipolar_cell&oldid=1033254616 An osmolarity quality inhering in a bearer by virtue of the total amount of ionic salts dissolved in the bearer. http://orcid.org/0000-0002-3410-4655 2020-10-30T08:08:48Z quality PATO:0085001 salinity An osmolarity quality inhering in a bearer by virtue of the total amount of ionic salts dissolved in the bearer. http://db0nus869y26v.cloudfront.net/en/Salinity https://en.wikipedia.org/wiki/Salinity https://rwu.pressbooks.pub/webboceanography/chapter/5-3-salinity-patterns/ https://www.sciencedirect.com/referencework/9780080983004/treatise-on-geochemistry https://www.sciencedirect.com/science/article/pii/B9780857096807500012 protein CD34 molecule cadherin cadherin-5 transferrin receptor protein 1 vascular endothelial growth factor receptor vascular endothelial growth factor receptor 2 fibroblast growth factor 8 sonic hedgehog protein T-cell acute lymphocytic leukemia protein 1 amino acid chain system An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity. uberon UBERON:0000000 processual entity An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity. span:ProcessualEntity FBbt:00005157 chemosensory sensory organ uberon UBERON:0000005 chemosensory organ chemosensory sensory organ FBbt:00005157 A layer of dense irregular connective tissue that lines organs and supports the mucosa, as well as joins the mucosa to the bulk of underlying smooth muscle. [WP,unvetted]. submucosal BTO:0002107 FMA:85391 FMA:85392 NCIT:C13167 SCTID:68439008 UMLS:C0225344 Wikipedia:Submucosa organ submucosa region of submucosa submucosa of organ submucosa of region of organ uberon submucous layer tela submucosa tunica submucosa UBERON:0000009 submucosa http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png A layer of dense irregular connective tissue that lines organs and supports the mucosa, as well as joins the mucosa to the bulk of underlying smooth muscle. [WP,unvetted]. Wikipedia:Submucosa UMLS:C0225344 ncithesaurus:Submucosa organ submucosa FMA:85391 region of submucosa FMA:85392 submucosa of organ FMA:85391 submucosa of region of organ FMA:85392 submucous layer BTO:0002107 tela submucosa BTO:0002107 A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands. Nervous structures including ganglia outside of the central nervous system. Kimmel et al, 1995.[TAO] Part of nervous system in which nerves extend throughout the body outside of the brain and spinal cord.[AAO] The peripheral nervous system (PNS) is the part of the nervous system connected to the CNS which contains cranial nerves III - XII, spinal, peripheral and autonomic nerves. (CUMBO) (...) specific vertebrate traits within the chordate phylum such as skeletal tissues, PNS, and spectacular head and brain development, are linked to the NC (neural crest) and its derivatives.[well established][VHOG] PNS AAO:0000429 BAMS:PNS BILA:0000081 BIRNLEX:1111 BTO:0001028 CALOHA:TS-0808 EFO:0000891 EHDAA2:0001445 EHDAA:2893 EMAPA:16665 EV:0100335 FBbt:00005098 FMA:9903 GAID:715 MA:0000218 MAT:0000338 MESH:D017933 MIAA:0000338 NCIT:C12465 SCTID:362292005 TAO:0000142 UMLS:C0206417 UMLS:C1305921 VHOG:0000399 Wikipedia:Peripheral_nervous_system XAO:0000178 ZFA:0000142 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=3232 pars peripherica systema nervosum periphericum uberon UBERON:0000010 peripheral nervous system http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png cjm A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands. GO:0007422 Nervous structures including ganglia outside of the central nervous system. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000142 TAO ZFIN:curator Part of nervous system in which nerves extend throughout the body outside of the brain and spinal cord.[AAO] 2012-06-20 AAO:0000429 AAO AAO:BJB The peripheral nervous system (PNS) is the part of the nervous system connected to the CNS which contains cranial nerves III - XII, spinal, peripheral and autonomic nerves. (CUMBO) http://neurolex.org/wiki/Cumbo_terms (...) specific vertebrate traits within the chordate phylum such as skeletal tissues, PNS, and spectacular head and brain development, are linked to the NC (neural crest) and its derivatives.[well established][VHOG] 2012-09-17 VHOG:0000399 VHOG DOI:10.1007/978-0-387-46954-6_6 Dupin E, Creuzet S, Le Douarin NM, The contribution of the neural crest to the vertebrate body. Advances in experimental medicine and biology (2006) http://bgee.unil.ch/ PNS UMLS:C0206417 BIRNLEX:1111 UMLS:C0206417 ncithesaurus:Peripheral_Nervous_System UMLS:C1305921 BIRNLEX:1111 pars peripherica FMA:9903 FMA:TA Wikipedia:Peripheral_nervous_system systema nervosum periphericum FMA:9903 FMA:TA Wikipedia:Peripheral_nervous_system Part of peripheral nervous system that includes the somatic parts of the cranial and spinal nerves and their ganglia and the peripheral sensory receptors. EFO:0000892 FMA:9904 MA:0002850 MAT:0000099 MIAA:0000099 NLXANAT:100301 Wikipedia:Somatic_nervous_system PNS - somatic somatic nervous system, somatic division somatic part of peripheral nervous system somatic peripheral nervous system uberon UBERON:0000012 somatic nervous system cjm Part of peripheral nervous system that includes the somatic parts of the cranial and spinal nerves and their ganglia and the peripheral sensory receptors. NLXANAT:100301 somatic nervous system, somatic division NLXANAT:100301 somatic part of peripheral nervous system UBERON:cjm somatic peripheral nervous system NLXANAT:100301 The sympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system (the other being the parasympathetic nervous system). The sympathetic preganglionic neurons have their cell bodies in the thoracic and lumbar regions of the spinal cord and connect to the paravertebral chain of sympathetic ganglia. Innervate heart and blood vessels, sweat glands, viscera and the adrenal medulla. Most sympathetic neurons, but not all, use noradrenaline as a post-ganglionic neurotransmitter [GO]. Part of the autonomic nervous system which has opposing physiological effects of the parasympathetic nervous system. Examples include increasing the heart rate or constricting the blood vessels.[AAO] The part of the autonomic nervous system which chiefly contains adrenergic fibres and tends to control and reduce secretions, decrease the contractility and hence the tone of smooth muscles and provoke the contraction of blood vessels. Essentially, it consists of preganglionic fibres from the thoracic and upper lumbar parts of the spinal cord. These fibres, by means of delicate rami communicantes, cross over to ganglia sited in a pair of ganglionated cords on each side of the vertebral column or to more peripheral ganglia. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] The autonomic nervous system is composed of three divisions: the sympathetic division, the parasympathetic division, and the enteric division. (...) In ray-finned teleost fishes, a sympathetic chain is present, and dual innervation of additional organs can be observed. A similar pattern can be found in amphibians (...). The evolution of the autonomic nervous system has been quite conservative, especially in the tetrapod lineage.[well established][VHOG] has developmental contribution from NC in verteberates (https://github.com/obophenotype/uberon/wiki/The-neural-crest) AAO:0010487 BIRNLEX:2516 BTO:0001832 CALOHA:TS-2050 EFO:0000893 EHDAA2:0001971 EHDAA:3769 EMAPA:16985 FMA:9906 GAID:710 MA:0000225 MESH:D013564 MIAA:0000100 NCIT:C12795 SCTID:362484004 TAO:0001576 UMLS:C0039044 UMLS:C1269646 VHOG:0000384 Wikipedia:Sympathetic_nervous_system ZFA:0001576 pars sympathica divisionis autonomici systematis nervosi sympathetic nervous system sympathetic part of autonomic division of nervous system uberon pars sympathica divisionis autonomici systematis nervosi UBERON:0000013 sympathetic nervous system http://upload.wikimedia.org/wikipedia/commons/7/77/Gray838.png cjm FMA MA ZFA-modified-from-isa The sympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system (the other being the parasympathetic nervous system). The sympathetic preganglionic neurons have their cell bodies in the thoracic and lumbar regions of the spinal cord and connect to the paravertebral chain of sympathetic ganglia. Innervate heart and blood vessels, sweat glands, viscera and the adrenal medulla. Most sympathetic neurons, but not all, use noradrenaline as a post-ganglionic neurotransmitter [GO]. GO:0048485 Part of the autonomic nervous system which has opposing physiological effects of the parasympathetic nervous system. Examples include increasing the heart rate or constricting the blood vessels.[AAO] 2012-06-20 AAO:0010487 AAO AAO:BJB The part of the autonomic nervous system which chiefly contains adrenergic fibres and tends to control and reduce secretions, decrease the contractility and hence the tone of smooth muscles and provoke the contraction of blood vessels. Essentially, it consists of preganglionic fibres from the thoracic and upper lumbar parts of the spinal cord. These fibres, by means of delicate rami communicantes, cross over to ganglia sited in a pair of ganglionated cords on each side of the vertebral column or to more peripheral ganglia. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000384 VHOG http://bgee.unil.ch/ The autonomic nervous system is composed of three divisions: the sympathetic division, the parasympathetic division, and the enteric division. (...) In ray-finned teleost fishes, a sympathetic chain is present, and dual innervation of additional organs can be observed. A similar pattern can be found in amphibians (...). The evolution of the autonomic nervous system has been quite conservative, especially in the tetrapod lineage.[well established][VHOG] 2012-09-17 VHOG:0000384 VHOG ISBN:978-0471210054 Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.461-463 http://bgee.unil.ch/ UMLS:C0039044 BIRNLEX:2516 UMLS:C0039044 ncithesaurus:Sympathetic_Nervous_System UMLS:C1269646 BIRNLEX:2516 pars sympathica divisionis autonomici systematis nervosi FMA:9906 FMA:TA pars sympathica divisionis autonomici systematis nervosi Wikipedia:Sympathetic_nervous_system Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis. Note the distinction between the entire skin of the body, of which there is only 1 in an organism, and zones of skin, of which there can be many. Examples: skin of knee (...) it is well-established that neural crest cells contribute to both the dermal skeleton (craniofacial bone, teeth, and the caudal fin rays of teleosts) and the integument, including craniofacial dermis and all pigment cells outside the retina (...).[well established][VHOG] we assume that mouse, HOG and GAID all mean zone of skin when they say skin. We also choose skin as an exact synonym, as it is more intuitive EHDAA2:0001844 EHDAA:6530 EMAPA:17525 EV:0100152 FMA:86166 GAID:933 MA:0000151 MAT:0000284 MESH:D012867 MIAA:0000284 OpenCyc:Mx4rvVjX3ZwpEbGdrcN5Y29ycA SCTID:20795001 VHOG:0000860 Wikipedia:Skin portion of skin region of skin skin skin region skin zone uberon UBERON:0000014 zone of skin http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg http://upload.wikimedia.org/wikipedia/commons/e/e8/HumanSkinDiagram.jpg FMA Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis. Wikipedia:Skin http://orcid.org/0000-0002-6601-2165 (...) it is well-established that neural crest cells contribute to both the dermal skeleton (craniofacial bone, teeth, and the caudal fin rays of teleosts) and the integument, including craniofacial dermis and all pigment cells outside the retina (...).[well established][VHOG] 2012-09-17 VHOG:0000860 VHOG DOI:10.1111/j.1469-7580.2008.01043.x Vickaryous MK, Sire JY, The integumentary skeleton of tetrapods: origin, evolution, and development. J Anat (2009) http://bgee.unil.ch/ skin MA:0000151 A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures. AEO:0000192 CARO:0000010 FMA:50705 anatomical boundary uberon UBERON:0000015 Except in the case of abstracted fiat boundaries such as the midline plane of an organism, all 2D anatomical entities have a 3 dimensional projection. For example, the surface of the shell of a muscle has a distinct shape that projects into the third dimension. Note that boundaries are 2D structures. They have no thickness - and so can not be sites of gene expression or gene product localisation. For this, use boundary region terms. non-material anatomical boundary CARO A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures. CARO:0000010 anatomical boundary CARO:0000010 An organ of sight that includes the camera-type eyeball and supporting structures such as the lacrimal apparatus, the conjunctiva, the eyelid. A cavitated compound organ that transduces light waves into neural signals.[TAO] The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] FMA distinguishes Eye (subdivision of face) which has its parts an Eyeball (organ), as well as other structures, and the orbit of skull. MA includes eyelid, conjunctiva and lacrimal apparatus as part of MA:eye - consistent with FMA - so we can infer that MA:eye is more like FMA:eye than FMA:eyeball. For other AOs this distinction is less meaningful - e.g. ZFA has no eyelid; XAO has no eyelid, but it has conjuctiva, which is considered part of the xao:eye. GO considers eyelid development part of eye development. See also notes on optic nerve - XAO, AAO and BTO consider this part of the eye. MA considers the eye muscles part of the eye, whereas FMA has a class 'orbital content' for this eye AAO:0010340 BIRNLEX:1169 BTO:0004688 EHDAA2:0000484 EHDAA:936 EMAPA:16198 FMA:54448 MA:0000261 NCIT:C12401 OpenCyc:Mx8Ngx4rwKSh9pwpEbGdrcN5Y29ycB4rvVil5pwpEbGdrcN5Y29ycB4rvViTvpwpEbGdrcN5Y29ycA SCTID:181143004 TAO:0000107 UMLS:C0015392 UMLS:C1280202 VHOG:0000275 XAO:0000179 ZFA:0000107 regio orbitalis vertebrate eye uberon camera-type eye plus associated structures eyes orbital part of face orbital region UBERON:0000019 camera-type eye definitional An organ of sight that includes the camera-type eyeball and supporting structures such as the lacrimal apparatus, the conjunctiva, the eyelid. GO:0043010 https://orcid.org/0000-0002-6601-2165 A cavitated compound organ that transduces light waves into neural signals.[TAO] 2012-08-14 TAO:0000107 TAO TAO:wd The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] 2012-09-17 VHOG:0000275 VHOG DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007) http://bgee.unil.ch/ FMA distinguishes Eye (subdivision of face) which has its parts an Eyeball (organ), as well as other structures, and the orbit of skull. MA includes eyelid, conjunctiva and lacrimal apparatus as part of MA:eye - consistent with FMA - so we can infer that MA:eye is more like FMA:eye than FMA:eyeball. For other AOs this distinction is less meaningful - e.g. ZFA has no eyelid; XAO has no eyelid, but it has conjuctiva, which is considered part of the xao:eye. GO considers eyelid development part of eye development. See also notes on optic nerve - XAO, AAO and BTO consider this part of the eye. MA considers the eye muscles part of the eye, whereas FMA has a class 'orbital content' for this FMA eye FMA:54448 UMLS:C0015392 BIRNLEX:1169 UMLS:C0015392 ncithesaurus:Eye UMLS:C1280202 BIRNLEX:1169 regio orbitalis FMA:54448 FMA:TA eyes TAO:0000107 orbital part of face FMA:54448 orbital region FMA:54448 An organ that is capable of transducing sensory stimulus to the nervous system. AEO:0000094 BSA:0000121 BTO:0000202 CALOHA:TS-2043 EHDAA2:0001824 EHDAA:500 EMAPA:35955 FBbt:00005155 GAID:63 HAO:0000930 MA:0000017 MESH:D012679 NCIT:C33224 SCTID:244485009 UMLS:C0935626 VHOG:0001407 WBbt:0006929 organ of sense organ system organ of sensory organ system organ of sensory system sense organ system organ sensory organ sensory organ system organ sensory system organ sensillum uberon Sinnesorgan sensor UBERON:0000020 sense organ http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png An organ that is capable of transducing sensory stimulus to the nervous system. https://github.com/obophenotype/uberon/issues/549 https://orcid.org/0000-0002-6601-2165 UMLS:C0935626 ncithesaurus:Organ_of_the_Special_Sense organ of sense organ system OBOL:accepted organ of sensory organ system OBOL:accepted organ of sensory system OBOL:accepted sense organ system organ OBOL:automatic sensory organ system organ OBOL:automatic sensory system organ OBOL:accepted sensillum WBbt:0006929 Sinnesorgan BTO:0000202 Appendage that is shaped in order to produce lift for flight through the air. alar This class is not monophyletic. See also: GO:0007629 BTO:0001463 EFO:0000885 GAID:1217 MAT:0000202 MESH:D014921 MIAA:0000202 Wikipedia:Wing aliform appendage uberon UBERON:0000023 wing Appendage that is shaped in order to produce lift for flight through the air. http://orcid.org/0000-0002-6601-2165 bgee Wikipedia:Flying_fish bgee bgee bgee bgee we do not consider flying frogs to have wings bgee bgee bgee bgee bgee bgee aliform appendage http://orcid.org/0000-0002-6601-2165 Any hollow cylindrical anatomical structure containing a lumen through which substances are transported. not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts) tubular galen:Tube anatomical tube duct uberon UBERON:0000025 tube Any hollow cylindrical anatomical structure containing a lumen through which substances are transported. http://orcid.org/0000-0002-6601-2165 Major subdivision of an organism that protrudes from the body[DOS, CARO]. An appendage is an external body part, or natural prolongation, that protrudes from an organism's body, such as a vertebrate's limbs[BILA][BILA:0000018]. Organ or organ part that is attached to the body of an organism. For example a limb[GO, modified][GO:0048736]. appendicular this is currently a subtype of organism subdivision - which would exclude feathers AEO:0000193 BILA:0000018 BTO:0001492 CARO:0010003 EFO:0000799 EHDAA2:0003193 EMAPA:37283 EV:0100155 FBbt:00007000 HAO:0000144 MAT:0000023 MESH:D005121 MIAA:0000023 NCIT:C61460 OpenCyc:Mx4rvViC-JwpEbGdrcN5Y29ycA UMLS:C0598782 VSAO:0000075 Wikipedia:Appendage XAO:0000218 uberon appendages extremitaet extremity limbs/digits/tail UBERON:0000026 appendage Major subdivision of an organism that protrudes from the body[DOS, CARO]. CARO:DOS An appendage is an external body part, or natural prolongation, that protrudes from an organism's body, such as a vertebrate's limbs[BILA][BILA:0000018]. BILA:0000018 Organ or organ part that is attached to the body of an organism. For example a limb[GO, modified][GO:0048736]. GO:0048736 EMAPA:37283 MA:th UMLS:C0598782 ncithesaurus:Appendage appendages XAO:0000218 extremitaet BTO:0001492 limbs/digits/tail MP:0000001 A thin layer of loose connective tissue which lies beneath the epithelium and together with the epithelium constitutes the mucosa[WP]. The lamina propria contains capillaries and a central lacteal (lymph vessel) in the small intestine, as well as lymphoid tissue. Lamina propria also contains glands with the ducts opening on to the mucosal epithelium, that secrete mucus and serous secretions. BTO:0002330 FMA:62517 NCIT:C32918 SCTID:298225002 UMLS:C1179187 Wikipedia:Lamina_propria lamina propria mucosa lamina propria mucosae uberon tunica propria UBERON:0000030 lamina propria GI:Organization.svg A thin layer of loose connective tissue which lies beneath the epithelium and together with the epithelium constitutes the mucosa[WP]. The lamina propria contains capillaries and a central lacteal (lymph vessel) in the small intestine, as well as lymphoid tissue. Lamina propria also contains glands with the ducts opening on to the mucosal epithelium, that secrete mucus and serous secretions. Wikipedia:Lamina_propria UMLS:C1179187 ncithesaurus:Lamina_Propria tunica propria BTO:0002330 A lamina propria that is part of a respiratory airway. EMAPA:35877 FMA:265157 MA:0001858 NCIT:C49305 UMLS:C1710457 lamina propria mucosa of trachea lamina propria mucosa of windpipe lamina propria mucosae of trachea lamina propria mucosae of windpipe lamina propria of windpipe trachea lamina propria trachea lamina propria mucosa trachea lamina propria mucosae tracheal lamina propria windpipe lamina propria windpipe lamina propria mucosa windpipe lamina propria mucosae uberon UBERON:0000031 lamina propria of trachea true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships A lamina propria that is part of a respiratory airway. OBOL:automatic UMLS:C1710457 ncithesaurus:Trachea_Lamina_Propria lamina propria mucosa of trachea OBOL:automatic lamina propria mucosa of windpipe OBOL:automatic lamina propria mucosae of trachea OBOL:automatic lamina propria mucosae of windpipe OBOL:automatic lamina propria of windpipe OBOL:automatic trachea lamina propria mucosa OBOL:automatic trachea lamina propria mucosae OBOL:automatic windpipe lamina propria OBOL:automatic windpipe lamina propria mucosa OBOL:automatic windpipe lamina propria mucosae OBOL:automatic The head is the anterior-most division of the body [GO]. Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO] Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO] Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG] AAO:0010335 AEO:0000106 BILA:0000115 BIRNLEX:1230 BTO:0000282 CALOHA:TS-0436 EFO:0000964 EHDAA2:0003106 EMAPA:31858 FBbt:00000004 FMA:7154 GAID:61 HAO:0000397 MA:0000023 MAT:0000294 MESH:D006257 MIAA:0000294 NCIT:C12419 OpenCyc:Mx4rEOLm4rgPEdmAAAACs6hRjg OpenCyc:Mx4rvVi6YJwpEbGdrcN5Y29ycA SCTID:302548004 SPD:0000016 TAO:0001114 TGMA:0000002 UMLS:C0018670 VHOG:0001644 WBbt:0005739 Wikipedia:Head XAO:0003024 ZFA:0001114 galen:Head head (volume) adult head uberon cephalic area UBERON:0000033 head The head is the anterior-most division of the body [GO]. GO:0060322 Wikipedia:Head Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO] 2012-06-20 AAO:0010335 AAO AAO:BJB Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO] 2012-08-14 TAO:0001114 TAO ZFIN:curator Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG] 2012-09-17 VHOG:0001644 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.82 http://bgee.unil.ch/ UMLS:C0018670 BIRNLEX:1230 UMLS:C0018670 ncithesaurus:Head head (volume) FMA:7154 cephalic area SPD:0000016 multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer. A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO] a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP] in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA. FMA:9581 GAID:19 MESH:D012704 NCIT:C13169 SCTID:362878009 TAO:0005425 UMLS:C0036760 Wikipedia:Serous_membrane ZFA:0005425 tunica serosa wall of serous sac uberon serosa UBERON:0000042 serous membrane http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer. Wikipedia:Serous_membrane https://github.com/obophenotype/uberon/issues/86 A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO] 2012-08-14 TAO:0005425 TAO Wikipedia:Serous_membrane a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP] Wikipedia:Serous_membrane in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA. FMA UMLS:C0036760 ncithesaurus:Serosa tunica serosa FMA:9581 wall of serous sac FMA:9581 serosa Wikipedia:Serous_membrane Dense regular connective tissue that connects muscle to bone[VSAO]. Dense regular connective tissue that connects muscle to bone.[VSAO] Phylogenetically, tendinous tissue first appears in the invertebrate chordate Branchiostoma as myosepta. This two-dimensional array of collagen fibers is highly organized, with fibers running along two primary axes. In hagfish the first linear tendons appear and the myosepta have developed specialized regions with unidirectional fiber orientation - a linear tendon within the flat sheet of myoseptum.[well established][VHOG] in FMA, tendon is an organ component that with parts dense-irregular-connective-tissue of tendon and dense-irregular-connective-tissue of tendon sheath; we follow VSAO in making it a subtype of the former. In VSAO tendons connect muscle to bone; in WP the def states integument (e.g. auricular muscles) - but JB confirms this is not actually tendon but aponeurosis AEO:0000091 BTO:0001356 CALOHA:TS-1021 EHDAA2:0003091 EMAPA:35854 EV:0100149 FMA:9721 GAID:276 MA:0000115 MESH:D013710 NCIT:C13045 OpenCyc:Mx4rvVjefJwpEbGdrcN5Y29ycA SCTID:256667004 UMLS:C0039508 VHOG:0001286 VSAO:0000073 Wikipedia:Tendon XAO:0000173 ZFA:0005647 galen:Tendon uberon sinew tendo UBERON:0000043 tendon http://upload.wikimedia.org/wikipedia/commons/3/3c/Achilles-tendon.jpg VSAO OG AEO Dense regular connective tissue that connects muscle to bone[VSAO]. GO_REF:0000034 VSAO:0000073 Wikipedia:Tendon http://dx.plos.org/10.1371/journal.pone.0051070 Dense regular connective tissue that connects muscle to bone.[VSAO] 2012-08-14 VSAO:0000073 VSAO PSPUB:0000170 Phylogenetically, tendinous tissue first appears in the invertebrate chordate Branchiostoma as myosepta. This two-dimensional array of collagen fibers is highly organized, with fibers running along two primary axes. In hagfish the first linear tendons appear and the myosepta have developed specialized regions with unidirectional fiber orientation - a linear tendon within the flat sheet of myoseptum.[well established][VHOG] 2012-09-17 VHOG:0001286 VHOG DOI:10.1016/S1095-6433(02)00241-6 Summers AP, Koob TJ, The evolution of tendon - morphology and material properties. Comparative Biochemistry and Physiology-Part A: Molecular and Integrative Physiology (2002) http://bgee.unil.ch/ in FMA, tendon is an organ component that with parts dense-irregular-connective-tissue of tendon and dense-irregular-connective-tissue of tendon sheath; we follow VSAO in making it a subtype of the former. In VSAO tendons connect muscle to bone; in WP the def states integument (e.g. auricular muscles) - but JB confirms this is not actually tendon but aponeurosis FMA UMLS:C0039508 ncithesaurus:Tendon sinew Wikipedia:Tendon tendo Wikipedia:Tendon A biological tissue mass, most commonly a mass of nerve cell bodies. TODO - check vert vs invert. Other species: Any of a number of aggregations of neurons, glial cells and their processes, surrounded by a glial cell and connective tissue sheath (plural: ganglia). // Subdivision of neural tree (organ) which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord); together with a nucleus and its associated nerve, it constitutes a neural tree (organ). Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion. // a cluster of nerve cells and associated glial cells (nuclear location) // Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system. A ganglion is a cluster of neurons. It is part of a nervous system. It may include glial cells. The neurons are arranged in a specific constellation: neuronal somata are concentrated at the surface, thus forming a cell cortex, and neurites are concentrated in the centre of the ganglion to form the neuropil. A ganglion is a distinct unit but several ganglia may be anterio-posteriorly joined by connectives or transversally by commissures Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system.[AAO] Structures containing a collection of nerve cell bodies. (Source: BioGlossary, www.Biology-Text.com)[TAO] Subdivision of nervous system which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord. Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion (adapted from Foundational Model of Anatomy)[NLXANAT:100302]. Cranial sensory placodes are focused areas of the head ectoderm of vertebrates that contribute to the development of the cranial sense organs and their associated ganglia. Placodes have long been considered a key character of vertebrates, and their evolution is proposed to have been essential for the evolution of an active predatory lifestyle by early vertebrates.[well established][VHOG] ganglionic AAO:0010426 AEO:0000135 BAMS:G BTO:0000497 CALOHA:TS-0397 EFO:0000899 EHDAA2:0003135 EHDAA:2897 EHDAA:4662 EHDAA:5621 EHDAA:918 EMAPA:32846 EV:0100372 FBbt:00005137 FMA:5884 MA:0002406 MAT:0000207 MAT:0000343 MESH:D005724 MIAA:0000207 MIAA:0000343 NCIT:C12719 NLXANAT:100302 TAO:0000190 TGMA:0001016 UMLS:C0017067 VHOG:0000156 WBbt:0005189 Wikipedia:Ganglion XAO:0000209 ZFA:0000190 uberon ganglia neural ganglion UBERON:0000045 ganglion https://github.com/obophenotype/uberon/issues/702 EHDAA2 Bgee:AN A biological tissue mass, most commonly a mass of nerve cell bodies. Wikipedia:Ganglion https://github.com/obophenotype/uberon/issues/300 A ganglion is a cluster of neurons. It is part of a nervous system. It may include glial cells. The neurons are arranged in a specific constellation: neuronal somata are concentrated at the surface, thus forming a cell cortex, and neurites are concentrated in the centre of the ganglion to form the neuropil. A ganglion is a distinct unit but several ganglia may be anterio-posteriorly joined by connectives or transversally by commissures PMID:21062451 Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system.[AAO] 2012-06-20 AAO:0010426 AAO AAO:EJS Structures containing a collection of nerve cell bodies. (Source: BioGlossary, www.Biology-Text.com)[TAO] 2012-08-14 TAO:0000190 TAO ZFIN:curator Subdivision of nervous system which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord. Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion (adapted from Foundational Model of Anatomy)[NLXANAT:100302]. NLXANAT:100302 Cranial sensory placodes are focused areas of the head ectoderm of vertebrates that contribute to the development of the cranial sense organs and their associated ganglia. Placodes have long been considered a key character of vertebrates, and their evolution is proposed to have been essential for the evolution of an active predatory lifestyle by early vertebrates.[well established][VHOG] 2012-09-17 VHOG:0000156 VHOG DOI:10.1016/j.ydbio.2005.02.021 Mazet F, Hutt JA, Milloz J, Millard J, Graham A, Shimeld SM, Molecular evidence from Ciona intestinalis for the evolutionary origin of vertebrate sensory placodes. Developmental Biology (2005) http://bgee.unil.ch/ UMLS:C0017067 ncithesaurus:Ganglion neural ganglion BTO:0000497 An eye with one concave chamber. Note that 'simple' does not imply a reduced level of complexity or acuity. TGMA:0000729 Wikipedia:Eye#Simple_eyes uberon UBERON:0000047 simple eye An eye with one concave chamber. Note that 'simple' does not imply a reduced level of complexity or acuity. Wikipedia:Eye#Simple_eyes A tubular structure that contains, conveys body fluid, such as blood or lymph. uberon UBERON:0000055 vessel A tubular structure that contains, conveys body fluid, such as blood or lymph. https://orcid.org/0000-0002-6601-2165 A tubular structure that transports secreted or excreted substances. A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171]. Most ducts, but not all, are exocrine gland ducts. Some ontologies classify structures such as the oviduct here. AAO:0011123 FBbt:00100314 FMA:30320 NCIT:C12948 SCTID:91726008 TAO:0005171 UMLS:C0687028 Wikipedia:Duct_(anatomy) XAO:0004000 ZFA:0005171 galen:Duct anatomical duct exocrine duct exocrine gland duct uberon ducts UBERON:0000058 duct A tubular structure that transports secreted or excreted substances. http://orcid.org/0000-0002-6601-2165 http://www.siumed.edu/~dking2/intro/glands.htm#ducts A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171]. ZFA:0005171 UMLS:C0687028 ncithesaurus:Duct ducts XAO:0004000 A subdivision of the digestive tract that connects the small intestine to the cloaca or anus. Lacks or has few villi[Kardong]. Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG] AAO:0010396 BTO:0000706 CALOHA:TS-1306 EFO:0000840 EMAPA:19252 EV:0100077 FMA:7201 GAID:306 MA:0000333 MESH:A03.492.411.495 MIAA:0000046 NCIT:C12379 OpenCyc:Mx4rvVkF5pwpEbGdrcN5Y29ycA SCTID:181254001 UMLS:C0021851 VHOG:0000054 Wikipedia:Large_intestine_(anatomy) XAO:0000131 galen:LargeIntestine uberon intestinum crassum UBERON:0000059 large intestine cjm A subdivision of the digestive tract that connects the small intestine to the cloaca or anus. Lacks or has few villi[Kardong]. ISBN:0073040584 Wikipedia:Large_intestine_(anatomy) Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG] 2012-09-17 VHOG:0000054 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.566 http://bgee.unil.ch/ UMLS:C0021851 ncithesaurus:Large_Intestine intestinum crassum BTO:0000706 Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers. in FMA, serosa is a wall UBERON:0009915 wall EMAPA:25036 FMA:82482 galen:Wall wall of organ uberon organ wall UBERON:0000060 anatomical wall Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers. FMA:82482 in FMA, serosa is a wall FMA wall of organ FMA:82482 organ wall FMA:82482 Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. AAO:0010825 AEO:0000003 BILA:0000003 CARO:0000003 EHDAA2:0003003 EMAPA:0 FBbt:00007001 FMA:305751 FMA:67135 GAID:781 HAO:0000003 MA:0003000 MESH:D000825 SCTID:362889002 TAO:0000037 TGMA:0001823 VHOG:0001759 XAO:0003000 ZFA:0000037 http://dbpedia.org/ontology/AnatomicalStructure biological structure connected biological structure uberon UBERON:0000061 anatomical structure Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. CARO:0000003 connected biological structure CARO:0000003 Anatomical structure that performs a specific function or group of functions [WP]. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4 BIRNLEX:4 CARO:0020004 EFO:0000634 EMAPA:35949 ENVO:01000162 FMA:67498 MA:0003001 NCIT:C13018 OpenCyc:Mx4rv5XMb5wpEbGdrcN5Y29ycA OpenCyc:Mx4rwP3iWpwpEbGdrcN5Y29ycA SCTID:272625005 UMLS:C0178784 WBbt:0003760 Wikipedia:Organ_(anatomy) uberon anatomical unit body organ element UBERON:0000062 organ Anatomical structure that performs a specific function or group of functions [WP]. Wikipedia:Organ_(anatomy) Wikipedia Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. GO:0048513 UMLS:C0178784 ncithesaurus:Organ element http://orcid.org/0000-0002-6601-2165 A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity. FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball. Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal. FMA:86140 uberon organ region with fixed fiat boundary organ segment segment of organ UBERON:0000063 organ subunit A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity. http://orcid.org/0000-0002-6601-2165 Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball. FMA:86140 3 Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal. FMA:86140 1 organ region with fixed fiat boundary FMA:86140 organ segment FMA:86140 segment of organ FMA:86140 A multicellular structure that is a part of an organ. currently defined in a very broad sense, may be replaced by more specific classes in the future AAO:0011124 BIRNLEX:16 EFO:0000635 FMA:82472 SCTID:113343008 SCTID:91717005 cardinal organ part uberon regional part of organ UBERON:0000064 organ part A multicellular structure that is a part of an organ. http://orcid.org/0000-0002-6601-2165 cardinal organ part FMA:82472 regional part of organ BIRNLEX:16 Anatomical structure that is part of the respiratory system. In mammals consists of upper and lower tracts EHDAA2:0001606 EHDAA:1568 EHDAA:2219 EMAPA:16737 FMA:265130 OpenCyc:Mx4rvvM--pwpEbGdrcN5Y29ycA SCTID:361110005 VHOG:0000393 uberon UBERON:0000065 respiratory tract NCBIBook:NBK10107 Anatomical structure that is part of the respiratory system. In mammals consists of upper and lower tracts https://orcid.org/0000-0002-6601-2165 The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage. adult stage BTO:0001043 BilaDO:0000004 EFO:0001272 FBdv:00005369 WBls:0000041 XtroDO:0000084 fully formed animal stage juvenile-adult stage uberon UBERON:0000066 fully formed stage https://github.com/obophenotype/uberon/issues/566 The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage. https://orcid.org/0000-0002-6601-2165 A life cycle stage that starts with fertilization and ends with the fully formed embryo. BilaDO:0000002 EV:0300001 FBdv:00005289 FMA:72652 HsapDv:0000002 MmusDv:0000002 OGES:000000 OGES:000022 SCTID:296280003 WBls:0000003 WBls:0000092 WBls:0000102 XAO:1000012 embryonic stage uberon embryogenesis UBERON:0000068 embryo stage A life cycle stage that starts with fertilization and ends with the fully formed embryo. http://orcid.org/0000-0002-6601-2165 End of the life of an organism. ncit:Death is an outcome XAO:0000437 XtroDO:0000085 uberon death UBERON:0000071 death stage End of the life of an organism. XAO:0000437 ncit:Death is an outcome ncit An section of a respiratory tract. MA:0000434 has subclasses upper and lower, so it corresponds to a segment of the tract, rather than the tract as a whole EMAPA:16737 FMA:45660 MA:0000434 uberon respiratory tract subdivision of respiratory tract UBERON:0000072 proximo-distal subdivision of respiratory tract An section of a respiratory tract. http://orcid.org/0000-0002-6601-2165 MA:0000434 has subclasses upper and lower, so it corresponds to a segment of the tract, rather than the tract as a whole MA respiratory tract MA:0000434 Any part or collection of parts of the central or peripheral nervous system. Parts may span both CNS and PNS. Melissa Haendel 2009-06-18T09:00:04Z BIRNLEX:1157 NCIT:C13040 SCTID:25087005 UMLS:C1518256 part of nervous system uberon UBERON:0000073 regional part of nervous system Any part or collection of parts of the central or peripheral nervous system. Parts may span both CNS and PNS. BIRNLEX:1157 UMLS:C1518256 ncithesaurus:Nervous_System_Part part of nervous system BIRNLEX:1157 Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism. UBERON:0010322 FMA:85544 NCIT:C34076 SCTID:118966000 UMLS:C1519343 galen:ComplexSkeletalStructure skeletal system subdivision uberon skeletal system part UBERON:0000075 subdivision of skeletal system cjm Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism. UBERONREF:0000003 https://orcid.org/0000-0002-6601-2165 UMLS:C1519343 ncithesaurus:Skeletal_System_Part skeletal system subdivision FMA:85544 The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm. merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube) (or external ectoderm) forms the following structures: Skin Epithelium of the mouth and nasal cavity saliavary glands, and glands of mouth and nasal cavity Enamel - as a side note dentin and dental pulp are formed from ectomesenchyme which is derived from ectoderm Epithelium of pineal and pituitary glands Lens and cornea of the eye Apical ectodermal ridge inducing development of the limb buds of the embryo. Sensory receptors in epidermis EHDAA2:0001968 EHDAA:1494 EHDAA:350 EHDAA:4784 EHDAA:4790 EHDAA:4796 EHDAA:7860 EMAPA:16096 FMA:87656 NCIT:C34309 UMLS:C1515087 Wikipedia:External_ectoderm surface (external) ectoderm surface ectoderm uberon UBERON:0000076 external ectoderm http://upload.wikimedia.org/wikipedia/commons/1/1d/Ectoderm.png EHDAA2 EHDAA2 The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm. MGI:anna MP:0012532 UMLS:C1515087 ncithesaurus:Surface_Ectoderm surface ectoderm MP:0012532 An anatomical structure that develops from the endoderm and the mesoderm. Grouping term for query purposes. Notes that the developmental relationships are being refined such that most structures should develop in whole from at most one layer, but may have contributions from multiple uberon UBERON:0000077 mixed endoderm/mesoderm-derived structure An anatomical structure that develops from the endoderm and the mesoderm. https://orcid.org/0000-0002-6601-2165 An anatomical structure that develops from the ectoderm, mesoderm and endoderm. Grouping term for query purposes. Notes that the developmental relationships are being refined such that most structures should develop in whole from at most one layer, but may have contributions from multiple uberon UBERON:0000078 mixed ectoderm/mesoderm/endoderm-derived structure An anatomical structure that develops from the ectoderm, mesoderm and endoderm. https://orcid.org/0000-0002-6601-2165 stage succeeding embryo, including mature structure In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997) BilaDO:0000003 OGES:000010 OGES:000014 OGES:000024 WBls:0000022 WBls:0000093 WBls:0000103 postembryonic stage post-hatching stage uberon postembryonic UBERON:0000092 post-embryonic stage https://github.com/obophenotype/uberon/issues/344 stage succeeding embryo, including mature structure https://orcid.org/0000-0002-6601-2165 Nonparenchymatous organ that primarily consists of dense connective tissue organized into a sheet which interconnects two or more organs, separates two or more body spaces from one another, or surrounds an organ or body part. Examples: interosseous membrane of forearm, obturator membrane, tympanic membrane, fibrous pericardium, fascia lata, dura mater. [FMA] cjm 2009-07-30T05:19:13Z membrane FMA:7145 membrane of organ uberon UBERON:0000094 membrane organ FMA-def Nonparenchymatous organ that primarily consists of dense connective tissue organized into a sheet which interconnects two or more organs, separates two or more body spaces from one another, or surrounds an organ or body part. Examples: interosseous membrane of forearm, obturator membrane, tympanic membrane, fibrous pericardium, fascia lata, dura mater. [FMA] FMA:7145 portion of neural crest that develops from the dorsal neural tube. It overlaps the vagal neural crest and migrates to populate the pharyngeal arches 3, 4 and 6 (producing structures in the head) and to the heart, forming connective tissue that separates the great vessels of the heart. [Wikipedia] A subpopulation of the cephalic neural crest that emerges from the otic level to the anterior limit of somite 4. It migrates to the heart and is essential for the septation of the outflow track[DOI:10.1242/dev.091751]. ZFA treats this as a subtype of NC. cjm 2009-07-30T07:57:38Z TAO:0002173 Wikipedia:Cardiac_neural_crest XAO:0004190 ZFA:0001648 uberon cardiac neural crest complex complexus cristae neuralis cardiacus UBERON:0000095 cardiac neural crest Wikipedia portion of neural crest that develops from the dorsal neural tube. It overlaps the vagal neural crest and migrates to populate the pharyngeal arches 3, 4 and 6 (producing structures in the head) and to the heart, forming connective tissue that separates the great vessels of the heart. [Wikipedia] Wikipedia:Cardiac_neural_crest A subpopulation of the cephalic neural crest that emerges from the otic level to the anterior limit of somite 4. It migrates to the heart and is essential for the septation of the outflow track[DOI:10.1242/dev.091751]. DOI:10.1242/dev.091751 ZFA treats this as a subtype of NC. ZFA cardiac neural crest complex Wikipedia:Cardiac_neural_crest complexus cristae neuralis cardiacus Wikipedia:Cardiac_neural_crest The lung vasculature is composed of the tubule structures that carry blood or lymph in the lungs[GO]. FMA:73750 lung vascular network pulmonary vasculature vascular network of lung vasculature of lung uberon UBERON:0000102 lung vasculature The lung vasculature is composed of the tubule structures that carry blood or lymph in the lungs[GO]. GOC:GO lung vascular network OBOL:automatic pulmonary vasculature FMA:73750 vascular network of lung OBOL:automatic vasculature of lung OBOL:automatic An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism. FBdv:00000000 HsapDv:0000001 MmusDv:0000001 OGES:000011 ncithesaurus:Life entire life cycle entire lifespan life lifespan uberon UBERON:0000104 life cycle https://github.com/obophenotype/uberon/issues/532 An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism. https://orcid.org/0000-0002-6601-2165 A spatiotemporal region encompassing some part of the life cycle of an organism. this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here the WBls class 'all stages' belongs here as it is the superclass of other WBls stages we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage BILS:0000105 EFO:0000399 FBdv:00007012 FMA:24120 HsapDv:0000000 MmusDv:0000000 OlatDv:0000010 PdumDv:0000090 WBls:0000002 XAO:1000000 ZFS:0000000 ZFS:0100000 ncithesaurus:Developmental_Stage developmental stage stage uberon UBERON:0000105 life cycle stage A spatiotemporal region encompassing some part of the life cycle of an organism. https://orcid.org/0000-0002-6601-2165 A stage at which the organism is a single cell produced by means of sexual reproduction. As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG] BILS:0000106 BilaDO:0000005 EFO:0001322 EHDAA:27 FBdv:00005288 NCIT:C12601 PdumDv:0000100 VHOG:0000745 Wikipedia:Zygote XAO:1000001 ZFS:0000001 1-cell stage fertilized egg stage one cell stage uberon fertilized egg stage one-cell stage zygote zygotum UBERON:0000106 zygote stage A stage at which the organism is a single cell produced by means of sexual reproduction. Wikipedia:Zygote As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG] 2012-09-17 VHOG:0000745 VHOG ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107 http://bgee.unil.ch/ fertilized egg stage BTO:0000854 one-cell stage VHOG:0000745 zygote VHOG:0000745 zygotum Wikipedia:Zygote The first few specialized divisions of an activated animal egg; Stage consisting of division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. The different cells derived from cleavage are called blastomeres and form a compact mass called the morula. Cleavage ends with the formation of the blastula. BILS:0000107 BilaDO:0000006 EFO:0001290 FBdv:00000054 MESH:A16.254.270 MmusDv:0000004 OGES:000015 OGES:000020 PdumDv:0000200 Wikipedia:Cleavage_(embryo) XAO:1000004 ZFS:0000046 uberon UBERON:0000107 cleavage stage The first few specialized divisions of an activated animal egg; Stage consisting of division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. The different cells derived from cleavage are called blastomeres and form a compact mass called the morula. Cleavage ends with the formation of the blastula. GO:0040016 Wikipedia:Cleavage_(embryo) An early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence. consider adding a preceding stage 'morula stage' as part of cleavage BILS:0000108 BilaDO:0000007 EFO:0001282 HsapDv:0000006 MmusDv:0000007 OGES:000003 OGES:000016 OGES:000021 OpenCyc:Mx4rEetFnKP2EdqAAAACs4vPlg WBls:0000005 Wikipedia:Blastula XAO:1000003 ZFS:0000045 uberon UBERON:0000108 blastula stage http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png An early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence. Wikipedia:Blastula A stage defined by complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm. BILS:0000109 BilaDO:0000008 EFO:0001296 FBdv:00005317 HsapDv:0000010 MmusDv:0000013 OGES:000004 OGES:000019 WBls:0000010 XAO:1000005 ZFS:0000047 uberon blastocystis trilaminaris stage trilaminar blastocyst stage trilaminar blastoderm stage trilaminar disk stage trilaminar germ stage trilaminar stage UBERON:0000109 gastrula stage BILS A stage defined by complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm. GO:0007369 blastocystis trilaminaris stage https://orcid.org/0000-0002-6601-2165 trilaminar blastocyst stage https://orcid.org/0000-0002-6601-2165 trilaminar blastoderm stage https://orcid.org/0000-0002-6601-2165 trilaminar disk stage https://orcid.org/0000-0002-6601-2165 trilaminar germ stage https://orcid.org/0000-0002-6601-2165 trilaminar stage https://orcid.org/0000-0002-6601-2165 Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system. BILS:0000110 BilaDO:0000009 HsapDv:0000012 MmusDv:0000017 XAO:1000006 uberon UBERON:0000110 neurula stage https://github.com/obophenotype/uberon/issues/343 Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system. GO:0001841 A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism. BILS:0000111 BilaDO:0000010 HsapDv:0000015 MmusDv:0000018 OGES:000005 OGES:000032 Wikipedia:Organogenesis uberon segmentation stage UBERON:0000111 organogenesis stage https://github.com/obophenotype/uberon/issues/533 A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism. Wikipedia:Organogenesis the connective tissue located between the respiratory (airway and alveolar) epithelium, the capillary endothelium and pleural mesothelium; it contains basement membrane composed of collagen, elastin, proteoglycans, and fibronectin it functions in the mechanical behavior of the lung, and forms a barrier to regulate the flow of plasma constituents from the capillaries to the airway and alveolar spaces EMAPA:35521 FMA:27533 MA:0001782 SCTID:201609008 connective tissue of lung pulmonary interstitium uberon lung interstitial tissue lung interstitium pulmonary connective tissue pulmonary interstitial tissue UBERON:0000114 lung connective tissue the connective tissue located between the respiratory (airway and alveolar) epithelium, the capillary endothelium and pleural mesothelium; it contains basement membrane composed of collagen, elastin, proteoglycans, and fibronectin ISBN:0-683-40008-8 MGI:anna MP:0002276 PMID:14635660 connective tissue of lung OBOL:automatic pulmonary interstitium FMA:27533 lung interstitial tissue MA:0001782 pulmonary connective tissue EMAPA:35521 The epithelial layer of the lung. A pseudostratified epithelium, containing basal cells, stem cells of the airway, submucosal glands and cartilage rings, is limited to the trachea and large lobar airways in the mouse (Morrisey and Hogan, 2010). This more complex epithelium extends to terminal bronchioles in the human[DOI:10.1242/dev.115469] BTO:0001653 EMAPA:32860 MA:0001783 epithelial tissue of lung epithelium of lung lung epithelial tissue uberon pulmonary epithelium UBERON:0000115 lung epithelium The epithelial layer of the lung. MP:0006382 epithelial tissue of lung OBOL:automatic epithelium of lung OBOL:automatic lung epithelial tissue OBOL:automatic pulmonary epithelium BTO:0001653 A tube in the respiratory system. Examples: bronchus, bronchiole, trachea. in GO lung development is part of respiratory tube development. This can lead to inconsistencies with other ontologies, e.g. VT. The GO structure may be better represented by a tree of tubes (see the FMA class) EMAPA:37946 FMA:12224 segment of tracheobronchial tree respiratory conducting tube segment of tracheobronchial tree tracheobronchial tree segment uberon airway UBERON:0000117 respiratory tube A tube in the respiratory system. Examples: bronchus, bronchiole, trachea. GO:0030323 http://orcid.org/0000-0002-6601-2165 in GO lung development is part of respiratory tube development. This can lead to inconsistencies with other ontologies, e.g. VT. The GO structure may be better represented by a tree of tubes (see the FMA class) GO EMAPA:37946 MA:th segment of tracheobronchial tree FMA:12224 respiratory conducting tube MP:0004391 segment of tracheobronchial tree FMA:12224 tracheobronchial tree segment FMA:12224 Structure derived from foregut that becomes a lung[GO]. clarify successors - include bronchi? BTO:0001643 EHDAA2:0004089 NCIT:C34260 NCIT:C34282 SCTID:361427007 UMLS:C1514420 UMLS:C1514897 Wikipedia:Respiratory_bud uberon gemma pulmonalis gemma respiratoria lung bud primary lung bud respiratory diverticulum UBERON:0000118 lung bud http://upload.wikimedia.org/wikipedia/commons/7/71/Gray948.png GO:0060441 EHDAA2 Structure derived from foregut that becomes a lung[GO]. GO:0060431 Wikipedia:Respiratory_bud UMLS:C1514420 ncithesaurus:Primary_Bronchial_Bud UMLS:C1514897 ncithesaurus:Respiratory_Diverticulum gemma pulmonalis Wikipedia:Lung_buds gemma respiratoria Wikipedia:Lung_buds lung bud primary lung bud GO:0060572 respiratory diverticulum Wikipedia:Lung_buds A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. UBERON:0005163 CARO:0001001 FBbt:00005099 NLX:147821 funiculus nerve fiber bundle neural fiber bundle uberon UBERON:0000122 neuron projection bundle A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. CARO:0001001 FBC:DOS FBbt:00005099 nerve fiber bundle FBbt:00005099 A spatially aggregated collection of nerve cell bodies in the CNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections, and including nearby cells that share the same cell type, chemical phenotype, and connections. (CUMBO) Anatomical structure consisting of a discrete aggregate of neuronal soma[GO][GO_REF:0000021]. Proposed CUMBO def from MM: A subcortical part of the nervous system consisting of a relatively compact group of cells that is distinguishable histologically that share a commonality of cytoarchitecture, chemoarchitecturel and connectivity. (comments: I put in 'subcortical' because I don't think we consider either the cerebellar cortex or cerebral cortex to be nuclei. Some people distinguish between a nucleus and a laminar structure (see Wikipedia definition). However, there are structures identified as nuclei that are laminar, e.g., lateral geniculate nucleus, although they are not laminated in all species. Also, I put in 'relatively compact' and 'distiguishable by histology' because we have groups of cells, e.g., cholinergic cell groups, doparminergic cell groups that are related on the 3 criteria but which we don't tend to consider nuclei because they don't occupy an easily defined territory. But all is open to debate. nucleus AEO:0000136 FMA:83686 NCIT:C13197 NLX:28443 Wikipedia:Nucleus_(neuroanatomy) nervous system nucleus neuraxis nucleus neuronal nucleus nucleus of CNS uberon nucleus of neuraxis UBERON:0000125 neural nucleus we limit this structure by definition to chordate and vertebrate nervous systems A spatially aggregated collection of nerve cell bodies in the CNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections, and including nearby cells that share the same cell type, chemical phenotype, and connections. (CUMBO) NLX:28443 Anatomical structure consisting of a discrete aggregate of neuronal soma[GO][GO_REF:0000021]. GO_REF:0000021 neuraxis nucleus FMA:83686 neuronal nucleus AEO:0000136 nucleus of CNS NLX:28443 Nucleus that receives projections from or contains neurons that send projections through one of the cranial nerves EMAPA:37066 FMA:54501 NLX:28532 SCTID:280160003 Wikipedia:Cranial_nerve_nucleus cranial neural nucleus nucleus of cranial nerve uberon nucleus nervi cranialis UBERON:0000126 cranial nerve nucleus http://upload.wikimedia.org/wikipedia/commons/3/30/Gray696.png Nucleus that receives projections from or contains neurons that send projections through one of the cranial nerves NLX:28532 EMAPA:37066 MA:th cranial neural nucleus FMA:54501 nucleus nervi cranialis Wikipedia:Cranial_nerve_nucleus uberon UBERON:0000153 anterior region of body lexical uberon UBERON:0000154 posterior region of body lexical The terminal part of the large intestine, continuous proximally with the rectum and distally terminates with the anus. requires alignment with EHDAA2 and complete developmental relationships BTO:0001978 CALOHA:TS-2160 EMAPA:18256 FMA:15703 MA:0000330 NCIT:C12375 SCTID:245438008 UMLS:C0227411 Wikipedia:Anal_canal galen:AnalCanal anal canal anal canal viewed anatomically anatomical anal canal uberon anal pad anus canalis analis cloaca cloacal chamber mesenteron pars analis recti UBERON:0000159 anal canal https://upload.wikimedia.org/wikipedia/commons/0/01/Gray1078.png Wikipathways:WP2062 The terminal part of the large intestine, continuous proximally with the rectum and distally terminates with the anus. Wikipedia:Anal_canal UMLS:C0227411 ncithesaurus:Anal_Canal canalis analis BTO:0001978 canalis analis Wikipedia:Anal_canal pars analis recti BTO:0001978 Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine. This class is probably too inclusive Portion of the alimentary canal bounded anteriorly by the pyloric sphincter and posteriorly by the cloacal sphincter.[AAO] The tract of the alimentary canal. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] intestinal In zebrafish, No stomach, small intestine, or large intestine can be distinguished. However, differences can be found in the morphology of the mucosa columnar epithelial cells and the number of goblet cells, suggesting functional differentiation. The intestine has numerous folds that become progressively shorter in a rostral-to-caudal direction. Proportionally, these folds are significantly larger than the finger-like intestinal villi of mammals and other amniotes (Wallace et al. 2005). Columnar-shaped absorptive enterocytes are the most numerous in the zebrafish intestinal epithelium. Goblet cells are the second most populous epithelial cell type. AAO:0000246 ANISEED:1235303 BSA:0000093 BTO:0000648 CALOHA:TS-0490 EFO:0000834 EMAPA:32874 EV:0100071 FMA:7199 GAID:295 MA:0000328 MA:0001524 MESH:A03.492.411 MIAA:0000043 NCIT:C12736 SCTID:256876008 TAO:0001338 UMLS:C0021853 VHOG:0000056 WBbt:0005772 Wikipedia:Intestine XAO:0000129 ZFA:0001338 galen:Intestine bowel uberon intestinal tract UBERON:0000160 intestine cjm Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine. GOC:GO Wikipedia:Intestine Portion of the alimentary canal bounded anteriorly by the pyloric sphincter and posteriorly by the cloacal sphincter.[AAO] 2012-06-20 AAO:0000246 AAO AAO:EJS The tract of the alimentary canal. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000056 VHOG http://bgee.unil.ch/ UMLS:C0021853 ncithesaurus:Intestine Anatomical conduit that connects two adjacent body spaces (or a body space with the space surrounding the organism)[FMA,modified]. in FMA, this is an anatomical conduit *space*, rather than anatomical conduit anatomical ostium ostium FMA:3724 SCTID:91837002 anatomical orifice hilum uberon UBERON:0000161 orifice Anatomical conduit that connects two adjacent body spaces (or a body space with the space surrounding the organism)[FMA,modified]. FMA:3724 in FMA, this is an anatomical conduit *space*, rather than anatomical conduit FMA anatomical ostium FMA:3724 anatomical orifice FMA:3724 Common chamber into which the intestines and excretory system opens. Arises during development in all vertebrates, but in many it becomes subdivided, lost or incorporated into other structures adding df link to embryonic cloaca leads to a cycle in uberon-simple, as cloaca is a suberclass of embryonic cloaca A common passage for fecal, urinary, and reproductive discharge in most lower vertebrates as well as the terminal end of the hindgut before division into rectum, bladder, and genital primordia in mammalian embryos. [TFD][VHOG] Anatomical structure which is the common receptacle for the alimentary canal, Wolffian ducts, oviducts, and the bladder.[AAO] A cloaca is apparently a primitive vertebrate feature because it occurs in most primitive gnathostomes and persists in the embryos of almost all vertebrates.[well established][VHOG] cloacal Human beings only have an embryonic cloaca, which is split up into separate tracts during the development of the urinary and reproductive organs hindgut endoderm and proctodeal ectoderm. AAO:0000095 GAID:1206 MESH:D002988 NCIT:C34127 SCTID:362857006 SCTID:370631000 UMLS:C0008987 VHOG:0001186 Wikipedia:Cloaca XAO:0000244 ZFA:0005781 uberon cloacal chamber vent UBERON:0000162 cloaca ZFA AAO Common chamber into which the intestines and excretory system opens. Arises during development in all vertebrates, but in many it becomes subdivided, lost or incorporated into other structures ISBN:0073040584 Wikipedia:Cloaca most adult placentals have no trace of a cloaca. However, the tenrecs and golden moles, small placental mammals native to Africa, retain a cloaca as adults. A common passage for fecal, urinary, and reproductive discharge in most lower vertebrates as well as the terminal end of the hindgut before division into rectum, bladder, and genital primordia in mammalian embryos. [TFD][VHOG] 2012-09-17 VHOG:0001186 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/cloaca Anatomical structure which is the common receptacle for the alimentary canal, Wolffian ducts, oviducts, and the bladder.[AAO] 2012-06-20 AAO:0000095 AAO AAO:BJB A cloaca is apparently a primitive vertebrate feature because it occurs in most primitive gnathostomes and persists in the embryos of almost all vertebrates.[well established][VHOG] 2012-09-17 VHOG:0001186 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.572 http://bgee.unil.ch/ hindgut endoderm and proctodeal ectoderm. WP UMLS:C0008987 ncithesaurus:Cloaca cloacal chamber AAO:0000095 vent XAO:0000244 endoderm-lined chamber that develops as pouch-like dilation of the caudal end of the hindgut and receives the allantois ventrally and two mesonephric ducts laterally; caudally it ends blindly at the cloacal membrane formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm[MP]. this class represents the embryonic form of the cloaca, as found in both mammals and non-mammals. EHDAA2:0000256 EHDAA:4895 EMAPA:27573 Wikipedia:Cloaca_(embryology) uberon cloaca UBERON:0000163 embryonic cloaca EHDAA2 EHDAA2 endoderm-lined chamber that develops as pouch-like dilation of the caudal end of the hindgut and receives the allantois ventrally and two mesonephric ducts laterally; caudally it ends blindly at the cloacal membrane formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm[MP]. MP:0010115 Wikipedia:Cloaca_(embryology) cloaca The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks). Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO] Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG] oral some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips AAO:0010355 BTO:0001090 BTO:0004698 CALOHA:TS-1315 EFO:0000825 EHDAA2:0001326 EHDAA:542 EMAPA:16262 FBbt:00003126 FMA:49184 GAID:75 MA:0000341 MA:0002474 MAT:0000038 MESH:D009055 MIAA:0000038 OpenCyc:Mx4rvVidh5wpEbGdrcN5Y29ycA SCTID:21082005 TADS:0000040 TAO:0000547 TAO:0000590 TGMA:0000131 VHOG:0000280 VHOG:0000812 Wikipedia:Mouth XAO:0003029 ZFA:0000547 ZFA:0000590 galen:Mouth http://purl.obolibrary.org/obo/uberon/images/lamprey_sucker_rosava_3238889218.jpg regio oralis adult mouth uberon cavital oralis cavitas oris cavum oris mouth cavity oral region oral vestibule rima oris stoma stomatodaeum trophic apparatus vestibule of mouth vestibulum oris UBERON:0000165 mouth https://github.com/obophenotype/uberon/issues/661 http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg the mouth contains structures such as jaw skeleton that may not strictly be considered tract parts exceptions in some taxa The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks). Wikipedia:Mouth https://github.com/obophenotype/uberon/wiki/The-digestive-tract Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO] 2012-06-20 AAO:0010355 AAO AAO:BJB Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG] 2012-09-17 VHOG:0000812 VHOG DOI:10.1038/nature07309 Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008) http://bgee.unil.ch/ in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips FMA regio oralis BTO:0004698 regio oralis FMA:49184 FMA:TA cavital oralis Wikipedia:Mouth cavitas oris BTO:0001090 cavum oris BTO:0001090 mouth cavity BTO:0001090 oral region EHDAA2:0001326 oral vestibule BTO:0001090 rima oris BTO:0001090 stomatodaeum VHOG:0000812 trophic apparatus http://orcid.org/0000-0002-6601-2165 vestibule of mouth BTO:0001090 vestibulum oris BTO:0001090 The orifice that connects the mouth to the exterior of the body. (...) mouth development is very similar in protostomes and 'basal' deuterostomes, whereas the chordate mouth seems to develop at a new position. Recent data for echinoderms and hemichordates further suggest that this change in mouth position may result from change in the influence of a conserved ectodermal patterning system on mouth development. It has been suggested that the mouths of vertebrates and urochordates may constitute a 'new' mouth.[well established][VHOG] FMA:59806 oral fissure oral orifice uberon mouth oral part of face UBERON:0000166 oral opening FMA The orifice that connects the mouth to the exterior of the body. https://github.com/obophenotype/uberon/wiki/The-digestive-tract (...) mouth development is very similar in protostomes and 'basal' deuterostomes, whereas the chordate mouth seems to develop at a new position. Recent data for echinoderms and hemichordates further suggest that this change in mouth position may result from change in the influence of a conserved ectodermal patterning system on mouth development. It has been suggested that the mouths of vertebrates and urochordates may constitute a 'new' mouth.[well established][VHOG] 2012-09-17 VHOG:0000280 VHOG DOI:10.1016/j.semcdb.2007.06.002 Christiaen L, Jaszczyszyn Y, Kerfant M, Kanob S, Thermes V, Joly JS, Evolutionary modification of mouth position in deuterostomes. Seminars in Cell and Developmental Biology (2007) http://bgee.unil.ch/ oral fissure FMA:59806 oral orifice FMA:59806 mouth Anatomical cavity at the start of the digestive tract that that is enclosed by the mouth. The boundaries and contents vary depending on the species. In vertebrates, the boundaries are the oral opening, the cheeks, the palate and (if present) the palatoglossal arch - if this is not present then the mouth and pharynx form the oropharyngeal cavity. The buccal cavity contains the teeth, tongue and palate (when present) Anatomical cavity bounded anteriorly by the mouth and posteriorly by the derivatives of the branchial arches.[AAO] The cavity of the mouth, bounded by the jaw bones and associated structures (muscles and mucosa). [TFD][VHOG] Echinoderms, hemichordates, and chordates are called deuterostomes because the mouth arises not from the blastopore but from a second invagination at the anterior end of the larva that pushes in to connect with the archenteron.[well established][VHOG] AAO:0000053 AAO:0000960 BSA:0000107 CALOHA:TS-1315 EFO:0001975 EHDAA2:0001324 EHDAA:6970 EMAPA:17411 EMAPA:18399 EV:0100057 FMA:20292 HAO:0000669 NCIT:C12421 SCTID:181220002 TAO:0001027 TGMA:0000102 UMLS:C0226896 VHOG:0000188 WBbt:0005255 XAO:0000126 ZFA:0001027 buccal cavity cavity of mouth uberon bucca UBERON:0000167 oral cavity Anatomical cavity at the start of the digestive tract that that is enclosed by the mouth. The boundaries and contents vary depending on the species. In vertebrates, the boundaries are the oral opening, the cheeks, the palate and (if present) the palatoglossal arch - if this is not present then the mouth and pharynx form the oropharyngeal cavity. The buccal cavity contains the teeth, tongue and palate (when present) ISBN:0073040584 https://github.com/obophenotype/uberon/wiki/The-digestive-tract https://orcid.org/0000-0002-6601-2165 Anatomical cavity bounded anteriorly by the mouth and posteriorly by the derivatives of the branchial arches.[AAO] 2012-06-20 AAO:0000960 AAO AAO:EJS The cavity of the mouth, bounded by the jaw bones and associated structures (muscles and mucosa). [TFD][VHOG] 2012-09-17 VHOG:0000188 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/oral+cavity Echinoderms, hemichordates, and chordates are called deuterostomes because the mouth arises not from the blastopore but from a second invagination at the anterior end of the larva that pushes in to connect with the archenteron.[well established][VHOG] 2012-09-17 VHOG:0000188 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.32 http://bgee.unil.ch/ UMLS:C0226896 ncithesaurus:Oral_Cavity buccal cavity FMA:20292 ISBN:0073040584 A section dividing a colon along a proximal-distal axis. FMA:222905 uberon segment of colon UBERON:0000168 proximal-distal subdivision of colon 4 cjm A section dividing a colon along a proximal-distal axis. http://orcid.org/0000-0002-6601-2165 segment of colon FMA:222905 1 1 1 1 The pair of anatomical structures comprised of a left lung and right lung. FMA:68877 OpenCyc:Mx4rvVjKy5wpEbGdrcN5Y29ycA lungs lungs pair pulmones set of lungs uberon UBERON:0000170 pair of lungs FMA-abduced The pair of anatomical structures comprised of a left lung and right lung. http://orcid.org/0000-0002-6601-2165 pulmones FMA:68877 FMA:TA Organ that functions in gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms. EMAPA:17607 SCTID:272626006 SPD:0000428 TGMA:0001247 apparatus respiratorius organ breathing organ organ of apparatus respiratorius organ of respiratory system respiratory organ respiratory system organ uberon gas exchange organ UBERON:0000171 respiration organ Organ that functions in gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms. GO:0007585 apparatus respiratorius organ OBOL:automatic organ of apparatus respiratorius OBOL:automatic organ of respiratory system OBOL:automatic respiratory system organ OBOL:automatic A portion of organism substance that is the product of an excretion process that will be eliminated from the body. An excretion process is elimination by an organism of the waste products that arise as a result of metabolic activity UBERON:0000324 UBERON:0007550 AEO:0000184 BTO:0000491 EHDAA2_RETIRED:0003184 ENVO:02000022 FMA:9674 galen:Excretion excreted substance portion of excreted substance waste substance uberon excretion UBERON:0000174 excreta A portion of organism substance that is the product of an excretion process that will be eliminated from the body. An excretion process is elimination by an organism of the waste products that arise as a result of metabolic activity GO:0007588 http://orcid.org/0000-0002-6601-2165 portion of excreted substance FMA:9674 waste substance AEO:0000184 excretion BTO:0000491 A fluid that is composed of blood plasma and erythrocytes. This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid. A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO] Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO] relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG] AAO:0000046 BTO:0000089 CALOHA:TS-0079 EFO:0000296 EHDAA2:0000176 EHDAA:418 EMAPA:16332 ENVO:02000027 EV:0100047 FMA:9670 GAID:965 MA:0000059 MESH:D001769 MIAA:0000315 NCIT:C12434 OpenCyc:Mx4rvVjI8JwpEbGdrcN5Y29ycA TAO:0000007 UMLS:C0005767 VHOG:0000224 Wikipedia:Blood XAO:0000124 ZFA:0000007 galen:Blood portion of blood vertebrate blood uberon whole blood UBERON:0000178 blood CL:tm https://github.com/obophenotype/uberon/issues/1330 Bgee:AN A fluid that is composed of blood plasma and erythrocytes. FMA:9670 Wikipedia:Blood http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/9 A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO] 2012-08-14 TAO:0000007 TAO ZFIN:curator Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO] 2012-06-20 AAO:0000046 AAO AAO:LAP relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] 2012-06-20 AAO:0000046 AAO Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG] 2012-09-17 VHOG:0000224 VHOG DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual review of cell and developmental biology (2006) http://bgee.unil.ch/ UMLS:C0005767 ncithesaurus:Blood whole blood BTO:0000089 Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs. cjm 2009-04-08T04:38:19Z CARO:0000081 uberon blood or blood analog circulating fluid UBERON:0000179 haemolymphatic fluid Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs. http://orcid.org/0000-0002-6601-2165 Dorsal part (roof region) of the telencephalon[GO]. In the anatomy of animals, an avian pallium is the dorsal telencephalon of a bird's brain. Pallium of avian species tend to be relatively large, comprising ~75% of the telencephalic volume. In humans the cerebrum has three parts: the archipallium, the paleopallium and the neopallium. The developing telencephalon or forebrain is divided into pallium and subpallium. In amphibians, the cerebrum includes archipallium, paleopallium and some of the basal nuclei. Reptiles first developed a neopallium, which continued to develop in the brains of more recent species to become the neocortex of humans and Old World monkeys. In fish, the archipallium is the largest part of the cerebrum. Some researchers suggest the early archipallium gave rise to the human hippocampus cjm 2009-04-18T12:03:09Z UBERON:0007333 BTO:0003399 DMBA:15903 EFO:0003534 SCTID:369224000 TAO:0000505 TAO:0007007 Wikipedia:Avian_pallium Wikipedia:Pallium_(neuroanatomy) ZFA:0000505 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=3240 area dorsalis telencephali dorsal part of telencephalon dorsal telencephalic area dorsal telencephalon uberon UBERON:0000203 pallium https://sourceforge.net/p/obo/zebrafish-anatomy-zfa-term-requests/87 Dorsal part (roof region) of the telencephalon[GO]. GO:0021543 ISBN:0471888893 Wikipedia:Pallium_(neuroanatomy) https://github.com/obophenotype/uberon/issues/287 PMID:8932866 In the anatomy of animals, an avian pallium is the dorsal telencephalon of a bird's brain. Pallium of avian species tend to be relatively large, comprising ~75% of the telencephalic volume. Wikipedia:Avian_pallium NCBITaxon:8782 In humans the cerebrum has three parts: the archipallium, the paleopallium and the neopallium. The developing telencephalon or forebrain is divided into pallium and subpallium. In amphibians, the cerebrum includes archipallium, paleopallium and some of the basal nuclei. Reptiles first developed a neopallium, which continued to develop in the brains of more recent species to become the neocortex of humans and Old World monkeys. In fish, the archipallium is the largest part of the cerebrum. Some researchers suggest the early archipallium gave rise to the human hippocampus WP area dorsalis telencephali ZFA:0000505 dorsal part of telencephalon ISBN:0471888893 dorsal telencephalic area ZFA:0000505 dorsal telencephalon ZFA:0000505 A layer of membrane around a tendon. It has 2 layers: synovial sheath + fibrous tendon sheath TODO - add layer relations. 'tendon sheath' GAT in FMA. BTO:0000051 FMA:45087 FMA:76715 NCIT:C96299 SCTID:361885006 UMLS:C0224856 Wikipedia:Tendon_sheath synovial tendon sheath uberon vagina tendinis UBERON:0000304 tendon sheath A layer of membrane around a tendon. It has 2 layers: synovial sheath + fibrous tendon sheath Wikipedia:Tendon_sheath UMLS:C0224856 ncithesaurus:Tendon_Sheath synovial tendon sheath FMA:45087 vagina tendinis Wikipedia:Tendon_sheath Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence. TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula UBERON:0007011 BILA:0000059 BTO:0000128 GAID:1294 MESH:A16.254.270.274 OGEM:000006 OpenCyc:Mx4rEetFnKP2EdqAAAACs4vPlg Wikipedia:Blastula blastula embryo uberon blastosphere UBERON:0000307 blastula http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence. Wikipedia:Blastula blastula embryo BILA:0000059 blastosphere Wikipedia:Blastula Mucosa that is part of a colon. The mucosa of the colon is lined by a simple columnar epithelium with a thin brush border and numerous goblet cells. UBERON:0003347 UBERON:0004981 BTO:0000271 CALOHA:TS-0164 EFO:0003038 EMAPA:27375 FMA:14984 FMA:85388 MA:0003194 SCTID:362157008 colon mucosa colon mucous membrane colonic mucosa colonic mucous membrane large bowel mucosa mucosa of colon mucosa of large bowel uberon UBERON:0000317 colonic mucosa Mucosa that is part of a colon. The mucosa of the colon is lined by a simple columnar epithelium with a thin brush border and numerous goblet cells. http://orcid.org/0000-0002-6601-2165 colon mucosa FMA:14984 colon mucous membrane OBOL:automatic colonic mucous membrane FMA:14984 large bowel mucosa OBOL:automatic mucosa of colon FMA:14984 mucosa of large bowel OBOL:automatic The branched tubular glands found in the mucosa of the fundus and body of the stomach which contain parietal cells that secrete hydrochloric acid and zymogenic cells that produce pepsin. BTO:0000503 EMAPA:27181 FMA:14919 uberon UBERON:0000325 gastric gland cjm ISBN:0073040584 The branched tubular glands found in the mucosa of the fundus and body of the stomach which contain parietal cells that secrete hydrochloric acid and zymogenic cells that produce pepsin. MGI:anna The wall of the digestive tract. This encompasses all parts of the digestive tract with the exception of the lumen (cavity). We model the digestive tract as consisting of two parts: the wall and the lumen. BTO:0000547 FMA:45653 digestive tract wall wall of digestive tract wall of gut uberon wall of alimentary tract UBERON:0000328 gut wall The wall of the digestive tract. This encompasses all parts of the digestive tract with the exception of the lumen (cavity). http://orcid.org/0000-0002-6601-2165 wall of gut FMA:45653 bone marrow in which the fat cells predominate in the meshes of the reticular network. BTO:0000635 FMA:74596 SCTID:328639002 SCTID:5023006 medulla ossium flava yellow marrow uberon fat marrow UBERON:0000332 yellow bone marrow bone marrow in which the fat cells predominate in the meshes of the reticular network. http://medical-dictionary.thefreedictionary.com/Yellow+Marrow medulla ossium flava BTO:0000635 yellow marrow BTO:0000635 fat marrow BTO:0000635 A gland that is part of the intestinal mucosa. Examples include the intestinal crypts, duodenal gland[cjm]. Note that some sources treat 'intestinal gland' as synonymous with crypts BTO:0000640 FMA:15052 SCTID:266297002 bowel mucosa gland bowel mucosa of organ gland bowel mucous membrane gland bowel organ mucosa gland gland of bowel mucosa gland of bowel mucosa of organ gland of bowel mucous membrane gland of bowel organ mucosa gland of intestinal mucosa gland of intestine mucosa gland of intestine mucosa of organ gland of intestine mucous membrane gland of intestine organ mucosa gland of mucosa of bowel gland of mucosa of intestine gland of mucosa of organ of bowel gland of mucosa of organ of intestine gland of mucous membrane of bowel gland of mucous membrane of intestine gland of organ mucosa of bowel gland of organ mucosa of intestine glandula intestinalis intestinal mucosa gland intestine mucosa gland intestine mucosa of organ gland intestine mucous membrane gland intestine organ mucosa gland mucosa of bowel gland mucosa of intestine gland mucosa of organ of bowel gland mucosa of organ of intestine gland mucous membrane of bowel gland mucous membrane of intestine gland organ mucosa of bowel gland organ mucosa of intestine gland uberon glandulae intestinales UBERON:0000333 intestinal gland A gland that is part of the intestinal mucosa. Examples include the intestinal crypts, duodenal gland[cjm]. https://orcid.org/0000-0002-6601-2165 bowel mucosa gland OBOL:automatic bowel mucosa of organ gland OBOL:automatic bowel mucous membrane gland OBOL:automatic bowel organ mucosa gland OBOL:automatic gland of bowel mucosa OBOL:automatic gland of bowel mucosa of organ OBOL:automatic gland of bowel mucous membrane OBOL:automatic gland of bowel organ mucosa OBOL:automatic gland of intestinal mucosa OBOL:automatic gland of intestine mucosa OBOL:automatic gland of intestine mucosa of organ OBOL:automatic gland of intestine mucous membrane OBOL:automatic gland of intestine organ mucosa OBOL:automatic gland of mucosa of bowel OBOL:automatic gland of mucosa of intestine OBOL:automatic gland of mucosa of organ of bowel OBOL:automatic gland of mucosa of organ of intestine OBOL:automatic gland of mucous membrane of bowel OBOL:automatic gland of mucous membrane of intestine OBOL:automatic gland of organ mucosa of bowel OBOL:automatic gland of organ mucosa of intestine OBOL:automatic glandula intestinalis FMA:15052 intestinal mucosa gland OBOL:automatic intestine mucosa gland OBOL:automatic intestine mucosa of organ gland OBOL:automatic intestine mucous membrane gland OBOL:automatic intestine organ mucosa gland OBOL:automatic mucosa of bowel gland OBOL:automatic mucosa of intestine gland OBOL:automatic mucosa of organ of bowel gland OBOL:automatic mucosa of organ of intestine gland OBOL:automatic mucous membrane of bowel gland OBOL:automatic mucous membrane of intestine gland OBOL:automatic organ mucosa of bowel gland OBOL:automatic organ mucosa of intestine gland OBOL:automatic A lining of mostly endodermal origin, covered in epithelium, which is involved in absorption and secretion. They line various body cavities that are exposed to the external environment and internal organs. It is at several places continuous with skin: at the nostrils, the lips, the ears, the genital area, and the anus. The sticky, thick fluid secreted by the mucous membranes and gland is termed mucus. The term mucous membrane refers to where they are found in the body and not every mucous membrane secretes mucus[WP] mucosal FMA has mucosa vs region of mucosa; these are subtypes of Mucosa: Mucosa of gallbladder, tongue, .... The following are subtypes of Region of mucosa: Mucosa of zone of stomach, trachea, bronchus, dorsum of tongue.... Depends on whether the covered area is an organ or organ component. Uberon does not regard organ vs organ component as crucial distinction and thus collapses these into a single class deliberately AEO:0000199 BTO:0000886 CALOHA:TS-2031 EHDAA2_RETIRED:0003234 EV:0100382 FMA:85355 FMA:85358 GAID:297 MESH:D009092 NCIT:C13166 OpenCyc:Mx4rvmKNOpwpEbGdrcN5Y29ycA SCTID:361693009 UMLS:C0026724 Wikipedia:Mucous_membrane galen:Mucosa mucosa of organ mucosa of organ part mucosal region mucous membrane organ mucosa uberon region of mucosa tunica mucosa UBERON:0000344 mucosa http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png A lining of mostly endodermal origin, covered in epithelium, which is involved in absorption and secretion. They line various body cavities that are exposed to the external environment and internal organs. It is at several places continuous with skin: at the nostrils, the lips, the ears, the genital area, and the anus. The sticky, thick fluid secreted by the mucous membranes and gland is termed mucus. The term mucous membrane refers to where they are found in the body and not every mucous membrane secretes mucus[WP] Wikipedia:Mucous_membrane FMA has mucosa vs region of mucosa; these are subtypes of Mucosa: Mucosa of gallbladder, tongue, .... The following are subtypes of Region of mucosa: Mucosa of zone of stomach, trachea, bronchus, dorsum of tongue.... Depends on whether the covered area is an organ or organ component. Uberon does not regard organ vs organ component as crucial distinction and thus collapses these into a single class deliberately FMA UMLS:C0026724 ncithesaurus:Mucosa mucosa of organ FMA:85355 mucosa of organ part FMA:85358 mucosal region FMA:85358 mucous membrane FMA:85355 organ mucosa FMA:85355 region of mucosa FMA:85358 tunica mucosa BTO:0000886 tunica mucosa Wikipedia:Mucous_membrane functional part of an organ in the body. This is in contrast to the stroma, which refers to the structural tissue of organs, being exactly, connective tissues. parenchymal Early in development the mammalian embryo has three distinct layers: ectoderm (external layer), endoderm (internal layer) and in between those two layers the middle layer or mesoderm. The parenchyma of most organs is of ectodermal (brain, skin) or endodermal origin (lungs, gastrointestinal tract, liver, pancreas). The parenchyma of a few organs (spleen, kidneys, heart) is of mesodermal origin. The stroma of all organs is of mesodermal origin the FMA definition is more restrictive, and limits this to solid organs. This would seem to cause problems for the lung parenchyma, except FMA classifies Lung as solid rather than cavitated EHDAA:3015 EHDAA:3905 EHDAA:3999 EHDAA:4005 EHDAA:6899 EHDAA:6903 EHDAA:6994 EHDAA:8086 EHDAA:9182 EHDAA:9190 EHDAA:9196 EHDAA:9202 FMA:45732 NCIT:C74601 UMLS:C0933845 Wikipedia:Parenchyma uberon UBERON:0000353 parenchyma functional part of an organ in the body. This is in contrast to the stroma, which refers to the structural tissue of organs, being exactly, connective tissues. Wikipedia:Parenchyma Early in development the mammalian embryo has three distinct layers: ectoderm (external layer), endoderm (internal layer) and in between those two layers the middle layer or mesoderm. The parenchyma of most organs is of ectodermal (brain, skin) or endodermal origin (lungs, gastrointestinal tract, liver, pancreas). The parenchyma of a few organs (spleen, kidneys, heart) is of mesodermal origin. The stroma of all organs is of mesodermal origin WP the FMA definition is more restrictive, and limits this to solid organs. This would seem to cause problems for the lung parenchyma, except FMA classifies Lung as solid rather than cavitated FMA UMLS:C0933845 ncithesaurus:Parenchyma A mucosa that is part of a pharynx [Automatically generated definition]. UBERON:0003344 BTO:0001047 EMAPA:26957 FMA:55031 MA:0003143 SCTID:362121003 mucosa of organ of pharynx mucosa of pharynx mucous membrane of pharynx organ mucosa of pharynx pharynx mucosa pharynx mucosa of organ pharynx mucous membrane pharynx organ mucosa tunica mucosa pharyngea tunica mucosa pharyngis uberon mucous membrane of the pharynx UBERON:0000355 pharyngeal mucosa A mucosa that is part of a pharynx [Automatically generated definition]. OBOL:automatic mucosa of organ of pharynx OBOL:automatic mucosa of pharynx OBOL:automatic mucous membrane of pharynx FMA:55031 mucous membrane of pharynx OBOL:automatic organ mucosa of pharynx OBOL:automatic pharynx mucosa OBOL:automatic pharynx mucosa of organ OBOL:automatic pharynx mucous membrane OBOL:automatic pharynx organ mucosa OBOL:automatic tunica mucosa pharyngea FMA:55031 FMA:TA mucous membrane of the pharynx BTO:0001047 The red vascular substance consisting of connective tissue and blood vessels, containing primitive blood cells, macrophages, megakaryocytes, and fat cells. Red marrow is found in the cavities of many bones. It manufactures and releases leukocytes and erythrocytes into the bloodstream. BTO:0001160 FMA:74595 SCTID:328538003 SCTID:75330005 medulla ossium rubra parenchymal red marrow red marrow uberon parenchyma of none marrow marrow UBERON:0000361 red bone marrow The red vascular substance consisting of connective tissue and blood vessels, containing primitive blood cells, macrophages, megakaryocytes, and fat cells. Red marrow is found in the cavities of many bones. It manufactures and releases leukocytes and erythrocytes into the bloodstream. http://medical-dictionary.thefreedictionary.com/red+marrow medulla ossium rubra BTO:0001160 parenchymal red marrow http://orcid.org/0000-0002-6601-2165 red marrow BTO:0001160 parenchyma of none marrow marrow http://orcid.org/0000-0002-6601-2165 The sensory nerve subdivision of the trigeminal nerve that transmits sensory information from the palate, upper teeth and gingiva, the skin between the palpebral fissure and the mouth, and from the nasal cavity and maxillary sinuses. Medial ramus (sensory) of the trigeminal nerve.[AAO] relationship loss: part_of trunk maxillary-mandibularis (AAO:0010669)[AAO] AAO:0010670 BTO:0001378 EHDAA2:0002087 EMAPA:17799 FMA:52724 GAID:836 MA:0001103 MESH:D008442 OpenCyc:Mx4rvWNU9JwpEbGdrcN5Y29ycA SCTID:280211001 VHOG:0001346 Wikipedia:Maxillary_nerve maxillary division [V2] maxillary division [Vb] maxillary division of fifth cranial nerve maxillary division of trigeminal nerve (Vb; V2) maxillary nerve [V2] maxillary nerve [Vb] nervus maxillaris (Vb; V2) nervus maxillaris [v2] nervus maxillaris [vb] ramus maxillaris (ramus V2) second division of fifth cranial nerve second division of trigeminal nerve trigeminal V nerve maxillary division uberon n. maxillaris nervus maxillaris trigeminal nerve maxillary division UBERON:0000377 maxillary nerve http://upload.wikimedia.org/wikipedia/commons/a/a9/Gray779.png The sensory nerve subdivision of the trigeminal nerve that transmits sensory information from the palate, upper teeth and gingiva, the skin between the palpebral fissure and the mouth, and from the nasal cavity and maxillary sinuses. MP:0009799 Wikipedia:Maxillary_nerve Medial ramus (sensory) of the trigeminal nerve.[AAO] 2012-06-20 AAO:0010670 AAO AAO:EJS relationship loss: part_of trunk maxillary-mandibularis (AAO:0010669)[AAO] 2012-06-20 AAO:0010670 AAO maxillary division [V2] FMA:52724 maxillary division [Vb] FMA:52724 maxillary division of fifth cranial nerve FMA:52724 maxillary division of trigeminal nerve (Vb; V2) FMA:52724 maxillary nerve [V2] FMA:52724 maxillary nerve [Vb] FMA:52724 nervus maxillaris (Vb; V2) FMA:52724 nervus maxillaris [v2] FMA:52724 FMA:TA nervus maxillaris [vb] FMA:52724 FMA:TA ramus maxillaris (ramus V2) AAO:0010670 second division of fifth cranial nerve FMA:52724 second division of trigeminal nerve FMA:52724 trigeminal V nerve maxillary division MA:0001103 n. maxillaris Wikipedia:Maxillary_nerve nervus maxillaris BTO:0001378 trigeminal nerve maxillary division EMAPA:17799 A mucosa that is part of a respiratory airway. BTO:0001390 FMA:7471 SCTID:660006 mucosa of organ of trachea mucosa of organ of windpipe mucosa of trachea mucosa of windpipe mucous membrane of trachea mucous membrane of windpipe organ mucosa of trachea organ mucosa of windpipe trachea mucosa trachea mucosa of organ trachea mucous membrane trachea organ mucosa tracheal mucous membrane tunica mucosa (tracheae) tunica mucosa tracheae windpipe mucosa windpipe mucosa of organ windpipe mucous membrane windpipe organ mucosa uberon UBERON:0000379 tracheal mucosa A mucosa that is part of a respiratory airway. OBOL:automatic mucosa of organ of trachea OBOL:automatic mucosa of organ of windpipe OBOL:automatic mucosa of trachea OBOL:automatic mucosa of windpipe OBOL:automatic mucous membrane of trachea FMA:7471 mucous membrane of trachea OBOL:automatic mucous membrane of windpipe OBOL:automatic organ mucosa of trachea OBOL:automatic organ mucosa of windpipe OBOL:automatic trachea mucosa OBOL:automatic trachea mucosa of organ OBOL:automatic trachea mucous membrane OBOL:automatic trachea organ mucosa OBOL:automatic tracheal mucous membrane FMA:7471 tunica mucosa (tracheae) FMA:7471 tunica mucosa tracheae FMA:7471 FMA:TA windpipe mucosa OBOL:automatic windpipe mucosa of organ OBOL:automatic windpipe mucous membrane OBOL:automatic windpipe organ mucosa OBOL:automatic The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified]. consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77 Anatomical system that consists of the muscles of the body.[VSAO] we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA AAO:0000307 BILA:0000088 BTO:0001369 BTO:0001485 EFO:0000801 EMAPA:35578 FBbt:00005069 FMA:72954 MA:0002888 MAT:0000025 MIAA:0000025 VSAO:0000033 XAO:0004042 muscle system muscle system of body muscular system musculature system set of all muscles set of muscles of body vertebrate muscular system uberon muskelsystem UBERON:0000383 musculature of body The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified]. VSAO:0000033 Anatomical system that consists of the muscles of the body.[VSAO] 2012-08-14 VSAO:0000033 VSAO VSAO:curator we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA MA muscular system FMA:72954 musculature system BILA:0000088 set of all muscles FMA:72954 set of muscles of body FMA:72954 vertebrate muscular system BTO:0001369 muskelsystem BTO:0001485 Tissue that surrounds the lens nucleus BTO:0001632 CALOHA:TS-0542 FMA:58970 MESH:A09.371.509.225 SCTID:280626006 cortex of lens uberon UBERON:0000389 lens cortex Tissue that surrounds the lens nucleus http://www.thefreedictionary.com/lens+cortex cortex of lens FMA:58970 The core of the crystalline lens, surrounded by the cortex. BTO:0001633 FMA:58971 MESH:A09.371.509.670 SCTID:280628007 nucleus of lens uberon UBERON:0000390 lens nucleus The core of the crystalline lens, surrounded by the cortex. BTO:0001633 nucleus of lens FMA:58971 An epithelium that is part of a colon [Automatically generated definition]. Intestinal epithelium which lines the lumen of the posterior intestine.[TAO] BTO:0001709 CALOHA:TS-0163 EMAPA:18941 FMA:17302 MA:0003195 SCTID:42978003 TAO:0005128 ZFA:0005128 colon epithelial tissue colon epithelium epithelial tissue of colon epithelial tissue of large bowel epithelium of colon epithelium of large bowel large bowel epithelial tissue large bowel epithelium posterior intestine epithelium uberon UBERON:0000397 colonic epithelium An epithelium that is part of a colon [Automatically generated definition]. OBOL:automatic Intestinal epithelium which lines the lumen of the posterior intestine.[TAO] 2012-08-14 TAO:0005128 TAO ZFIN:curator colon epithelial tissue OBOL:automatic colon epithelium FMA:17302 colon epithelium OBOL:automatic epithelial tissue of colon OBOL:automatic epithelial tissue of large bowel OBOL:automatic epithelium of colon OBOL:automatic epithelium of large bowel OBOL:automatic large bowel epithelial tissue OBOL:automatic large bowel epithelium OBOL:automatic posterior intestine epithelium ZFA:0005128 A gland in which the principal secretory cells are serous secreting cells. glands that secrete watery albuminous material that often contains enzymes[MP:0008052]. BTO:0001837 EMAPA:37950 FMA:62889 Wikipedia:Serous_gland uberon UBERON:0000409 serous gland http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray1021.png A gland in which the principal secretory cells are serous secreting cells. http://orcid.org/0000-0002-6601-2165 http://www.siumed.edu/~dking2/intro/glands.htm glands that secrete watery albuminous material that often contains enzymes[MP:0008052]. MP:0008052 EMAPA:37950 MA:th An anatomical wall that is part of an artery [Automatically generated definition]. BTO:0002009 FMA:14155 galen:ArterialWall arterial wall wall of artery uberon UBERON:0000415 artery wall An anatomical wall that is part of an artery [Automatically generated definition]. OBOL:automatic arterial wall FMA:14155 wall of artery FMA:14155 A portion of organism substance that is produced by exocrine glands. BTO has two distunct classes, with exocrine glandular secretion a subtype of secretion - however, all examples in BTO directly under secretion appear to be exocrine gland secretions UBERON:0006540 secretion AEO:0001005 BTO:0002977 BTO:0002979 EMAPA:36535 FMA:9675 MA:0002504 MESH:D012634 NCIT:C34062 UMLS:C1516992 galen:Secretion bodily secretion exocrine gland fluid/secretion secreted substance uberon exocrine gland fluid exocrine gland fluid or secretion exocrine gland secretion external secretion UBERON:0000456 secretion of exocrine gland A portion of organism substance that is produced by exocrine glands. http://orcid.org/0000-0002-6601-2165 BTO has two distunct classes, with exocrine glandular secretion a subtype of secretion - however, all examples in BTO directly under secretion appear to be exocrine gland secretions BTO secretion FMA:9675 UMLS:C1516992 ncithesaurus:Exocrine_Gland_Fluid_or_Secretion bodily secretion MESH:D012634 exocrine gland fluid/secretion MA:0002504 external secretion BTO:0002977 Any of several small branches of the internal carotid artery that supply the trigeminal ganglion and the walls of the cavernous and petrosal sinuses. BTO:0002996 FMA:70527 cavernous branch of cavernous part of internal carotid artery ramus sinus cavernosi (pars cavernosa) (arteria carotis interna) uberon UBERON:0000457 cavernous artery Any of several small branches of the internal carotid artery that supply the trigeminal ganglion and the walls of the cavernous and petrosal sinuses. BTO:0002996 cavernous branch of cavernous part of internal carotid artery FMA:70527 ramus sinus cavernosi (pars cavernosa) (arteria carotis interna) FMA:70527 FMA:TA Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. AAO:0010839 AEO:0000004 BILA:0000004 CALOHA:TS-2101 CARO:0000004 EHDAA2:0003004 EMAPA:35178 FBbt:00007019 FMA:9669 HAO:0000004 MA:0002450 NCIT:C13236 SPD:0000008 TAO:0001487 TGMA:0001824 VHOG:0001726 XAO:0004001 ZFA:0001487 galen:BodySubstance body fluid or substance body substance organism substance portion of body substance portion of organism substance uberon UBERON:0000463 organism substance this relationship may be too strong and may be weakened in future Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. http://orcid.org/0000-0001-9114-8737 body fluid or substance MA:0002450 body substance FMA:9669 organism substance CARO:0000004 portion of body substance FMA:9669 portion of organism substance ZFA:0001487 Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures. lumen space AAO:0010110 AEO:0000005 BILA:0000005 CARO:0000005 EHDAA2:0003005 FBbt:00007017 FMA:5897 HAO:0000005 NCIT:C94478 TAO:0001668 TGMA:0001825 UMLS:C0524461 VHOG:0001728 XAO:0003190 ZFA:0001643 lumen space uberon anatomical spaces UBERON:0000464 anatomical space Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures. http://orcid.org/0000-0001-9114-8737 UMLS:C0524461 ncithesaurus:Lumen_Space anatomical spaces ZFA:0001643 Anatomical entity that has mass. AAO:0010264 AEO:0000006 BILA:0000006 CARO:0000006 EHDAA2:0003006 FBbt:00007016 FMA:67165 HAO:0000006 TAO:0001836 TGMA:0001826 VHOG:0001721 uberon UBERON:0000465 material anatomical entity Anatomical entity that has mass. http://orcid.org/0000-0001-9114-8737 Anatomical entity that has no mass. AAO:0010265 AEO:0000007 BILA:0000007 CARO:0000007 EHDAA2:0003007 FBbt:00007015 FMA:67112 HAO:0000007 TAO:0001835 TGMA:0001827 VHOG:0001727 immaterial physical anatomical entity uberon UBERON:0000466 immaterial anatomical entity Anatomical entity that has no mass. http://orcid.org/0000-0001-9114-8737 immaterial physical anatomical entity FMA:67112 Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function. system AAO:0000007 AEO:0000011 BILA:0000011 BIRNLEX:14 BSA:0000049 CALOHA:TS-2088 CARO:0000011 EHDAA2:0003011 EHDAA:392 EMAPA:16103 EV:0100000 FBbt:00004856 FMA:7149 HAO:0000011 MA:0000003 NCIT:C12919 OpenCyc:Mx4rCWM0QCtDEdyAAADggVbxzQ SCTID:278195005 TAO:0001439 TGMA:0001831 UMLS:C0460002 VHOG:0001725 WBbt:0005746 WBbt:0005763 Wikipedia:Organ_system XAO:0003002 ZFA:0001439 galen:AnatomicalSystem body system connected anatomical system organ system uberon anatomical systems UBERON:0000467 anatomical system Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function. CARO:0000011 system GO:0048731 UMLS:C0460002 ncithesaurus:Organ_System body system BIRNLEX:14 connected anatomical system CARO:0000011 anatomical systems ZFA:0001439 Anatomical structure that is an individual member of a species and consists of more than one cell. TODO - split body and mc organism? body continues after death stage organismal organism AAO:0010026 AEO:0000191 BILA:0000012 BIRNLEX:18 BSA:0000038 BTO:0000042 CARO:0000012 EFO:0002906 EHDAA2:0003103 EHDAA2:0003191 EHDAA:1 EMAPA:25765 EV:0100016 FBbt:00000001 FMA:256135 HAO:0000012 NCIT:C13041 SCTID:243928005 TADS:0000001 TAO:0001094 TGMA:0001832 VHOG:0000671 WBbt:0007833 Wikipedia:Multi-cellular_organism XAO:0003004 ZFA:0001094 galen:Organism ncithesaurus:Whole_Organism multi-cellular organism animal uberon Koerper body whole body whole organism UBERON:0000468 multicellular organism Anatomical structure that is an individual member of a species and consists of more than one cell. CARO:0000012 Wikipedia:Multi-cellular_organism http://orcid.org/0000-0001-9114-8737 organism FBbt:00000001 VHOG:0000671 WBbt:0007833 multi-cellular organism CARO:0000012 animal BTO:0000042 Koerper BTO:0001489 body AEO:0000103 BIRNLEX:18 FMA:256135 NCIT:C13041 whole body BTO:0001489 whole organism FBbt:00000001 The organs and associated structures associated with bearing offspring in a female animal. By far, sexual reproduction is the more common pattern among living vertebrate forms and its widespread occurrence suggests that it is the plesiomorphic, or primitive, reproductive mode among the vertebrates.[well established][VHOG] BTO:0000083 CALOHA:TS-1303 EFO:0000969 EHDAA2:0000506 EHDAA:8116 EMAPA:17959 EV:0100110 FBbt:00004864 FMA:45663 GAID:364 HAO:0000324 MA:0000381 MESH:D005836 MIAA:0000028 NCIT:C12402 OpenCyc:Mx4rvVipTZwpEbGdrcN5Y29ycA SCTID:361386004 TGMA:0000635 UMLS:C0700038 VHOG:0000726 Wikipedia:Female_genitalia WikipediaCategory:Female_reproductive_system XAO:0000156 female organism genitalia female organism reproductive system genitalia of female organism reproductive system of female organism uberon female genital system female genital tract female genitalia female genitals female reproductive tract gynaecological tissue systema genitale femininum UBERON:0000474 female reproductive system http://upload.wikimedia.org/wikipedia/commons/6/68/Scheme_female_reproductive_system-en.svg The organs and associated structures associated with bearing offspring in a female animal. MP:0001119 Wikipedia:Female_genitalia http://orcid.org/0000-0002-6601-2165 By far, sexual reproduction is the more common pattern among living vertebrate forms and its widespread occurrence suggests that it is the plesiomorphic, or primitive, reproductive mode among the vertebrates.[well established][VHOG] 2012-09-17 VHOG:0000726 VHOG ISBN:978-0792383369 Lombardi J, Comparative vertebrate reproduction (1998) p.43 http://bgee.unil.ch/ UMLS:C0700038 ncithesaurus:Female_Reproductive_System female organism genitalia OBOL:automatic female organism reproductive system OBOL:automatic genitalia of female organism OBOL:automatic reproductive system of female organism OBOL:automatic female genitals XAO:0000156 female reproductive tract MA:0000381 gynaecological tissue BTO:0000083 systema genitale femininum BTO:0000083 Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument. Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency AAO:0010053 AEO:0000032 BILA:0000032 BIRNLEX:7 CALOHA:TS-2084 CARO:0000032 EFO:0000808 EHDAA2:0003032 EMAPA:36031 FBbt:00007009 FMA:7153 HAO:0000032 MA:0002433 MAT:0000293 MESH:D001829 MIAA:0000293 NCIT:C32221 OpenCyc:Mx4rvViAHJwpEbGdrcN5Y29ycA TAO:0001308 TGMA:0001840 UMLS:C0229962 VHOG:0001758 Wikipedia:Body_part XAO:0003013 ZFA:0001308 galen:BodyPart anatomic region uberon body part body region cardinal body part UBERON:0000475 organism subdivision CARO Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument. CARO:0000032 CARO:DOS http://orcid.org/0000-0001-9114-8737 UMLS:C0229962 ncithesaurus:Body_Part anatomic region MA:0002433 body region FMA:7153 cardinal body part FMA:7153 Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue. AAO:0010268 AEO:0000040 BILA:0000040 CARO:0000040 EHDAA2:0003040 FBbt:00007013 FMA:63863 HAO:0000040 TAO:0000382 TGMA:0001841 XAO:0003162 ZFA:0000382 uberon acellular anatomical structures UBERON:0000476 acellular anatomical structure CARO Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue. http://orcid.org/0000-0001-9114-8737 acellular anatomical structures ZFA:0000382 Anatomical group that has its parts adjacent to one another. Will be obsoleted in CARO v2 [https://github.com/obophenotype/caro/issues/3] AAO:0010009 AEO:0000041 BILA:0000041 CARO:0000041 EHDAA2:0003041 FBbt:00007277 FMA:49443 HAO:0000041 TADS:0000605 TAO:0001478 TGMA:0001842 VHOG:0001737 XAO:0003160 ZFA:0001478 uberon UBERON:0000477 anatomical cluster Anatomical group that has its parts adjacent to one another. http://orcid.org/0000-0001-9114-8737 A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis. AAO:0010020 AEO:0000042 BILA:0000042 CALOHA:TS-2119 CARO:0000042 EHDAA2:0003042 EHDAA:46 FBbt:00005835 FMA:85537 HAO:0000042 NCIT:C34055 SCTID:314908006 TAO:0000020 TGMA:0001843 UMLS:C1282438 VHOG:0000292 XAO:0004005 ZFA:0000020 extra-embryonic structure uberon extraembryonic structures extraembryonic tissue UBERON:0000478 see also conceptus extraembryonic component in EHDAA2. extraembryonic structure A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis. CARO:DOS http://orcid.org/0000-0001-9114-8737 https://cedar.bio.indiana.edu/trac/env/ontologies/ticket/279 UMLS:C1282438 ncithesaurus:Extraembryonic_Structure extraembryonic structures ZFA:0000020 Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. changed label and definition to reflect CARO2 AAO:0000607 AAO:0010054 AEO:0000043 BILA:0000043 BIRNLEX:19 CALOHA:TS-2090 CARO:0000043 EHDAA2:0003043 EMAPA:35868 FBbt:00007003 FMA:9637 HAO:0000043 MA:0003002 MESH:D014024 NCIT:C12801 TAO:0001477 TGMA:0001844 UMLS:C0040300 VHOG:0001757 WBbt:0005729 XAO:0003040 ZFA:0001477 galen:Tissue portion of tissue tissue portion simple tissue uberon UBERON:0000479 tissue CARO Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. CARO:0000043 UMLS:C0040300 ncithesaurus:Tissue portion of tissue CARO:0000043 simple tissue AEO:0000043 Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types. AAO:0010048 AEO:0000055 BILA:0000055 CARO:0000055 EHDAA2:0003055 FBbt:00007010 HAO:0000055 TAO:0001488 TGMA:0001847 VHOG:0001762 XAO:0003037 ZFA:0001488 uberon multi-tissue structures UBERON:0000481 multi-tissue structure CARO Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types. CARO:0000055 http://orcid.org/0000-0001-9114-8737 multi-tissue structures ZFA:0001488 Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO]. The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG] epithelial AAO:0000144 AAO:0010055 AEO:0000066 BILA:0000066 BTO:0000416 CALOHA:TS-0288 CARO:0000066 EHDAA2:0003066 EMAPA:32738 FBbt:00007005 FMA:9639 GAID:402 HAO:0000066 MA:0003060 MESH:D004848 NCIT:C12710 SCTID:31610004 TAO:0001486 UMLS:C0014609 VHOG:0000387 Wikipedia:Epithelium XAO:0003045 ZFA:0001486 epithelial tissue portion of epithelium uberon UBERON:0000483 Editor note: surface epithelium may contain non-epithelial cells, such as melanocytes, lymphocytes and dendritic cells, within the sheet of epithelial cells. Do we consider these part of the epithelium, or located-in it? epithelium Tkanka:nablonkowa.png Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO]. Wikipedia:Epithelium http://orcid.org/0000-0001-9114-8737 The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG] 2012-09-17 VHOG:0000387 VHOG ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.59 http://bgee.unil.ch/ UMLS:C0014609 ncithesaurus:Epithelium portion of epithelium FMA:9639 Unilaminar epithelium that consists of a single layer of cuboidal cells. needs to be synchronized with CL - there is no distinct cuboidal cell in CL AAO:0010064 AEO:0000067 BILA:0000067 CARO:0000067 EHDAA2:0003067 FMA:45566 HAO:0000067 NCIT:C33553 TAO:0001497 UMLS:C0836134 Wikipedia:Simple_cuboidal_epithelium XAO:0004009 ZFA:0001497 epithelium simplex cuboideum uberon simple cuboidal epithelia UBERON:0000484 simple cuboidal epithelium http://upload.wikimedia.org/wikipedia/commons/d/d0/Gray1133.png Unilaminar epithelium that consists of a single layer of cuboidal cells. Wikipedia:Simple_cuboidal_epithelium http://orcid.org/0000-0001-9114-8737 UMLS:C0836134 ncithesaurus:Simple_Cuboidal_Epithelium simple cuboidal epithelia ZFA:0001497 Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA] columnar epithelium columnar epithlium AAO:0010063 AEO:0000068 BILA:0000068 CARO:0000068 EHDAA2_RETIRED:0003068 FBbt:00007027 FMA:45567 HAO:0000068 NCIT:C33552 SCTID:32210007 TAO:0001496 UMLS:C0836135 Wikipedia:Simple_columnar_epithelium XAO:0004008 ZFA:0001496 epithelium simplex columnare simple columnar epithelium uberon simple columnar epithelia UBERON:0000485 simple columnar epithelium http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray1059.png Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA] FMA:FMA Wikipedia:Simple_columnar_epithelium http://orcid.org/0000-0001-9114-8737 columnar epithelium EHDAA2:0003068 columnar epithlium AEO:0000068 UMLS:C0836135 ncithesaurus:Simple_Columnar_Epithelium simple columnar epithelia ZFA:0001496 Epithelium which consists of more than one layer of epithelial cells that may or may not be in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, ciliated stratified columnar epithelium.[FMA] Epithelium that consists of more than one layer of epithelial cells.[CARO] AAO:0010059 AEO:0000069 BILA:0000069 BTO:0002074 CARO:0000069 EHDAA2:0003069 FMA:45562 HAO:0000069 NCIT:C33622 SCTID:309044005 TAO:0001494 UMLS:C0682575 Wikipedia:Stratified_epithelium XAO:0004006 ZFA:0001494 stratified epithelium uberon laminated epithelium UBERON:0000486 multilaminar epithelium Epithelium which consists of more than one layer of epithelial cells that may or may not be in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, ciliated stratified columnar epithelium.[FMA] FMA:FMA Wikipedia:Stratified_epithelium http://orcid.org/0000-0001-9114-8737 Epithelium that consists of more than one layer of epithelial cells.[CARO] 2012-06-20 CARO:0000069 CARO FMA:45562 http://orcid.org/0000-0001-9114-8737 UMLS:C0682575 ncithesaurus:Stratified_Epithelium laminated epithelium BTO:0002074 Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA] Unilaminar epithelium that consists of a single layer of squamous cells.[CARO] AAO:0010066 AEO:0000070 BILA:0000070 BTO:0002073 CARO:0000070 EHDAA2:0003070 FMA:45565 HAO:0000070 NCIT:C13178 TAO:0001498 UMLS:C0836133 Wikipedia:Simple_squamous_epithelium XAO:0004010 ZFA:0001498 epithelium simplex squamosum uberon simple squamous epithelia UBERON:0000487 simple squamous epithelium Illu:epithelium.jpg Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA] FMA:45565 Wikipedia:Simple_squamous_epithelium http://orcid.org/0000-0001-9114-8737 Unilaminar epithelium that consists of a single layer of squamous cells.[CARO] 2012-06-20 CARO:0000070 CARO FMA:45565 http://orcid.org/0000-0001-9114-8737 UMLS:C0836133 ncithesaurus:Simple_Squamous_Epithelium simple squamous epithelia ZFA:0001498 Epithelium that consists of epithelial cells not arranged in one ore more layers. AAO:0010057 AEO:0000071 BILA:0000071 CARO:0000071 EHDAA2:0003071 FMA:61741 HAO:0000071 TAO:0001493 XAO:0004004 ZFA:0001493 heterogenous epithelium uberon atypical epithelia UBERON:0000488 atypical epithelium Epithelium that consists of epithelial cells not arranged in one ore more layers. http://orcid.org/0000-0001-9114-8737 atypical epithelia ZFA:0001493 Compound organ that contains one or more macroscopic anatomical spaces. this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future AAO:0010016 AEO:0000072 BILA:0000072 CARO:0000072 EHDAA2:0003072 FMA:55671 HAO:0000072 TAO:0001490 TGMA:0001857 VHOG:0001730 XAO:0003165 ZFA:0001490 cavitated organ uberon cavitated compound organs UBERON:0000489 cavitated compound organ Compound organ that contains one or more macroscopic anatomical spaces. http://orcid.org/0000-0001-9114-8737 cavitated organ FMA:55671 cavitated compound organs ZFA:0001490 Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA] consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable Epithelium that consists of a single layer of epithelial cells.[CARO] AAO:0010062 AEO:0000073 BILA:0000073 BTO:0002073 CARO:0000073 EHDAA2:0003073 FMA:45561 HAO:0000073 NCIT:C33554 SCTID:309043004 TAO:0001495 UMLS:C0682574 XAO:0004007 ZFA:0001495 simple epithelium uberon unilaminar epithelia UBERON:0000490 unilaminar epithelium Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA] FMA:45561 http://orcid.org/0000-0001-9114-8737 Epithelium that consists of a single layer of epithelial cells.[CARO] 2012-06-20 CARO:0000073 CARO FMA:45561 http://orcid.org/0000-0001-9114-8737 UMLS:C0682574 ncithesaurus:Simple_Epithelium simple epithelium FMA:45561 unilaminar epithelia ZFA:0001495 Subdivision of trunk that lies between the head and the abdomen. note that we use the slightly verbose term 'thoracic segment of trunk' to avoid confusuon with insect thorax. todo - taxonomic constraints. Also, in FMA 'thorax' is a synonym for chest EMAPA:35862 FMA:259209 MA:0000022 SCTID:302551006 Wikipedia:Thorax thorax uberon anterior subdivision of trunk upper body upper trunk UBERON:0000915 thoracic segment of trunk FMA Subdivision of trunk that lies between the head and the abdomen. http://orcid.org/0000-0002-6601-2165 thorax MA:0000022 upper trunk FMA:259209 The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column. Vertebrate specific. In arthropods 'abdomen' is the most distal section of the body which lies behind the thorax or cephalothorax. If need be we can introduce some grouping class abdominal celiac BTO:0000020 CALOHA:TS-0001 EFO:0000968 EMAPA:35102 EV:0100011 FMA:9577 GAID:16 MA:0000029 MAT:0000298 MESH:A01.047 MIAA:0000298 OpenCyc:Mx4rvVjgyZwpEbGdrcN5Y29ycA SCTID:302553009 Wikipedia:Abdomen galen:Abdomen abdominopelvic region abdominopelvis uberon adult abdomen belly celiac region UBERON:0000916 abdomen MA The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column. http://orcid.org/0000-0002-6601-2165 abdominopelvic region FMA:9577 abdominopelvis FMA:9577 Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. embryonic Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo AAO:0011035 AEO:0000169 BILA:0000056 BSA:0000039 BTO:0000379 CALOHA:TS-0229 EFO:0001367 EHDAA2:0000002 EHDAA2_RETIRED:0003236 EHDAA:38 EMAPA:16039 FBbt:00000052 FMA:69068 GAID:963 MAT:0000226 MESH:D004622 MIAA:0000019 NCIT:C28147 OGEM:000001 OpenCyc:Mx4rwP1ceZwpEbGdrcN5Y29ycA SCTID:57991002 UMLS:C0013935 VHOG:0001766 Wikipedia:Embryo XAO:0000113 ZFA:0000103 http://neurolex.org/wiki/Category:Embryonic_organism embryonic organism uberon developing organism developmental tissue UBERON:0000922 embryo https://github.com/obophenotype/uberon/issues/503 Wrinkledfrog:embryos.jpg Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. BTO:0000379 FB:FBrf0039741 FB:FBrf0041814 GO:0009790 Wikipedia:Embryo Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo ZFA UMLS:C0013935 ncithesaurus:Embryo embryonic organism BILA:0000056 developing organism BILA:0000056 A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm. The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] embryonic tissue AAO:0000480 BILA:0000035 BTO:0000556 EMAPA:36033 FBbt:00000110 FMA:69069 GAID:1303 MESH:A16.254.425 NCIT:C12950 NCIT:C54105 TAO:0001122 UMLS:C0920502 UMLS:C1708239 VHOG:0001223 Wikipedia:Germ_layer XAO:0003011 ZFA:0001122 germinal layer primary germ layer uberon embryonic germ layer embryonic germ layers UBERON:0000923 Classically the germ layers are ectoderm, mesoderm and endoderm. Alternatively: primary = ectoderm, endoderm; secondary=mesoderm; tertiary=dorsal mesoderm, NC[https://github.com/obophenotype/uberon/wiki/The-neural-crest] germ layer A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm. Wikipedia:Germ_layer https://github.com/obophenotype/uberon/issues/203 The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] 2012-09-17 VHOG:0001223 VHOG ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 http://bgee.unil.ch/ embryonic tissue FMA:69069 UMLS:C0920502 ncithesaurus:Embryonic_Tissue UMLS:C1708239 ncithesaurus:Germinal_Layer germinal layer ncithesaurus:Germinal_Layer primary germ layer GO:0001704 ZFA:0001122 Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO] The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] ectodermal AAO:0000137 BILA:0000036 BTO:0000315 CALOHA:TS-0216 EFO:0000414 EHDAA2:0000428 EMAPA:16069 EV:0100003 FBbt:00000111 FMA:69070 GAID:1304 MAT:0000155 MAT:0000173 MESH:A16.254.425.273 MIAA:0000173 NCIT:C12703 SCTID:362851007 TAO:0000016 UMLS:C0013574 VHOG:0000153 Wikipedia:Ectoderm XAO:0000001 ZFA:0000016 embryonic ectoderm uberon UBERON:0000924 ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png Bgee:AN Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. Wikipedia:Ectoderm Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO] 2012-06-20 AAO:0000137 AAO AAO:EJS The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] 2012-09-17 VHOG:0000153 VHOG ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 http://bgee.unil.ch/ UMLS:C0013574 ncithesaurus:Ectoderm embryonic ectoderm VHOG:0000153 Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] endodermal AAO:0000139 BILA:0000038 BTO:0000800 CALOHA:TS-0273 EFO:0002545 EHDAA2:0000436 EMAPA:16062 EV:0100005 FBbt:00000125 FMA:69071 GAID:1305 MAT:0000175 MESH:A16.254.425.407 MIAA:0000175 NCIT:C12706 SCTID:362855003 TAO:0000017 UMLS:C0014144 VHOG:0000154 Wikipedia:Endoderm XAO:0000090 ZFA:0000017 uberon entoderm UBERON:0000925 endoderm http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png Bgee:AN Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. Wikipedia:Endoderm The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] 2012-09-17 VHOG:0000154 VHOG ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 http://bgee.unil.ch/ UMLS:C0014144 ncithesaurus:Endoderm entoderm DOI:10.5962/bhl.title.1013 The middle germ layer of the embryo, between the endoderm and ectoderm. Primary germ layer that is the middle of the embryonic germ layers.[AAO] The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] mesodermal sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates UBERON:0003263 AAO:0000304 BILA:0000037 BTO:0000839 CALOHA:TS-0623 EFO:0001981 EHDAA2:0001128 EHDAA:124 EHDAA:160 EHDAA:183 EMAPA:16083 EV:0100006 FBbt:00000126 FMA:69072 GAID:522 MAT:0000174 MESH:A16.254.425.660 MIAA:0000174 NCIT:C12750 SCTID:362854004 TAO:0000041 UMLS:C0025485 VHOG:0000152 Wikipedia:Mesoderm XAO:0000050 ZFA:0000041 uberon embryonic mesoderm entire mesoderm mesodermal mantle UBERON:0000926 mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png sometimes not considered primary Bgee:AN The middle germ layer of the embryo, between the endoderm and ectoderm. Wikipedia:Mesoderm Primary germ layer that is the middle of the embryonic germ layers.[AAO] 2012-06-20 AAO:0000304 AAO AAO:EJS The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] 2012-09-17 VHOG:0000152 VHOG ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 http://bgee.unil.ch/ sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates https://github.com/obophenotype/uberon/wiki/The-neural-crest UMLS:C0025485 ncithesaurus:Mesoderm embryonic mesoderm VHOG:0000152 entire mesoderm SCTID:362854004 https://orcid.org/0000-0002-6601-2165 Anterior part of the embryonic digestive tract that develops into a mouth. The stomodeum includes as parts an invagination of the ectoderm and the stomodeal cavity. consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO] the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx stomodeal This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity. stomodeal-hypophyseal primordium BTO:0004224 EHDAA2:0001929 EMAPA:16263 FBbt:00000439 FMA:295846 NCIT:C34306 TAO:0001290 TGMA:0000135 UMLS:C1514977 Wikipedia:Stomodeum XAO:0000269 ZFA:0001290 mouth primordium primitive oral cavity stomatodeum stomodaeum uberon mouth pit oral ectoderm oral pit UBERON:0000930 stomodeum http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png Anterior part of the embryonic digestive tract that develops into a mouth. The stomodeum includes as parts an invagination of the ectoderm and the stomodeal cavity. Wikipedia:Stomodeum http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/326 Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO] 2012-08-14 TAO:0001290 TAO ZFIN:curator the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx MP:0012522 NCBITaxon:40674 stomodeal-hypophyseal primordium XAO:0000269 UMLS:C1514977 ncithesaurus:Stomodeum mouth primordium XAO:0000269 primitive oral cavity https://orcid.org/0000-0002-6601-2165 stomatodeum Wikipedia:Stomodeum mouth pit EMAPA:16263 oral ectoderm ZFA:0001290 ZFIN:ZDB-PUB-100726-23 oral pit EMAPA:16263 Inward fold on the surface of the embryonic ectoderm that develops into an ectodermal terminal part of the digestive tract. removed WBbt:0006795 'proctodeum' - junction between the alimentary and genital tracts in the male. An inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[TAO] Inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[AAO] proctodeal AAO:0011087 EHDAA2:0000121 EMAPA:25038 FBbt:00000123 NCIT:C34278 TAO:0000066 UMLS:C0231054 VHOG:0000139 Wikipedia:Proctodeum XAO:0001019 ZFA:0000066 embryonic proctodaeum proctodaeum amnioproctodeal invagination uberon anal pit anus porus UBERON:0000931 proctodeum https://github.com/obophenotype/uberon/issues/685 EHDAA2 EHDAA2 Inward fold on the surface of the embryonic ectoderm that develops into an ectodermal terminal part of the digestive tract. ZFA:0000066 https://github.com/obophenotype/uberon/issues/685 https://sourceforge.net/p/fbbtdv/tickets/52 An inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[TAO] 2012-08-14 TAO:0000066 TAO ZFIN:curator Inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[AAO] 2012-06-20 AAO:0011087 AAO ZFA:0000066 UMLS:C0231054 ncithesaurus:Proctodeum amnioproctodeal invagination FBbt:00000123 anal pit VHOG:0000139 anus porus XAO:0001019 An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium. Portion of alimentary canal with increased circular and longitudinal smooth muscle. Bounded posteriorly by the pyloric sphincter. Mucosal lining has increased folding.[AAO] It appears that the stomach has an ancient origin. The stomach first appears in the fish lineage. The prevertebrate chordates do not have a true stomach, whereas the cartilaginous and bony fish do. Although most fish do have a true stomach, some fish species appear to have lost the stomach secondarily. The remaining vertebrate lineages do have a true stomach (at least in the adult animal), although there is great variation in the size and shape of the stomach.[well established][VHOG] We restrict this to the vertebrate specific structure - see the grouping class 'food storage organ' for analogous structures in other species. Teleosts: Zebrafish is functionally stomach-less, but may retain ontogenic footprint. Although the precise shape and size of the stomach varies widely among different vertebrates, the relative positions of the oesophageal and duodenal openings remain relatively constant. As a result, the organ always curves somewhat to the left before curving back to meet the pyloric sphincter. However, lampreys, hagfishes, chimaeras, lungfishes, and some teleost fish have no stomach at all, with the oesophagus opening directly into the intestine. The gastric lining is usually divided into two regions, an anterior portion lined by fundic glands, and a posterior with pyloric glands. Cardiac glands are unique to mammals, and even then are absent in a number of species. The distributions of these glands vary between species, and do not always correspond with the same regions as in man. Furthermore, in many non-human mammals, a portion of the stomach anterior to the cardiac glands is lined with epithelium essentially identical to that of the oesophagus. Ruminants, in particular, have a complex stomach, the first three chambers of which are all lined with oesophageal mucosa AAO:0000579 ANISEED:1235297 BTO:0001307 CALOHA:TS-0980 EFO:0000837 EHDAA2:0001915 EHDAA:2993 EMAPA:17021 EV:0100070 FMA:7148 GAID:293 MA:0000353 MAT:0000051 MESH:A03.492.766 MIAA:0000051 NCIT:C12391 OpenCyc:Mx4rvVjlqpwpEbGdrcN5Y29ycA SCTID:181246003 TAO:0002121 UMLS:C0038351 VHOG:0000408 Wikipedia:Stomach XAO:0000128 galen:Stomach stomach chamber uberon anterior intestine gaster mesenteron ventriculus UBERON:0000945 stomach Stomach:diagram.svg cjm cjm absent in lampreys and hagfishes ISBN:0073040584 ISBN:0486692132 An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium. ISBN:0073040584 Wikipedia:Stomach https://orcid.org/0000-0002-6601-2165 Wikipedia Wikipedia ZFA Wikipedia Portion of alimentary canal with increased circular and longitudinal smooth muscle. Bounded posteriorly by the pyloric sphincter. Mucosal lining has increased folding.[AAO] 2012-06-20 AAO:0000579 AAO AAO:EJS It appears that the stomach has an ancient origin. The stomach first appears in the fish lineage. The prevertebrate chordates do not have a true stomach, whereas the cartilaginous and bony fish do. Although most fish do have a true stomach, some fish species appear to have lost the stomach secondarily. The remaining vertebrate lineages do have a true stomach (at least in the adult animal), although there is great variation in the size and shape of the stomach.[well established][VHOG] 2012-09-17 VHOG:0000408 VHOG DOI:10.1046/j.1525-142x.2000.00076.x Smith DM, Grasty RC, Theodosiou NA, Tabin CJ, Nascone-Yoder NM, Evolutionary relationships between the amphibian, avian, and mammalian stomachs. Evolution and development (2000) http://bgee.unil.ch/ We restrict this to the vertebrate specific structure - see the grouping class 'food storage organ' for analogous structures in other species. Teleosts: Zebrafish is functionally stomach-less, but may retain ontogenic footprint. Although the precise shape and size of the stomach varies widely among different vertebrates, the relative positions of the oesophageal and duodenal openings remain relatively constant. As a result, the organ always curves somewhat to the left before curving back to meet the pyloric sphincter. However, lampreys, hagfishes, chimaeras, lungfishes, and some teleost fish have no stomach at all, with the oesophagus opening directly into the intestine. The gastric lining is usually divided into two regions, an anterior portion lined by fundic glands, and a posterior with pyloric glands. Cardiac glands are unique to mammals, and even then are absent in a number of species. The distributions of these glands vary between species, and do not always correspond with the same regions as in man. Furthermore, in many non-human mammals, a portion of the stomach anterior to the cardiac glands is lined with epithelium essentially identical to that of the oesophagus. Ruminants, in particular, have a complex stomach, the first three chambers of which are all lined with oesophageal mucosa WP:Stomach#In_other_animals UMLS:C0038351 ncithesaurus:Stomach gaster BTO:0001307 ventriculus Wikipedia:Stomach The main trunk of the systemic arterial system that carries blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation This class is currently a mixed bag, encompassing (1) the entirety of the mammalian aorta together with (2) the developmental and phylogenetic homologs of its segments: the ventral aorta and dorsal aortae. The main artery of the circulatory system which carries oxygenated blood from the heart to all the arteries of the body except those of the lungs.[AAO] When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG] aortic All amniotes have a broadly similar arrangement to that of humans, albeit with a number of individual variations. In fish, however, there are two separate vessels referred to as aortas. The ventral aorta carries de-oxygenated blood from the heart to the gills; part of this vessel forms the ascending aorta in tetrapods (the remainder forms the pulmonary artery). A second, dorsal aorta carries oxygenated blood from the gills to the rest of the body, and is homologous with the descending aorta of tetrapods. The two aortas are connected by a number of vessels, one passing through each of the gills. Amphibians also retain the fifth connecting vessel, so that the aorta has two parallel arches AAO:0010213 BTO:0000135 CALOHA:TS-0046 EFO:0000265 EMAPA:18601 EV:0100027 FMA:3734 GAID:469 MA:0000062 MAT:0000035 MESH:D001011 MIAA:0000035 NCIT:C12669 OpenCyc:Mx4rvVjvTpwpEbGdrcN5Y29ycA SCTID:181298001 UMLS:C0003483 VHOG:0001523 Wikipedia:Aorta XAO:0003010 galen:Aorta trunk of aortic tree trunk of systemic arterial tree dorsal aorta uberon arteria maxima UBERON:0000947 aorta Aorta:scheme.jpg MA EHDAA2 The main trunk of the systemic arterial system that carries blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation ISBN:0-683-40008-8 MESH:A07.231.114.056 MP:0000272 Wikipedia:Aorta http://orcid.org/0000-0002-6601-2165 This class is currently a mixed bag, encompassing (1) the entirety of the mammalian aorta together with (2) the developmental and phylogenetic homologs of its segments: the ventral aorta and dorsal aortae. WP The main artery of the circulatory system which carries oxygenated blood from the heart to all the arteries of the body except those of the lungs.[AAO] 2012-06-20 AAO:0010213 AAO AAO:BJB When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG] 2012-09-17 VHOG:0001523 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620 http://bgee.unil.ch/ UMLS:C0003483 ncithesaurus:Aorta dorsal aorta Wikipedia:Aorta#In_other_animals ZFA:0000014 arteria maxima Wikipedia:Aorta A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ. Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO] Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO] relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO] As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG] cardiac AAO:0010210 BILA:0000020 BTO:0000562 CALOHA:TS-0445 EFO:0000815 EHDAA2:0000738 EHDAA:420 EMAPA:16105 EV:0100018 FMA:7088 GAID:174 MA:0000072 MAT:0000036 MESH:D006321 MIAA:0000036 NCIT:C12727 OpenCyc:Mx4rvVjvDpwpEbGdrcN5Y29ycA SCTID:302509004 TAO:0000114 UMLS:C0018787 VHOG:0000276 Wikipedia:Heart XAO:0000064 ZFA:0000114 galen:Heart chambered heart vertebrate heart branchial heart uberon cardium UBERON:0000948 Taxon notes:" the ascidian tube-like heart lacks chambers....The ascidian heart is formed after metamorphosis as a simple tube-like structure with a single-layered myoepithelium that is continuous with a single-layered pericar- dial wall. It lacks chambers and endocardium.... The innovation of the chambered heart was a key event in vertebrate evolution, because the chambered heart generates one-way blood flow with high pressure, a critical requirement for the efficient blood supply of large-body vertebrates... all extant vertebrates have hearts with two or more chambers (Moorman and Christoffels 2003)" DOI:10.1101/gad.1485706 heart MA A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ. Wikipedia:Heart http://orcid.org/0000-0002-6601-2165 Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO] 2012-08-14 TAO:0000114 TAO ZFIN:curator Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO] 2012-06-20 AAO:0010210 AAO AAO:BJB relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO] 2012-06-20 AAO:0010210 AAO As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG] 2012-09-17 VHOG:0000276 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481 http://bgee.unil.ch/ UMLS:C0018787 ncithesaurus:Heart chambered heart https://orcid.org/0000-0002-6601-2165 branchial heart cardium EMAPA:16105 Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity. Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO] Multicellular organisms have complex endocrine systems, allowing responses to environmental stimuli, regulation of development, reproduction, and homeostasis. Nuclear receptors (NRs), a metazoan-specific family of ligand-activated transcription factors, play central roles in endocrine responses, as intermediates between signaling molecules and target genes. The NR family includes ligand-bound and orphan receptors, that is, receptors with no known ligand or for which there is no ligand Pocket. Understanding NR evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...).[well established][VHOG] endocrine AAO:0010279 CALOHA:TS-1301 EFO:0002969 EHDAA2:0002224 EMAPA:35306 EV:0100128 FBbt:00005068 FMA:9668 GAID:439 MA:0000012 MESH:D004703 NCIT:C12705 SCTID:278876000 TAO:0001158 UMLS:C0014136 VHOG:0000098 Wikipedia:Endocrine_system XAO:0000158 ZFA:0001158 endocrine glandular system endocrine system systema endocrinum uberon UBERON:0000949 endocrine system Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity. NLM:endocrine+system Wikipedia:Endocrine_system Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO] 2012-06-20 AAO:0010279 AAO AAO:BJB Multicellular organisms have complex endocrine systems, allowing responses to environmental stimuli, regulation of development, reproduction, and homeostasis. Nuclear receptors (NRs), a metazoan-specific family of ligand-activated transcription factors, play central roles in endocrine responses, as intermediates between signaling molecules and target genes. The NR family includes ligand-bound and orphan receptors, that is, receptors with no known ligand or for which there is no ligand Pocket. Understanding NR evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...).[well established][VHOG] 2012-09-17 VHOG:0000098 VHOG DOI:10.1073/pnas.0812138106 Markov GV, Tavares R, Dauphin-Villemant C, Demeneix BA, Baker ME, Laudet V, Independent elaboration of steroid hormone signaling pathways in metazoans. PNAS (2009) http://bgee.unil.ch/ UMLS:C0014136 ncithesaurus:Endocrine_System endocrine glandular system EHDAA2:0002224 The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]. requires review for applicability to invertebrate structures, e.g. synganglion Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO] Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO] The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO) (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG] AAO:0010478 ABA:Brain BAMS:Br BAMS:Brain BILA:0000135 BIRNLEX:796 BTO:0000142 CALOHA:TS-0095 DHBA:10155 EFO:0000302 EHDAA2:0000183 EHDAA:2641 EHDAA:6485 EMAPA:16894 EV:0100164 FBbt:00005095 FMA:50801 GAID:571 HBA:4005 MA:0000168 MAT:0000098 MBA:8 MBA:997 MESH:D001921 MIAA:0000098 NCIT:C12439 OpenCyc:Mx4rvVjT65wpEbGdrcN5Y29ycA PBA:3999 SCTID:258335003 TAO:0000008 UMLS:C0006104 UMLS:C1269537 VHOG:0000157 Wikipedia:Brain XAO:0000010 ZFA:0000008 galen:Brain http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=21 uberon encephalon suprasegmental levels of nervous system suprasegmental structures synganglion the brain UBERON:0000955 brain GO FMA Bgee:AN The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]. Wikipedia:Brain https://github.com/obophenotype/uberon/issues/300 Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO] 2012-08-14 TAO:0000008 TAO ZFIN:curator Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO] 2012-06-20 AAO:0010478 AAO AAO:BJB The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO) http://neurolex.org/wiki/Cumbo_terms (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000157 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 http://bgee.unil.ch/ UMLS:C0006104 BIRNLEX:796 UMLS:C0006104 ncithesaurus:Brain UMLS:C1269537 BIRNLEX:796 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=21 BIRNLEX:796 encephalon BTO:0000142 suprasegmental levels of nervous system NeuroNames:21 suprasegmental structures NeuroNames:21 the brain NeuroNames:21 The thin layer of gray matter on the surface of the cerebral hemisphere that develops from the telencephalon. It consists of the neocortex (6 layered cortex or isocortex), the hippocampal formation and the olfactory cortex. We follow NIFSTD in defining cerebral cortex and including both neocortex and hippocampal formation (DG+hippocampus). The cerebral cortex is a structure within the brain that plays a key role in memory, attention, perceptual awareness, thought, language, and consciousness. It constitutes the outermost layer of the cerebrum. In preserved brains, it has a grey color, hence the name 'grey matter'. Grey matter is formed by neurons and their unmyelinated fibers, whereas the white matter below the grey matter of the cortex is formed predominantly by myelinated axons interconnecting different regions of the central nervous system. The human cerebral cortex is 2-4 mm (0.08-0.16 inches) thick. The surface of the cerebral cortex is folded in large mammals, such that more than two-thirds of the cortical surface is buried in the grooves, called 'sulci. ' The phylogenetically most recent part of the cerebral cortex, the neocortex, also called isocortex, is differentiated into six horizontal layers; the more ancient part of the cerebral cortex, the hippocampus (also called archicortex), has at most three cellular layers, and is divided into subfields. Relative variations in thickness or cell type (among other parameters) allow us to distinguish between different neocortical architectonic fields. The geometry of at least some of these fields seems to be related to the anatomy of the cortical folds, and, for example, layers in the upper part of the cortical ridges seem to be more clearly differentiated than in its deeper parts. [WP,unvetted][Wikipedia:Cerebral_cortex]. Migration of neurons from the basal or striatal portions of the anterior part of the neural tube occurs to varying degrees in different vertebrate classes, but a true cerebral cortex is generally acknowledged to have made its first appearance in reptiles. The definition can be unambiguous, since 'cortex' simply implies the existence of a surface neuronal layer with an overlying 'zonal lamina' or 'molecular' layer containing dendrites and axons, which is separated from the underlying basal 'matrix' by white matter. Although reptilian cerebral cortex does indeed fulfill these conditions in certain locations, the separation from striatal structures is often indistinct, so that it may even be argued that some primitive dipnoans possess a pallium or cortex. Nevertheless, an extensive laminated layer separated by underlying white matter is well represented only in reptiles and mammals.[well established][VHOG] hagfishes have independently evolved a highly laminated cerebral cortex, comparable in many ways to the cerebral cortex of mammals [http://icb.oxfordjournals.org/content/42/4/743] BAMS:C BAMS:CTX BAMS:Cerebral_cortex BAMS:Cx BIRNLEX:1494 BM:Tel-Cx BTO:0000233 CALOHA:TS-0091 DHBA:10159 EFO:0000328 EHDAA2:0000234 EHDAA:5464 EMAPA:17544 EV:0100166 FMA:61830 GAID:629 HBA:4008 MA:0000185 MAT:0000108 MBA:688 MESH:A08.186.211.730.885.213 MIAA:0000108 NCIT:C12443 PBA:128011354 SCTID:362880003 UMLS:C0007776 VHOG:0000722 Wikipedia:Cerebral_cortex http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=39 cortex of cerebral hemisphere uberon brain cortex cortex cerebralis cortex cerebri cortical plate (CTXpl) cortical plate (areas) pallium of the brain UBERON:0000956 cerebral cortex http://upload.wikimedia.org/wikipedia/commons/7/7b/Cerebral_Cortex_location.jpg http://upload.wikimedia.org/wikipedia/commons/9/9a/Brainmaps-macaque-hippocampus.jpg FMA GO ISBN:0471888893 FMA MA Wikipedia The thin layer of gray matter on the surface of the cerebral hemisphere that develops from the telencephalon. It consists of the neocortex (6 layered cortex or isocortex), the hippocampal formation and the olfactory cortex. BIRNLEX:1494 The cerebral cortex is a structure within the brain that plays a key role in memory, attention, perceptual awareness, thought, language, and consciousness. It constitutes the outermost layer of the cerebrum. In preserved brains, it has a grey color, hence the name 'grey matter'. Grey matter is formed by neurons and their unmyelinated fibers, whereas the white matter below the grey matter of the cortex is formed predominantly by myelinated axons interconnecting different regions of the central nervous system. The human cerebral cortex is 2-4 mm (0.08-0.16 inches) thick. The surface of the cerebral cortex is folded in large mammals, such that more than two-thirds of the cortical surface is buried in the grooves, called 'sulci. ' The phylogenetically most recent part of the cerebral cortex, the neocortex, also called isocortex, is differentiated into six horizontal layers; the more ancient part of the cerebral cortex, the hippocampus (also called archicortex), has at most three cellular layers, and is divided into subfields. Relative variations in thickness or cell type (among other parameters) allow us to distinguish between different neocortical architectonic fields. The geometry of at least some of these fields seems to be related to the anatomy of the cortical folds, and, for example, layers in the upper part of the cortical ridges seem to be more clearly differentiated than in its deeper parts. [WP,unvetted][Wikipedia:Cerebral_cortex]. Wikipedia:Cerebral_cortex Migration of neurons from the basal or striatal portions of the anterior part of the neural tube occurs to varying degrees in different vertebrate classes, but a true cerebral cortex is generally acknowledged to have made its first appearance in reptiles. The definition can be unambiguous, since 'cortex' simply implies the existence of a surface neuronal layer with an overlying 'zonal lamina' or 'molecular' layer containing dendrites and axons, which is separated from the underlying basal 'matrix' by white matter. Although reptilian cerebral cortex does indeed fulfill these conditions in certain locations, the separation from striatal structures is often indistinct, so that it may even be argued that some primitive dipnoans possess a pallium or cortex. Nevertheless, an extensive laminated layer separated by underlying white matter is well represented only in reptiles and mammals.[well established][VHOG] 2012-09-17 VHOG:0000722 VHOG DOI:10.1111/j.1749-6632.1969.tb20437.x Kruger L, Experimental analyses of the reptilian nervous system. Annals of the New York Academy of Sciences (1969) http://bgee.unil.ch/ UMLS:C0007776 BIRNLEX:1494 UMLS:C0007776 ncithesaurus:Cortex http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=39 BIRNLEX:1494 cortex of cerebral hemisphere BTO:0000233 FMA:61830 brain cortex BTO:0000233 cortex cerebralis NeuroNames:39 cortex cerebri Wikipedia:Cerebral_cortex cortical plate (CTXpl) NeuroNames:39 cortical plate (areas) NeuroNames:39 pallium of the brain BTO:0000233 Any thin layer or plate. TODO - merge with cell layer? laminar Wikipedia:Lamina_of_the_vertebral_arch laminar tissue uberon UBERON:0000957 lamina http://upload.wikimedia.org/wikipedia/commons/8/80/Laminaarcusvertebrae.png Any thin layer or plate. Wikipedia:Lamina_of_the_vertebral_arch The cervical nerves are the spinal nerves from the cervical vertebrae. Although there are seven cervical vertebrae (C1-C7), there are eight cervical nerves (C1-C8). All nerves except C8 emerge above their corresponding vertebrae, while the C8 nerve emerges below the C7 vertebra. (In the other portions of the spine, the nerve emerges below the vertebra with the same name. Dorsal (posterior) distribution includes the greater occipital (C2) and third occipital (C3). Ventral (anterior) distribution includes the cervical plexus (C1-C4) and brachial plexus (C5-C8) [WP,unvetted]. BAMS:cern FMA:5859 NCIT:C32299 NLXANAT:20090207 SCTID:360497008 UMLS:C0228815 Wikipedia:Cervical_nerves http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=2351 cervical nerve cervical nerve tree cervical spinal nerve nervus cervicalis uberon UBERON:0000962 Innervates: sternohyoid muscle, sternothyroid muscle, omohyoid muscle[WP] nerve of cervical vertebra http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray795.png The cervical nerves are the spinal nerves from the cervical vertebrae. Although there are seven cervical vertebrae (C1-C7), there are eight cervical nerves (C1-C8). All nerves except C8 emerge above their corresponding vertebrae, while the C8 nerve emerges below the C7 vertebra. (In the other portions of the spine, the nerve emerges below the vertebra with the same name. Dorsal (posterior) distribution includes the greater occipital (C2) and third occipital (C3). Ventral (anterior) distribution includes the cervical plexus (C1-C4) and brachial plexus (C5-C8) [WP,unvetted]. Wikipedia:Cervical_nerves UMLS:C0228815 ncithesaurus:Cervical_Nerve cervical nerve FMA:5859 nervus cervicalis FMA:5859 FMA:TA the transparent anterior portion of the fibrous coat of the eye that serves as the chief refractory structure corneal Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals. In fish, and aquatic vertebrates in general, the cornea plays no role in focusing light, since it has virtually the same refractive index as water AAO:0010344 BTO:0000286 CALOHA:TS-0171 EFO:0000377 EHDAA2:0000316 EHDAA:10199 EMAPA:17161 EV:0100341 FMA:58238 GAID:892 MA:0000266 MESH:D003315 NCIT:C12342 OpenCyc:Mx4rvViBa5wpEbGdrcN5Y29ycA SCTID:181162001 TAO:0000640 UMLS:C0010031 VHOG:0000164 Wikipedia:Cornea XAO:0000180 ZFA:0000640 cornea of camera-type eye uberon corneas tunica cornea UBERON:0000964 cornea http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg XAO MA MA FMA-isa definitional the transparent anterior portion of the fibrous coat of the eye that serves as the chief refractory structure ISBN:0-683-40008-8 MESH:A09.371.060.217 MP:0001312 UMLS:C0010031 ncithesaurus:Cornea cornea of camera-type eye GO:0061303 corneas ZFA:0000640 Transparent part of camera-type eye that helps to refract light to be focused on the retina. The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] This class excludes compound eye corneal lenses. AAO:0010348 BTO:0000723 CALOHA:TS-0545 EHDAA:9057 EMAPA:17838 EV:0100343 FMA:58241 MA:0000275 MAT:0000141 MESH:A09.371.509 MIAA:0000141 NCIT:C12743 OpenCyc:Mx4rvVj0fZwpEbGdrcN5Y29ycA RETIRED_EHDAA2:0000975 SCTID:181169005 TAO:0000035 UMLS:C0023317 VHOG:0000169 Wikipedia:Lens_(anatomy) XAO:0000008 ZFA:0000035 camera-type eye lens eye lens lens lens crystallina uberon crystalline lens lenses ocular lens UBERON:0000965 The lens is avascular and nourished by diffusion from the aqueous and vitreous lens of camera-type eye Transparent part of camera-type eye that helps to refract light to be focused on the retina. Wikipedia:Lens_(anatomy) http://orcid.org/0000-0002-6601-2165 The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] 2012-09-17 VHOG:0000169 VHOG DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007) http://bgee.unil.ch/ UMLS:C0023317 ncithesaurus:Crystalline_Lens camera-type eye lens GO:0002088 eye lens lens lens crystallina Wikipedia:Lens_(anatomy) crystalline lens BTO:0000723 lenses ZFA:0000035 ocular lens BTO:0000723 The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates. The portion of the eye developing from the optic primordium and including the neural retina and the retinal pigment layer. Kimmel et al, 1995.[TAO] The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] retinal AAO:0010352 BAMS:R BIRNLEX:1153 BTO:0001175 CALOHA:TS-0865 EFO:0000832 EHDAA2:0001627 EHDAA:4757 EMAPA:17168 EV:0100348 FMA:58301 GAID:755 MA:0000276 MAT:0000142 MBA:304325711 MESH:D012160 MIAA:0000142 NCIT:C12343 NIFSTD_RETIRED:birnlex_1156 OpenCyc:Mx4rvViTfpwpEbGdrcN5Y29ycA SCTID:181171005 TAO:0000152 UMLS:C0035298 UMLS:C1278894 VHOG:0000229 Wikipedia:Retina XAO:0000009 ZFA:0000152 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1862 inner layer of eyeball retina of camera-type eye tunica interna of eyeball uberon Netzhaut retinas UBERON:0000966 Currently this class encompasses only verteberate AOs but could in theory also include cephalopod - we may want to make a more specific class for vertebrate retina. note that this class excludes ommatidial retinas, as the retina must be part of an eyeball. Use the parent class photoreceptor array / light-sensitive tissue for arthropods retina http://upload.wikimedia.org/wikipedia/commons/e/ed/Human_eye_cross-sectional_view_grayscale.png FMA FMA FMA EHDAA2 The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates. Wikipedia:Retina ZFIN:curator The portion of the eye developing from the optic primordium and including the neural retina and the retinal pigment layer. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000152 TAO ZFIN:curator The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] 2012-09-17 VHOG:0000229 VHOG DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007) http://bgee.unil.ch/ UMLS:C0035298 BIRNLEX:1153 UMLS:C0035298 ncithesaurus:Retina UMLS:C1278894 BIRNLEX:1153 retina of camera-type eye GO:0060041 Netzhaut BTO:0001175 retinas ZFA:0000152 An organ that detects light. This class encompasses a variety of light-detecting structures from different phyla with no implication of homology, from the compound insect eye to the vertebrate camera-type eye (distinct classes are provided for each) ocular optic Note that whilst this is classified as an organ, it is in fact more of a unit composed of different structures: in Drosophila, it includes the interommatidial bristle as a part; we consider here the vertebrate eye to include the eyeball/eye proper as a part, with the eye having as parts (when present): eyelids, conjuctiva, BILA:0000017 BTO:0000439 CALOHA:TS-0309 EFO:0000827 EV:0100336 FBbt:00005162 GAID:69 MAT:0000140 MESH:D005123 MIAA:0000140 OpenCyc:Mx4rvViTvpwpEbGdrcN5Y29ycA Wikipedia:Eye uberon light-detecting organ visual apparatus UBERON:0000970 eye PMID:21062451 PMID:21062451 An organ that detects light. https://orcid.org/0000-0002-6601-2165 visual apparatus EV:0100336 An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column. true necks are considered to be present when the pectoral girdle is separate from the skull - Tiktaalik is the earliest known fish to have a true neck. cervical AEO:0000108 BTO:0000420 CALOHA:TS-2045 EFO:0000967 EHDAA2:0003108 EMAPA:35587 FMA:7155 GAID:86 MA:0000024 MAT:0000297 MESH:D009333 MIAA:0000297 NCIT:C13063 OpenCyc:Mx4rvVjLF5wpEbGdrcN5Y29ycA SCTID:302550007 UMLS:C0027530 Wikipedia:Neck galen:Neck uberon collum neck (volume) UBERON:0000974 neck Female:neck.jpg An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column. http://orcid.org/0000-0002-6601-2165 ISBN:9780674021839 UMLS:C0027530 ncithesaurus:Neck collum Wikipedia:Neck neck (volume) FMA:7155 The invaginated serous membrane that surrounds the lungs (the visceral portion) and lines the walls of the pleural cavity (parietal portion). The serous membrane that covers the lungs and lines the pleural cavity. [Kaufman_MH_and_Bard_JBL, The_anatomical_basis_of_mouse_development_(1999)_San_Diego:_Academic_Press, p.264][VHOG] pleural In MA, is_a cavity lining (which we equate to parietal). In FMA, is_a (viscous) serous membrane (which includes mesothelium plus connective tissue). Note the MA structure should probably be associated with the mesothelium of pleura in FMA. JB/EHDAA2 argues the term 'pleura' is best used for the mesothelial lining (thus excluding connective tissue). See https://github.com/obophenotype/uberon/issues/86 BTO:0001791 CALOHA:TS-2081 EFO:0001980 EMAPA:16775 EV:0100044 FMA:9583 GAID:360 MA:0000433 MESH:D010994 NCIT:C12469 OpenCyc:Mx4rv3zwLZwpEbGdrcN5Y29ycA SCTID:181609007 UMLS:C0032225 VHOG:0000394 Wikipedia:Pleura wall of pleural sac uberon pleura pleural tissue UBERON:0000977 pleura http://upload.wikimedia.org/wikipedia/commons/a/ab/Gray965.png https://github.com/obophenotype/uberon/issues/86 The invaginated serous membrane that surrounds the lungs (the visceral portion) and lines the walls of the pleural cavity (parietal portion). ISBN:0-683-40008-8 MP:0010820 UBERON:cjm Wikipedia:Pulmonary_pleurae https://github.com/obophenotype/uberon/issues/1231 BGEE:AN ISBN:978-0030223693 The serous membrane that covers the lungs and lines the pleural cavity. [Kaufman_MH_and_Bard_JBL, The_anatomical_basis_of_mouse_development_(1999)_San_Diego:_Academic_Press, p.264][VHOG] 2012-09-17 VHOG:0000394 VHOG ISBN:0124020607 http://bgee.unil.ch/ UMLS:C0032225 ncithesaurus:Pleural_Tissue pleural tissue BTO:0001791 NCIT:C12469 Anatomical cluster that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO]. Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO] Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO] articulation joint AEO:0000182 BTO:0001686 CALOHA:TS-2023 EFO:0000948 EMAPA:35456 FMA:7490 GAID:102 MA:0000319 MAT:0000188 MESH:D007596 MIAA:0000188 NCIT:C13044 OpenCyc:Mx4rvVjjdpwpEbGdrcN5Y29ycA RETIRED_EHDAA2:0003182 SCTID:302536002 TAO:0000367 UMLS:C0022417 VHOG:0001276 VSAO:0000101 Wikipedia:Joint XAO:0000171 ZFA:0001596 galen:Joint uberon articular joint joints UBERON:0000982 skeletal joint Anatomical cluster that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO]. GO_REF:0000034 VSAO:0000101 Wikipedia:Joint http://dx.plos.org/10.1371/journal.pone.0051070 Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO] 2012-08-14 VSAO:0000101 VSAO PSPUB:0000170 Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO] 2012-08-14 TAO:0000367 TAO TAO:pem articulation VSAO:0000101 joint FMA:7490 VSAO:0000101 UMLS:C0022417 ncithesaurus:Joint articular joint BTO:0001686 joints ZFA:0001596 The part of the central nervous system lying between the medulla oblongata and the midbrain, ventral to the cerebellum. The pons is not present in zebrafish. In this ontology we currently have some structures which are applicable to zebrafish appearing as parts of the pons. Currently we only include the weaker dubious_for_taxon relationship ubtil this is resolved The part of the central nervous system lying between the medulla oblongata and the midbrain, ventral to the cerebellum. [TFD][VHOG] During the embryonic development of birds and mammals, neuroblasts migrate from the cerebellum into the ventral part of the rhombencephalon and differentiate into pontine and other nuclei, which relay information from between the cerebrum and cerebellum, and a conspicuous band of transverse fibers. This region is known as the pons. A pons does not differentiate in reptiles and anamniotes (...).[well established][VHOG] BAMS:PONS BAMS:Pons BIRNLEX:733 BM:Pons BTO:0001101 CALOHA:TS-0813 DHBA:10661 EFO:0001394 EHDAA2:0004394 EMAPA:17563 EV:0100253 FMA:67943 GAID:578 HBA:9131 MA:0000204 MAT:0000115 MBA:771 MESH:D011149 MIAA:0000115 NCIT:C12511 SCTID:279103004 UMLS:C0032639 UMLS:C1280999 VHOG:0001176 Wikipedia:Pons http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=547 pons Varolii pons of Varolius uberon pons cerebri UBERON:0000988 pons http://upload.wikimedia.org/wikipedia/commons/3/36/Gray768.png neuronames The part of the central nervous system lying between the medulla oblongata and the midbrain, ventral to the cerebellum. VHOG:0001176 The part of the central nervous system lying between the medulla oblongata and the midbrain, ventral to the cerebellum. [TFD][VHOG] 2012-09-17 VHOG:0001176 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/pons During the embryonic development of birds and mammals, neuroblasts migrate from the cerebellum into the ventral part of the rhombencephalon and differentiate into pontine and other nuclei, which relay information from between the cerebrum and cerebellum, and a conspicuous band of transverse fibers. This region is known as the pons. A pons does not differentiate in reptiles and anamniotes (...).[well established][VHOG] 2012-09-17 VHOG:0001176 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.474 http://bgee.unil.ch/ UMLS:C0032639 BIRNLEX:733 UMLS:C0032639 ncithesaurus:Pons_Varolii UMLS:C1280999 BIRNLEX:733 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=547 BIRNLEX:733 pons Varolii ncithesaurus:Pons_Varolii pons cerebri NeuroNames:547 Anatomical system that has as its parts the organs concerned with reproduction. consider splitting genitalia from reproductive system Anatomical system which consists of organs and tissues associated with sexual reproduction of the organism.[AAO] Arguably, one of the most important aspects of urbilaterian organogenesis would have been gonadogenesis, since Urbilateria must have successfully generated gametes and developed a strategy for extrusion and fertilization, in order to be the ancestor of all living Bilateria.[well established][VHOG] AAO:0010258 BILA:0000103 BTO:0000081 CALOHA:TS-1318 EFO:0000809 EHDAA2:0001603 EHDAA:5923 EMAPA:17381 EV:0100100 FBbt:00004857 FMA:7160 GAID:363 HAO:0000374 HAO:0000895 MA:0000326 MIAA:0000305 NCIT:C12841 OpenCyc:Mx4rvVja4ZwpEbGdrcN5Y29ycA SCTID:278875001 TAO:0000632 UMLS:C1261210 VHOG:0000182 WBbt:0005747 Wikipedia:Reproductive_system XAO:0000142 ZFA:0000632 uberon Geschlechtsorgan animal reproductive system genital system genital tract genitalia organa genitalia reproductive tissue reproductive tract systemata genitalia UBERON:0000990 reproductive system http://upload.wikimedia.org/wikipedia/commons/5/52/Penis.svg Anatomical system that has as its parts the organs concerned with reproduction. Wikipedia:Reproductive_system Anatomical system which consists of organs and tissues associated with sexual reproduction of the organism.[AAO] 2012-06-20 AAO:0010258 AAO AAO:BJB Arguably, one of the most important aspects of urbilaterian organogenesis would have been gonadogenesis, since Urbilateria must have successfully generated gametes and developed a strategy for extrusion and fertilization, in order to be the ancestor of all living Bilateria.[well established][VHOG] 2012-09-17 VHOG:0000182 VHOG PMID:21672850 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across Bilateria. Integrative and Comparative Biology (2007) http://bgee.unil.ch/ UMLS:C1261210 ncithesaurus:Reproductive_System Geschlechtsorgan BTO:0000081 animal reproductive system BTO:0000081 genitalia organa genitalia BTO:0000081 reproductive tissue BTO:0000081 systemata genitalia Wikipedia:Reproductive_system Reproductive organ that produces and releases eggs (ovary) or sperm (testis). Anatomical structure which produces gametes as well as certain sex hormones controlled by the pituitary gonadotropins.[AAO] The part of the reproductive system that produces and releases eggs (ovary) or sperm (testis).[TAO] Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved.[uncertain][VHOG] gonadal FMA xref is a 'general anatomical term' AAO:0000213 BILA:0000123 BSA:0000079 BTO:0000534 EMAPA:17383 FBbt:00004858 FMA:18250 GAID:368 HAO:0000379 MA:0002420 MESH:D006066 NCIT:C12725 OpenCyc:Mx4rwQvdiZwpEbGdrcN5Y29ycA SCTID:304623008 TAO:0000413 UMLS:C0018067 VHOG:0000397 WBbt:0005175 Wikipedia:Gonad XAO:0003146 ZFA:0000413 gonada uberon gonads UBERON:0000991 gonad Reproductive organ that produces and releases eggs (ovary) or sperm (testis). ISBN:0140512888 Wikipedia:Gonad ZFA:0000413 ZFIN:curator Anatomical structure which produces gametes as well as certain sex hormones controlled by the pituitary gonadotropins.[AAO] 2012-06-20 AAO:0000213 AAO AAO:BJB The part of the reproductive system that produces and releases eggs (ovary) or sperm (testis).[TAO] 2012-08-14 TAO:0000413 TAO ZFIN:curator Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved.[uncertain][VHOG] 2012-09-17 VHOG:0000397 VHOG DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T, Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009) http://bgee.unil.ch/ FMA xref is a 'general anatomical term' FMA UMLS:C0018067 ncithesaurus:Gonad gonads ZFA:0000413 the gonad of a female organism which contains germ cells Either of paired female reproductive organs involved in production of ova and female sex hormones.[AAO] Female reproductive organ.[TAO] (...) while it is likely that Urbilateria lacked a complex somatic reproductive system, it is at present impossible to speculate on whether or not it possessed a true gonad, let alone any other somatic adaptations for reproduction (reference 1); Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved (reference 2).[uncertain][VHOG] ovarian Ovaries of some kind are found in the female reproductive system of many animals that employ sexual reproduction, including invertebrates. However, they develop in a very different way in most invertebrates than they do in vertebrates, and are not truly homologous. Many of the features found in human ovaries are common to all vertebrates, including the presence of follicular cells, tunica albuginea, and so on. However, many species produce a far greater number of eggs during their lifetime than do humans, so that, in fish and amphibians, there may be hundreds, or even millions of fertile eggs present in the ovary at any given time. In these species, fresh eggs may be developing from the germinal epithelium throughout life. Corpora lutea are found only in mammals, and in some elasmobranch fish; in other species, the remnants of the follicle are quickly resorbed by the ovary. In birds, reptiles, and monotremes, the egg is relatively large, filling the follicle, and distorting the shape of the ovary at maturity. Amphibians and reptiles have no ovarian medulla; the central part of the ovary is a hollow, lymph-filled space. The ovary of teleosts is also often hollow, but in this case, the eggs are shed into the cavity, which opens into the oviduct. Although most normal female vertebrates have two ovaries, this is not the case in all species. In birds and platypuses, the right ovary never matures, so that only the left is functional. In some elasmobranchs, the reverse is true, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo AAO:0000371 BILA:0000125 BSA:0000080 BTO:0000975 CALOHA:TS-0730 EFO:0000973 EHDAA2:0001360 EHDAA:8124 EMAPA:17962 EV:0100111 FBbt:00004865 FMA:7209 GAID:367 MA:0000384 MESH:D010053 MIAA:0000125 NCIT:C12404 OpenCyc:Mx4rvVi9QJwpEbGdrcN5Y29ycA SCTID:181464007 TAO:0000403 UMLS:C0029939 VHOG:0000251 Wikipedia:Ovary XAO:0000258 ZFA:0000403 animal ovary female gonad female organism genitalia gonad female organism genitalia gonada female organism reproductive system gonad female organism reproductive system gonada female reproductive system gonad female reproductive system gonada genitalia of female organism gonad genitalia of female organism gonada gonad of female organism genitalia gonad of female organism reproductive system gonad of female reproductive system gonad of genitalia of female organism gonad of reproductive system of female organism gonada of female organism genitalia gonada of female organism reproductive system gonada of female reproductive system gonada of genitalia of female organism gonada of reproductive system of female organism ovum-producing ovary reproductive system of female organism gonad reproductive system of female organism gonada uberon ovaries ovarium UBERON:0000992 ovary Female:anatomy.png http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray589.png the gonad of a female organism which contains germ cells ISBN:0-683-40008-8 MP:0001126 Wikipedia:Ovary Either of paired female reproductive organs involved in production of ova and female sex hormones.[AAO] 2012-06-20 AAO:0000371 AAO AAO:BJB Female reproductive organ.[TAO] 2012-08-14 TAO:0000403 TAO ZFIN:curator (...) while it is likely that Urbilateria lacked a complex somatic reproductive system, it is at present impossible to speculate on whether or not it possessed a true gonad, let alone any other somatic adaptations for reproduction (reference 1); Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved (reference 2).[uncertain][VHOG] 2012-09-17 VHOG:0000251 VHOG DOI:10.1093/icb/icm052 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across the Bilateria. Integrative and Comparative Biology (2007), DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T and Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009) http://bgee.unil.ch/ Ovaries of some kind are found in the female reproductive system of many animals that employ sexual reproduction, including invertebrates. However, they develop in a very different way in most invertebrates than they do in vertebrates, and are not truly homologous. Many of the features found in human ovaries are common to all vertebrates, including the presence of follicular cells, tunica albuginea, and so on. However, many species produce a far greater number of eggs during their lifetime than do humans, so that, in fish and amphibians, there may be hundreds, or even millions of fertile eggs present in the ovary at any given time. In these species, fresh eggs may be developing from the germinal epithelium throughout life. Corpora lutea are found only in mammals, and in some elasmobranch fish; in other species, the remnants of the follicle are quickly resorbed by the ovary. In birds, reptiles, and monotremes, the egg is relatively large, filling the follicle, and distorting the shape of the ovary at maturity. Amphibians and reptiles have no ovarian medulla; the central part of the ovary is a hollow, lymph-filled space. The ovary of teleosts is also often hollow, but in this case, the eggs are shed into the cavity, which opens into the oviduct. Although most normal female vertebrates have two ovaries, this is not the case in all species. In birds and platypuses, the right ovary never matures, so that only the left is functional. In some elasmobranchs, the reverse is true, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo WP UMLS:C0029939 ncithesaurus:Ovary animal ovary EFO:0000973 female organism genitalia gonad OBOL:automatic female organism genitalia gonada OBOL:automatic female organism reproductive system gonad OBOL:automatic female organism reproductive system gonada OBOL:automatic female reproductive system gonad OBOL:automatic female reproductive system gonada OBOL:automatic genitalia of female organism gonad OBOL:automatic genitalia of female organism gonada OBOL:automatic gonad of female organism genitalia OBOL:automatic gonad of female organism reproductive system OBOL:automatic gonad of female reproductive system OBOL:automatic gonad of genitalia of female organism OBOL:automatic gonad of reproductive system of female organism OBOL:automatic gonada of female organism genitalia OBOL:automatic gonada of female organism reproductive system OBOL:automatic gonada of female reproductive system OBOL:automatic gonada of genitalia of female organism OBOL:automatic gonada of reproductive system of female organism OBOL:automatic ovum-producing ovary GO:0061039 reproductive system of female organism gonad OBOL:automatic reproductive system of female organism gonada OBOL:automatic ovaries ovarium Wikipedia:Ovary The outer epithelial layer of the skin that is superficial to the dermis. A cellular, multilayered epithelium derived from the ectoderm. Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. Le Guellec et al, 2004.[TAO] The outer epithelial layer of the external integument of the body that is derived from the embryonic epiblast.[AAO] relationship loss: subclass external integument structures (AAO:0000961)[AAO] (...) outer epithelia in all metazoan animals are homologous. (...) The ancestor of all metazoans likely had an epidermis with a basal extracellular matrix (ECM), an apical extracellular glycocalyx, and one cilium with a striated rootlet per cell.[well established][VHOG] epidermal Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. In terrestrial vertebrates the epidermis often forms an outer keratinized or cornified layer, the stratum corneum. Interaction between the epideris and dermis gives rise to feathers (birds), hair and mammary glands (mammals), teeth and scales (placoid: chondrichthyans; cosmoids, ganoid, cycloid in bony fishes). epidermis skin AAO:0000143 BTO:0000404 CALOHA:TS-0283 EFO:0000954 EMAPA:17528 EV:0100153 FMA:70596 GAID:932 MA:0000153 MAT:0000154 MESH:D004817 MIAA:0000154 NCIT:C12708 SCTID:361694003 TAO:0000105 UMLS:C0014520 VHOG:0000077 Wikipedia:Epidermis_(skin) XAO:0000028 ZFA:0000105 vertebrate epidermis uberon UBERON:0001003 skin epidermis The outer epithelial layer of the skin that is superficial to the dermis. ISBN:0073040584 http://orcid.org/0000-0002-6601-2165 A cellular, multilayered epithelium derived from the ectoderm. Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. Le Guellec et al, 2004.[TAO] 2012-08-14 TAO:0000105 TAO ZFIN:curator The outer epithelial layer of the external integument of the body that is derived from the embryonic epiblast.[AAO] 2012-06-20 AAO:0000143 AAO AAO:BJB relationship loss: subclass external integument structures (AAO:0000961)[AAO] 2012-06-20 AAO:0000143 AAO (...) outer epithelia in all metazoan animals are homologous. (...) The ancestor of all metazoans likely had an epidermis with a basal extracellular matrix (ECM), an apical extracellular glycocalyx, and one cilium with a striated rootlet per cell.[well established][VHOG] 2012-09-17 VHOG:0000077 VHOG ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.71-72 http://bgee.unil.ch/ UMLS:C0014520 ncithesaurus:Epidermis Functional system which consists of structures involved in respiration. The anatomical system in which the exchange of oxygen and carbon dioxide between the organism and its environment.[AAO] There is no doubt that the primitive pattern of vertebrate air-breathing is the buccal pulse pump found in actinopterygian fishes.[well established][VHOG] AAO:0000541 BTO:0000203 CALOHA:TS-1319 EFO:0000804 EHDAA2:0001604 EHDAA:2203 EMAPA:16727 EV:0100036 FMA:7158 GAID:78 MA:0000327 MAT:0000030 MESH:D012137 MIAA:0000030 NCIT:C12779 OpenCyc:Mx4rvVjzFJwpEbGdrcN5Y29ycA SCTID:278197002 TAO:0000272 UMLS:C0035237 VHOG:0000202 Wikipedia:Respiratory_system XAO:0000117 ZFA:0000272 apparatus respiratorius respiratory system uberon Atmungssystem apparatus respiratorius systema respiratorium UBERON:0001004 respiratory system http://upload.wikimedia.org/wikipedia/commons/5/5e/Respiratory_system_complete_en.svg Functional system which consists of structures involved in respiration. Wikipedia:Respiratory_system http://orcid.org/0000-0002-6601-2165 Wikipedia:Acoelomorpha The anatomical system in which the exchange of oxygen and carbon dioxide between the organism and its environment.[AAO] 2012-06-20 AAO:0000541 AAO AAO:BJB There is no doubt that the primitive pattern of vertebrate air-breathing is the buccal pulse pump found in actinopterygian fishes.[well established][VHOG] 2012-09-17 VHOG:0000202 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.599 and Figure 18-23 http://bgee.unil.ch/ UMLS:C0035237 ncithesaurus:Respiratory_System Atmungssystem BTO:0000203 apparatus respiratorius BTO:0000203 systema respiratorium Wikipedia:Respiratory_system An airway through which respiratory air passes in organisms. This class generically groups trachea and analagous structures throughout metazoa. Consider renaming, as the term could be taken to mean lumen of tracheal system (e.g. in SNOMED). As a grouping class this is quite vague, as it is not clear where the airway begins and ends airway airways FMA:265130 SCTID:361380005 Wikipedia:Trachea uberon UBERON:0001005 respiratory airway An airway through which respiratory air passes in organisms. Wikipedia:Trachea airway http://orcid.org/0000-0002-6601-2165 airways http://orcid.org/0000-0002-6601-2165 Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes. An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO] digestive many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class AAO:0000129 BILA:0000082 BTO:0000058 CALOHA:TS-1293 EFO:0000793 EV:0100056 FBbt:00005055 FMA:7152 GAID:278 MA:0002431 MAT:0000018 MESH:D004064 MIAA:0000018 SCTID:278859004 TADS:0000170 TAO:0000339 WBbt:0005748 Wikipedia:Digestive_system XAO:0000125 ZFA:0000339 galen:DigestiveSystem ncithesaurus:Digestive_System uberon alimentary system alimentary tract gastrointestinal system gut UBERON:0001007 digestive system Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes. FB:gg NLM:alimentary+system Wikipedia:Digestive_system An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO] 2012-06-20 AAO:0000129 AAO AAO:BJB many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class MA The renal system in an anatomical system that maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products.. In various sources such as Encyclopedia Britannica, the excretory and urinary systems are indeed the same system (see wikipedia talk page); we merge two BTO classes here An anatomical system which consists of organs and tissues which produce, store, and excrete urine.[AAO] Evolution of vertebrate renal anatomy appears quite conservative when compared, for example, to evolution of respiratory and cardiovascular systems in vertebrates. Major anatomical changes in vertebrates kidneys separate those of birds and mammals from kidneys of lower vertebrates. General increase in animal size from fish to mammals is reflected by an increase in total number of nephrons per kidney, rather than by constant change in tubular dimensions.[well established][VHOG] In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels This definition is inclusive of the organs of the vertebrate renal system, as well as the Malpighian tubules of insects, and allows for future incorporation of structures such as the antennal glands of crustaceans AAO:0010257 BILA:0000015 BTO:0001244 BTO:0003092 CALOHA:TS-1323 EFO:0000803 EHDAA2:0001601 EHDAA:5901 EMAPA:17366 EV:0100095 FBbt:00005056 FMA:7159 GAID:391 MA:0000325 MAT:0000027 MESH:D014551 MIAA:0000027 NCIT:C12413 SCTID:362204003 TADS:0000162 TAO:0000163 UMLS:C1508753 VHOG:0000723 WBbt:0005736 Wikipedia:Excretory_system XAO:0000143 ZFA:0000163 galen:UrinaryTract excretory system renal system systema urinaria systema urinarium urinary system urinary tract uberon renal or urinary system renal/urinary system UBERON:0001008 renal system The renal system in an anatomical system that maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products.. DOI:10.1371/journal.pone.0099864 GO:0072001 Wikipedia Wikipedia:Acoelomorpha An anatomical system which consists of organs and tissues which produce, store, and excrete urine.[AAO] 2012-06-20 AAO:0010257 AAO AAO:BJB Evolution of vertebrate renal anatomy appears quite conservative when compared, for example, to evolution of respiratory and cardiovascular systems in vertebrates. Major anatomical changes in vertebrates kidneys separate those of birds and mammals from kidneys of lower vertebrates. General increase in animal size from fish to mammals is reflected by an increase in total number of nephrons per kidney, rather than by constant change in tubular dimensions.[well established][VHOG] 2012-09-17 VHOG:0000723 VHOG ISBN:978-3540428541 Kapoor BG, Bhavna Khanna, Ichthyology Handbook (2004) p.406 http://bgee.unil.ch/ In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels GO This definition is inclusive of the organs of the vertebrate renal system, as well as the Malpighian tubules of insects, and allows for future incorporation of structures such as the antennal glands of crustaceans DOI:10.1371/journal.pone.0099864 UMLS:C1508753 ncithesaurus:Urinary_System renal system GO:0001977 systema urinaria FMA:7159 systema urinarium BTO:0003092 renal or urinary system EHDAA:5901 organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP]. the cardiovascular system and the lymphatic system are parts of the circulatory system Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO] We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG] AAO:0000959 CALOHA:TS-2103 FBbt:00005057 OpenCyc:Mx4rvVjzG5wpEbGdrcN5Y29ycA VHOG:0001248 Wikipedia:Circulatory_system uberon systema cardiovasculare UBERON:0001009 circulatory system http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP]. Wikipedia:Circulatory_system Wikipedia:Acoelomorpha WBbt coelomocyte currently classified as circulating cell Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO] 2012-06-20 AAO:0000959 AAO AAO:BJB We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG] 2012-09-17 VHOG:0001248 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.493 http://bgee.unil.ch/ systema cardiovasculare Wikipedia:Circulatory_system Portion of connective tissue composed of adipocytes enmeshed in areolar tissue Connective tissue in which fat is stored.[TAO] Tissue that contains adipocytes, used for cushioning, thermal insulation, lubrication (primarily in the pericardium) and energy storage.[AAO] relationship loss: subclass connective tissue proper (AAO:0000099)[AAO] Adipose tissue is unique to vertebrates. It is found in mostmammals, birds, reptiles and amphibians, and a variety is found in some species of fish. Furthermore, in insects the fat body found in larvae as well as in adults shares some homology with adipose tissue.[well established][VHOG] adipose In humans, adipose tissue is located beneath the skin (subcutaneous fat), around internal organs (visceral fat), in bone marrow (yellow bone marrow) and in breast tissue. Adipose tissue is found in specific locations, which are referred to as adipose depots. Adipose tissue contains several cell types, with the highest percentage of cells being adipocytes, which contain fat droplets. Other cell types include fibroblasts, macrophages, and endothelial cells. Adipose tissue contains many small blood vessels.; Mice have eight major adipose depots, four of which are within the abdominal cavity. The paired gonadal depots are attached to the uterus and ovaries in females and the epididymis and testes in males; the paired retroperitoneal depots are found along the dorsal wall of the abdomen, surrounding the kidney, and, when massive, extend into the pelvis. The mesenteric depot forms a glue-like web that supports the intestines, and the omental depot, which originates near the stomach and spleen, and, when massive, extends into the ventral abdomen. in FMA this is dense irregular connective tissue AAO:0000001 AEO:000020 BTO:0001487 CALOHA:TS-0013 EFO:0000790 EHDAA2:0003120 EMAPA:35112 EV:0100381 FMA:20110 GAID:920 MA:0000009 MAT:0000015 MESH:D000273 MIAA:0000015 NCIT:C12472 OpenCyc:Mx4rvVjc_ZwpEbGdrcN5Y29ycA SCTID:55603005 TAO:0002134 UMLS:C0001527 VHOG:0001284 Wikipedia:Adipose_tissue XAO:0003049 ZFA:0005345 galen:FattyTissue fat fat tissue fatty tissue uberon adipose bodyfat fatty depot UBERON:0001013 adipose tissue FMA Portion of connective tissue composed of adipocytes enmeshed in areolar tissue MESH:A10.165.114 MGI:cwg MP:0000003 Wikipedia:Adipose_tissue http://orcid.org/0000-0002-6601-2165 Connective tissue in which fat is stored.[TAO] 2012-08-14 TAO:0002134 TAO ZFIN:curator Tissue that contains adipocytes, used for cushioning, thermal insulation, lubrication (primarily in the pericardium) and energy storage.[AAO] 2012-06-20 AAO:0000001 AAO AAO:LAP relationship loss: subclass connective tissue proper (AAO:0000099)[AAO] 2012-06-20 AAO:0000001 AAO Adipose tissue is unique to vertebrates. It is found in mostmammals, birds, reptiles and amphibians, and a variety is found in some species of fish. Furthermore, in insects the fat body found in larvae as well as in adults shares some homology with adipose tissue.[well established][VHOG] 2012-09-17 VHOG:0001284 VHOG DOI:10.1017/S0029665107005423 Haugen F, Drevon CA, The interplay between nutrients and the adipose tissue. The Proceedings of the Nutrition Society (2007) http://bgee.unil.ch/ in FMA this is dense irregular connective tissue FMA UMLS:C0001527 ncithesaurus:Adipose_Tissue fat MA:0000009 adipose BTO:0001487 bodyfat BTO:0001487 A subdivision of the muscular system corresponding to a subdisivision of an organism. In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here. AAO:0011066 BTO:0000887 EFO:0001949 EMAPA:32715 EMAPA:35577 FMA:32558 MA:0000165 NCIT:C13056 OpenCyc:Mx4rvVjmr5wpEbGdrcN5Y29ycA TAO:0000548 UMLS:C0026845 VSAO:0005038 WBbt:0005737 Wikipedia:Muscular_system ZFA:0000548 muscle group muscles set musculature musculi set of muscles set of skeletal muscles uberon muscle system muscles musculature system UBERON:0001015 musculature http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png A subdivision of the muscular system corresponding to a subdisivision of an organism. Wikipedia:Muscular_system https://orcid.org/0000-0002-6601-2165 In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here. FMA UMLS:C0026845 ncithesaurus:Muscle musculi FMA:32558 FMA:TA set of muscles FMA:32558 set of skeletal muscles MA:0000165 The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]. A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO] Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO] Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG] nervous neural AAO:0000324 BILA:0000079 BIRNLEX:844 BTO:0001484 CALOHA:TS-1313 EFO:0000802 EHDAA2:0001246 EHDAA:826 EMAPA:16469 EV:0100162 FBbt:00005093 FMA:7157 GAID:466 MA:0000016 MAT:0000026 MESH:D009420 MIAA:0000026 NCIT:C12755 OpenCyc:Mx4rvViT_pwpEbGdrcN5Y29ycA SCTID:278196006 TAO:0000396 UMLS:C0027763 VHOG:0000402 WBbt:0005735 Wikipedia:Nervous_system XAO:0000177 ZFA:0000396 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=3236 neurological system nerve net uberon systema nervosum UBERON:0001016 nervous system http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png Bgee:AN The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]. BIRNLEX:844 ISBN:0-14-051288-8 ISBN:3110148986 NLM:nervous+system WB:rynl Wikipedia:Nervous_system ZFIN:curator A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO] 2012-08-14 TAO:0000396 TAO ZFIN:curator Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO] 2012-06-20 AAO:0000324 AAO AAO:BJB Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG] 2012-09-17 VHOG:0000402 VHOG ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.117 http://bgee.unil.ch/ UMLS:C0027763 ncithesaurus:Nervous_System neurological system GO:0050877 nerve net Wikipedia:Nerve_net systema nervosum Wikipedia:Nervous_system The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. Part of the nervous system which includes the brain and spinal cord.[AAO] The brain and spinal cord. Kimmel et al, 1995.[TAO] The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO). (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG] AAO:0000090 BAMS:CNS BILA:0000080 BIRNLEX:1099 BTO:0000227 CALOHA:TS-0150 EFO:0000908 EHDAA2:0000225 EHDAA:828 EMAPA:16470 EMAPA:16754 EV:0100163 FBbt:00005094 FMA:55675 GAID:570 MA:0000167 MAT:0000457 MESH:D002490 NCIT:C12438 OpenCyc:Mx4rvzYt3pwpEbGdrcN5Y29ycA SCTID:278199004 TAO:0000012 UMLS:C0927232 VHOG:0000293 Wikipedia:Central_nervous_system XAO:0000215 ZFA:0000012 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=854 CNS systema nervosum centrale cerebrospinal axis uberon neuraxis UBERON:0001017 central nervous system FBbt cjm Bgee:AN The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. GO:0021551 http://www.frontiersinzoology.com/content/7/1/29 https://sourceforge.net/p/geneontology/ontology-requests/11422/ Wikipedia:Acoelomorpha Part of the nervous system which includes the brain and spinal cord.[AAO] 2012-06-20 AAO:0000090 AAO AAO:BJB The brain and spinal cord. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000012 TAO ZFIN:curator The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO). BIRNLEX:1099 (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG] 2012-09-17 VHOG:0000293 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 (reference 1), ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 (reference 2), DOI:10.1016/j.cell.2007.02.040 Denes AS, Jekely G, Steinmetz PRH, Raible F, Snyman H, Prud'homme B, Ferrier DEK, Balavoine G and Arendt D, Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in Bilateria. Cell (2007) (reference 3) http://bgee.unil.ch/ UMLS:C0927232 BIRNLEX:1099 UMLS:C0927232 ncithesaurus:Central_Nervous_System CNS systema nervosum centrale FMA:55675 FMA:TA cerebrospinal axis FMA:55675 neuraxis FMA:55675 An enclosed, cable-like bundle of axons in the peripheral nervous system originating in a nerve root in the central nervous system (or a condensed nervous structure) connecting with peripheral structures. A portion of tissue which is a fasiculated group of axons.[TAO] nervous AAO:0011070 AEO:0000137 BAMS:n BIRNLEX:1615 BSA:0000098 BTO:0000925 BTO:0001027 CALOHA:TS-0772 EHDAA2:0003137 EHDAA:2851 EHDAA:3776 EHDAA:4657 EMAPA:32808 EMAPA:32815 EV:0100371 FBbt:00005105 FMA:65132 FMA:65239 GAID:747 GAID:758 MA:0000217 MA:0000228 MESH:D010525 NCIT:C12466 NCIT:C12768 NLX:147826 OpenCyc:Mx4rwP3lkpwpEbGdrcN5Y29ycA SCTID:244457007 SCTID:256864008 TAO:0007009 UMLS:C0027740 UMLS:C0031119 VHOG:0000901 Wikipedia:Nervous_system XAO:0000204 XAO:0003047 ZFA:0007009 galen:Nerve nerves peripheral nerve uberon neural subtree UBERON:0001021 nerve FBbt An enclosed, cable-like bundle of axons in the peripheral nervous system originating in a nerve root in the central nervous system (or a condensed nervous structure) connecting with peripheral structures. FBbt:00005105 http://orcid.org/0000-0002-6601-2165 A portion of tissue which is a fasiculated group of axons.[TAO] 2012-08-14 TAO:0007009 TAO ZFIN:curator UMLS:C0027740 ncithesaurus:Nerve UMLS:C0031119 ncithesaurus:Peripheral_Nerve nerves TAO:0007009 peripheral nerve http://orcid.org/0000-0002-6601-2165 neural subtree FMA:65132 A nerve that transmits from sensory receptors on the surface of the body to the central nervous system. AEO:0000201 EHDAA2:0003200 FBbt:00005136 FMA:5868 OpenCyc:Mx4rv0GdXpwpEbGdrcN5Y29ycA Wikipedia:Sensory_nerve nervus sensorius uberon afferent nerve UBERON:0001027 sensory nerve AEO A nerve that transmits from sensory receptors on the surface of the body to the central nervous system. UBERON:cjm Wikipedia:Sensory_nerve nervus sensorius Wikipedia:Sensory_nerve Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information. An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG] note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs AAO:0000555 BAMS:SEN BILA:0000099 EFO:0000805 EHDAA2:0003094 EMAPA:16192 FBbt:00007692 FMA:75259 MA:0002442 MAT:0000031 MIAA:0000031 NLXANAT:090816 TAO:0000282 VHOG:0001674 Wikipedia:Sensory_system XAO:0003194 ZFA:0000282 organa sensuum sense organ subsystem sense organs sense organs set sensory subsystem sensory systems uberon organa sensuum sensory organ system set of sense organs UBERON:0001032 sensory system http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information. Wikipedia:Sensory_system An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG] 2012-09-17 VHOG:0001674 VHOG DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) http://bgee.unil.ch/ organa sensuum FMA:75259 FMA:TA sense organs FMA:75259 sense organs set FMA:75259 sensory systems TAO:0000282 organa sensuum Wikipedia:Sensory_system set of sense organs FMA:75259 The sensory system for the sense of taste. The sensory system for the sense of taste[NLXANAT:090803]. The sensory system used for the sense of taste.[AAO] gustatory in ZFA and MA this is a subtype of sensory system. we should change sensory system to disambiguate parts and wholes AAO:0010577 BILA:0000143 EFO:0000830 FMA:7194 MA:0002446 MAT:0000275 MIAA:0000275 NLXANAT:090803 SCTID:423940004 TAO:0001101 Wikipedia:Gustatory_system XAO:0003197 ZFA:0001101 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=2889 gustatory organ system taste system uberon UBERON:0001033 gustatory system The sensory system for the sense of taste. NLXANAT:090803 The sensory system for the sense of taste[NLXANAT:090803]. NLXANAT:090803 The sensory system used for the sense of taste.[AAO] 2012-06-20 AAO:0010577 AAO AAO:EJS in ZFA and MA this is a subtype of sensory system. we should change sensory system to disambiguate parts and wholes ZFA Anterior subdivision of a digestive tract. Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. In vertebrates the term may refer to a developmental structure The anterior portion of the primitive digestive tube of the embryo that lies cephalic to the junction of the yolk stalk, consists of endodermal tissue, and gives rise to the the pharynx, lower respiratory system, esophagus, stomach, duodenum proximal to the biliary tract, liver, pancreas, biliary tract, and gall bladder. The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] AAO:0011042 BILA:0000085 BTO:0000507 EHDAA2:0000557 EHDAA:520 EMAPA:16548 FBbt:00005379 FMA:45616 MA:0001526 NCIT:C34180 SCTID:361409009 TGMA:0001014 UMLS:C0231051 VHOG:0000285 Wikipedia:Foregut XAO:0000232 uberon praeenteron proenteron UBERON:0001041 foregut http://upload.wikimedia.org/wikipedia/commons/9/9a/Gray27.png Anterior subdivision of a digestive tract. http://orcid.org/0000-0002-6601-2165 The anterior portion of the primitive digestive tube of the embryo that lies cephalic to the junction of the yolk stalk, consists of endodermal tissue, and gives rise to the the pharynx, lower respiratory system, esophagus, stomach, duodenum proximal to the biliary tract, liver, pancreas, biliary tract, and gall bladder. MP:0000474 The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000285 VHOG ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 http://bgee.unil.ch/ UMLS:C0231051 ncithesaurus:Foregut praeenteron Wikipedia:Foregut proenteron Wikipedia:Foregut A portion of the respiratory and digestive tracts; its distal limit is the superior part of the esophagus and it connects the nasal and oral cavities with the esophagus and larynx; it contains the valleculae and the pyriform recesses; its upper limits are the nasal cavity and cranial base.[FEED]. A funnel-shaped fibromuscular tube that conducts food to the ESOPHAGUS, and air to the LARYNYX and LUNGS. It is located posterior to the NASAL CAVITY; ORAL CAVITY; and LARYNX, and extends from the SKULL BASE to the inferior border of the CRICOID CARTILAGE anteriorly and to the inferior border of the C6 vertebra posteriorly. It is divided into the NASOPHARYNX; OROPHARYNX; and HYPOPHARYNX (laryngopharynx)[MESH:A03.867]. Anatomical cavity bounded by the derivatives of the branchial arches.[AAO] Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills. Kimmel et al, 1995.[TAO] Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills[ZFA:0000056, ZFIN:ZDB-PUB-961014-576]. The portion of the alimentary canal between the mouth and the oesophagus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: develops_from respiratory system (UBERON:0001004)[AAO] relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: part_of respiratory system (UBERON:0001004)[AAO] (...) the earliest vertebrates possessed unjointed internal and external branchial arches, and musculature encircling the pharynx.[well established][VHOG] MA/FMA pharynx not part of digestive/alimentary system, we are consistent with this scheme pharynx AAO:0000967 BTO:0001049 CALOHA:TS-0785 EFO:0000836 EHDAA2:0001458 EHDAA:2947 EMAPA:16706 EV:0100065 FMA:46688 GAID:155 MA:0000432 MESH:A03.867 NCIT:C12425 OpenCyc:Mx4rvViv7ZwpEbGdrcN5Y29ycA SCTID:181211006 TAO:0000056 UMLS:C0031354 VHOG:0000462 Wikipedia:Pharynx XAO:0003227 ZFA:0000056 galen:Pharynx uberon UBERON:0001042 Consider generalizing to deuterostome pharynx chordate pharynx EHDAA2 A portion of the respiratory and digestive tracts; its distal limit is the superior part of the esophagus and it connects the nasal and oral cavities with the esophagus and larynx; it contains the valleculae and the pyriform recesses; its upper limits are the nasal cavity and cranial base.[FEED]. http://www.feedexp.org A funnel-shaped fibromuscular tube that conducts food to the ESOPHAGUS, and air to the LARYNYX and LUNGS. It is located posterior to the NASAL CAVITY; ORAL CAVITY; and LARYNX, and extends from the SKULL BASE to the inferior border of the CRICOID CARTILAGE anteriorly and to the inferior border of the C6 vertebra posteriorly. It is divided into the NASOPHARYNX; OROPHARYNX; and HYPOPHARYNX (laryngopharynx)[MESH:A03.867]. MESH:A03.867 Anatomical cavity bounded by the derivatives of the branchial arches.[AAO] 2012-06-20 AAO:0000967 AAO AAO:EJS Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000056 TAO ZFIN:curator Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills[ZFA:0000056, ZFIN:ZDB-PUB-961014-576]. ZFIN:ZDB-PUB-961014-576 The portion of the alimentary canal between the mouth and the oesophagus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000462 VHOG http://bgee.unil.ch/ relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: develops_from respiratory system (UBERON:0001004)[AAO] 2012-06-20 AAO:0000967 AAO relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: part_of respiratory system (UBERON:0001004)[AAO] 2012-06-20 AAO:0000967 AAO (...) the earliest vertebrates possessed unjointed internal and external branchial arches, and musculature encircling the pharynx.[well established][VHOG] 2012-09-17 VHOG:0000462 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) Box essay 13.1 and Box figure I, p.502-503 http://bgee.unil.ch/ MA/FMA pharynx not part of digestive/alimentary system, we are consistent with this scheme MA pharynx FMA:46688 UMLS:C0031354 ncithesaurus:Pharynx Tube that connects the pharynx to the stomach. In mammals, the oesophagus connects the buccal cavity with the stomach. The stratified squamous non-keratinised epithelium lining the buccal cavity is continued through the pharynx down into the oesophagus. The lowest part of the oesophagus (ca. 2 cm) is lined with gastric mucosa and covered by peritoneum. The main body of the oesophagus is lined with small, simple mucous glands. Each gland opens into the lumen by a long duct which pierces the muscularis mucosae (Wilson and Washington, 1989). A sphincter is situated at the point where the oesophagus enters the stomach to prevent gastro-oesophageal reflux, i.e. to prevent acidic gastric contents from reaching stratified epithelia of the oesophagus, where they can cause inflammation and irritation (Wilson and Washington, 1989; Brown et al., 1993). Anterior end of the alimentary canal lined with smooth muscle. Bounded anteriorly by a constriction in the pharynx. Bounded posteriorly by and increase in circular and/or longitudinal smooth muscle associated with the stomach.[AAO] The few structural specializations in (adult lampreys) pharynx include complex valves on the external gill openings that direct the tidal flow, and the division of the ancestral pharynx into an oesophagus and a respiratory pharynx.[well established][VHOG] esophageal esophagus NOT part of gut in MA. part of gut in ZFA. part_of gut (via UGIT) in FMA. Consider splitting. Interspecies: The human oesophagus is 25 cm long and has a diameter of ca. 2 cm. Only little information was found on the oesophagus in rat, rabbit and pig. The oesophagus of rat (75 x 2 mm) and rabbit has no mucous glands and the cardia of the stomach has a well-developed sphincter, which prevents them from vomiting (Hebel and Stromberg, 1988; Manning et al., 1994). Morphologically the oesophagus is similar in man and pig; both are omnivores and have a non-keratinised epithelium, submucous glands and similar membrane enzymes. Like in humans, pigs can suffer from reflux oesophagitis and stress ulceration of the oesophagus. The pig oesophagus may therefore be a good model for investigation compared to the human oesophagus (Christie et al., 1995) AAO:0000145 ANISEED:1235301 BTO:0000959 CALOHA:TS-0700 EFO:0000835 EHDAA2:0001285 EHDAA:2937 EMAPA:16833 EV:0100069 FMA:7131 GAID:291 MA:0000352 MAT:0000048 MESH:A03.365 MIAA:0000048 NCIT:C12389 OpenCyc:Mx4rvVj9Q5wpEbGdrcN5Y29ycA SCTID:181245004 TAO:0000204 UMLS:C0014876 VHOG:0000450 Wikipedia:Esophagus XAO:0000127 ZFA:0000204 galen:Esophagus gullet oesophagus uberon UBERON:0001043 esophagus http://upload.wikimedia.org/wikipedia/commons/d/d4/Illu01_head_neck.jpg Tube that connects the pharynx to the stomach. In mammals, the oesophagus connects the buccal cavity with the stomach. The stratified squamous non-keratinised epithelium lining the buccal cavity is continued through the pharynx down into the oesophagus. The lowest part of the oesophagus (ca. 2 cm) is lined with gastric mucosa and covered by peritoneum. The main body of the oesophagus is lined with small, simple mucous glands. Each gland opens into the lumen by a long duct which pierces the muscularis mucosae (Wilson and Washington, 1989). A sphincter is situated at the point where the oesophagus enters the stomach to prevent gastro-oesophageal reflux, i.e. to prevent acidic gastric contents from reaching stratified epithelia of the oesophagus, where they can cause inflammation and irritation (Wilson and Washington, 1989; Brown et al., 1993). Wikipedia:Esophagus http://www.rivm.nl/interspeciesinfo/inter/oesophagus/ Anterior end of the alimentary canal lined with smooth muscle. Bounded anteriorly by a constriction in the pharynx. Bounded posteriorly by and increase in circular and/or longitudinal smooth muscle associated with the stomach.[AAO] 2012-06-20 AAO:0000145 AAO AAO:EJS The few structural specializations in (adult lampreys) pharynx include complex valves on the external gill openings that direct the tidal flow, and the division of the ancestral pharynx into an oesophagus and a respiratory pharynx.[well established][VHOG] 2012-09-17 VHOG:0000450 VHOG DOI:10.1111/j.1096-3642.1996.tb01658.x Mallatt J, Ventilation and the origin of jawed vertebrates: a new mouth. Zoological Journal of the Linnean Society (1996) http://bgee.unil.ch/ esophagus NOT part of gut in MA. part of gut in ZFA. part_of gut (via UGIT) in FMA. Consider splitting. Interspecies: The human oesophagus is 25 cm long and has a diameter of ca. 2 cm. Only little information was found on the oesophagus in rat, rabbit and pig. The oesophagus of rat (75 x 2 mm) and rabbit has no mucous glands and the cardia of the stomach has a well-developed sphincter, which prevents them from vomiting (Hebel and Stromberg, 1988; Manning et al., 1994). Morphologically the oesophagus is similar in man and pig; both are omnivores and have a non-keratinised epithelium, submucous glands and similar membrane enzymes. Like in humans, pigs can suffer from reflux oesophagitis and stress ulceration of the oesophagus. The pig oesophagus may therefore be a good model for investigation compared to the human oesophagus (Christie et al., 1995) MA UMLS:C0014876 ncithesaurus:Esophagus Middle subdivision of a digestive tract[CJM]. In vertebrates: The middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine[GO]. Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. We may explicitly make this a developmental class The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] In humans: originates from the foregut at the opening of the bile duct into the duodenum and continues through the small intestine and much of the large intestine until the transition to the hindgut about two-thirds of the way through the transverse colon in FMA this represents an embryonic region. BILA:0000086 BTO:0000863 EFO:0001950 EHDAA2:0001185 EHDAA:983 EMAPA:16255 FBbt:00005383 FMA:45617 MA:0001564 NCIT:C34210 SCTID:361410004 TGMA:0001036 UMLS:C0231052 VHOG:0000290 Wikipedia:Midgut XAO:0000103 uberon mesenteron UBERON:0001045 midgut http://upload.wikimedia.org/wikipedia/commons/3/3d/Illu_small_intestine.jpg Middle subdivision of a digestive tract[CJM]. In vertebrates: The middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine[GO]. GO:0007494 Wikipedia:Midgut The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000290 VHOG ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 http://bgee.unil.ch/ In humans: originates from the foregut at the opening of the bile duct into the duodenum and continues through the small intestine and much of the large intestine until the transition to the hindgut about two-thirds of the way through the transverse colon WP in FMA this represents an embryonic region. FMA UMLS:C0231052 ncithesaurus:Midgut mesenteron Wikipedia:Midgut The caudalmost subdivision of a digestive tract. Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future (vertebrates have some contribution from NC - https://github.com/obophenotype/uberon/wiki/The-neural-crest). We may explicitly make this a developmental class the caudal portion of the primitive digestive tube of the embryo The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] in FMA this class has no children. In MA it has a single child hindgut epithelium AAO:0011052 BILA:0000087 BTO:0000510 EHDAA2:0000779 EHDAA:975 EMAPA:16715 FBbt:00005384 FMA:45618 MA:0001527 NCIT:C34188 SCTID:362856002 TGMA:0001020 UMLS:C0231053 VHOG:0000459 Wikipedia:Hindgut XAO:0000104 uberon metenteron UBERON:0001046 hindgut http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray472.png Wikipedia The caudalmost subdivision of a digestive tract. http://orcid.org/0000-0002-6601-2165 the caudal portion of the primitive digestive tube of the embryo MP:0008786 The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000459 VHOG ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 http://bgee.unil.ch/ in FMA this class has no children. In MA it has a single child hindgut epithelium FMA UMLS:C0231053 ncithesaurus:Hindgut metenteron Wikipedia:Hindgut Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt, Hartenstein, V. (2004)]. AEO:0000171 BTO:0001886 EFO:0001652 EHDAA2:0003171 FBbt:00005495 FMA:86589 MAT:0000482 NCIT:C34275 UMLS:C0678727 Wikipedia:Primordium XAO:0003043 uberon bud future organ placode primordia rudiment UBERON:0001048 primordium EHDAA2 Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt, Hartenstein, V. (2004)]. BTO:0001886 FB:DJS FB:FBrf0089570 http://flybase.org/reports/FBrf0178740.html UMLS:C0678727 ncithesaurus:Primordium placode FBbt:00005495 primordia XAO:0003043 In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted]. Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO] The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG] (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium AAO:0010617 BTO:0001057 CALOHA:TS-2371 DHBA:10154 EHDAA2:0001254 EHDAA:2869 EHDAA:908 EMAPA:16164 EMAPA:16757 FMA:293882 MAT:0000069 MIAA:0000069 NCIT:C34226 SCTID:362852000 TAO:0001135 UMLS:C0231024 VHOG:0000307 Wikipedia:Neural_tube XAO:0003204 ZFA:0001135 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1365 uberon neural primordium presumptive central nervous system tubus neuralis UBERON:0001049 neural tube http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png EHDAA2 In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted]. Wikipedia:Neural_tube Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO] 2012-06-20 AAO:0010617 AAO AAO:JOR The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG] 2012-09-17 VHOG:0000307 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/neural+tube (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] 2012-09-17 VHOG:0000307 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 http://bgee.unil.ch/ The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium GO:0021915 UMLS:C0231024 ncithesaurus:Neural_Tube tubus neuralis Wikipedia:Neural_tube the terminal portion of the intestinal tube, terminating with the anus The terminal portion of the large intestine between the ileo-pelvic colon and the anus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] rectal In the lungfish, sharks and rays the rectum opens into the cloaca which also receives wastes (urine) from the kidneys and material from the reproductive organs. In bony fish the rectum reaches the outside environment through the anus, which is normally situated just in front the urinary and reproductive openings. However in some fish the digestive tract may be curled back on itself, and in the Electric Eel (Electrophorus electricus) the anus is situated in the fish's throat. -- http://www.earthlife.net/fish/digestion.html AAO:0010401 BTO:0001158 CALOHA:TS-1180 EFO:0000848 EHDAA2:0001592 EHDAA:5836 EMAPA:17896 EV:0100081 FMA:14544 GAID:311 MA:0000336 MAT:0000050 MESH:A03.492.411.495.767 MIAA:0000050 NCIT:C12390 OpenCyc:Mx4rvVjaU5wpEbGdrcN5Y29ycA SCTID:181261002 UMLS:C0034896 VHOG:0001751 Wikipedia:Rectum XAO:0000238 galen:Rectum terminal portion of intestine uberon intestinum rectum rectal sac terminal portion of large intestine UBERON:0001052 rectum http://upload.wikimedia.org/wikipedia/commons/7/75/Anorectum.gif 4 cjm MA EHDAA2 ISBN:0073040584 the terminal portion of the intestinal tube, terminating with the anus ISBN:0-683-40008-8 MP:0000492 http://orcid.org/0000-0002-6601-2165 The terminal portion of the large intestine between the ileo-pelvic colon and the anus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0001751 VHOG http://bgee.unil.ch/ UMLS:C0034896 ncithesaurus:Rectum intestinum rectum BTO:0001158 Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. AAO:0010841 AEO:0000000 BILA:0000000 BIRNLEX:6 CARO:0000000 EHDAA2:0002229 FBbt:10000000 FBbt_root:00000000 FMA:62955 HAO:0000000 MA:0000001 NCIT:C12219 TAO:0100000 TGMA:0001822 UMLS:C1515976 WBbt:0000100 XAO:0000000 ZFA:0100000 uberon UBERON:0001062 anatomical entity Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. FMA:62955 http://orcid.org/0000-0001-9114-8737 UMLS:C1515976 ncithesaurus:Anatomic_Structure_System_or_Substance A zone of skin that is part of a back [Automatically generated definition]. TODO - distinguish between entire skin of region and arbitrary zone of skin on region EMAPA:36392 FMA:10462 FMA:22985 MA:0000498 SCTID:181492002 back skin back zone of skin skin, dorsal region zone of skin of back uberon UBERON:0001068 skin of back MA MA A zone of skin that is part of a back [Automatically generated definition]. OBOL:automatic back zone of skin OBOL:automatic skin, dorsal region https://orcid.org/0000-0002-6601-2165 zone of skin of back OBOL:automatic A terminal branch of the left or right common carotid artery which supplies oxygenated blood to to the throat, neck glands, tongue, face, mouth, ear, scalp and dura mater of the meninges[MP] not homologous to the external carotid of zebrafish (Goodrich, 1958) - http://zfish.nichd.nih.gov/zfatlas/Intro%20Page/comparative.html; check XAO AAO:0010218 AAO:0010416 BTO:0004696 EFO:0001953 EHDAA2:0000461 EMAPA:18611 FMA:10635 GAID:480 MA:0001929 MESH:D002342 NCIT:C32551 OpenCyc:Mx4rwVJkPZwpEbGdrcN5Y29ycA SCTID:362044002 UMLS:C0007275 VHOG:0000265 Wikipedia:External_carotid_artery XAO:0000345 external carotid uberon arteria carotis externa UBERON:0001070 external carotid artery https://sourceforge.net/tracker/?func=detail&aid=3486863&group_id=76834&atid=1127722 http://upload.wikimedia.org/wikipedia/commons/1/13/External_carotid_a.gif MA FMA EHDAA2 FMA A terminal branch of the left or right common carotid artery which supplies oxygenated blood to to the throat, neck glands, tongue, face, mouth, ear, scalp and dura mater of the meninges[MP] MGI:anna UMLS:C0007275 ncithesaurus:External_Carotid_Artery external carotid AAO:0010218 arteria carotis externa Wikipedia:External_carotid_artery It ascends beneath the anterior margin of the trapezius, distributing branches to it, and to the neighboring muscles and lymph glands in the neck, and anastomosing with the superficial branch of the descending branch of the occipital artery. EMAPA:37117 FMA:10665 MA:0002052 NCIT:C53005 SCTID:161746006 UMLS:C0226271 Wikipedia:Superficial_part_of_transverse_cervical_artery superficial branch of transverse cervical artery uberon UBERON:0001071 The transverse cervical artery splits into two branches, a superficial one and a deep one[WP] superficial cervical artery It ascends beneath the anterior margin of the trapezius, distributing branches to it, and to the neighboring muscles and lymph glands in the neck, and anastomosing with the superficial branch of the descending branch of the occipital artery. Wikipedia:Superficial_part_of_transverse_cervical_artery EMAPA:37117 MA:th UMLS:C0226271 ncithesaurus:Superficial_Cervical_Artery superficial branch of transverse cervical artery Wikipedia:Superficial_part_of_transverse_cervical_artery A potential space between the visceral and parietal layers of the pericardium. Anatomical space in which the heart is located and is surrounded by the pericardium.[TAO] In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart (of other tetrapods) is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG] check ZFA, should actually be thoracic cavity. Note that Hyman defines the cavity as the space between the heart and the sac (but defines the sac as parietal) BSA:0000091 EHDAA2:0001434 EMAPA:16131 EMAPA:16132 FMA:11350 MA:0000053 NCIT:C38662 SCTID:362027001 TAO:0002220 UMLS:C0225972 VHOG:0000556 Wikipedia:Pericardial_cavity ZFA:0001655 galen:PericardialSpace cavity of pericardial sac pericardial space uberon cavitas pericardiaca UBERON:0001074 pericardial cavity MA FMA Wikipedia A potential space between the visceral and parietal layers of the pericardium. Wikipedia:Pericardium PMID:20959416 Anatomical space in which the heart is located and is surrounded by the pericardium.[TAO] 2012-08-14 TAO:0002220 TAO ZFIN:curator In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart (of other tetrapods) is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG] 2012-09-17 VHOG:0000556 VHOG ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206 http://bgee.unil.ch/ check ZFA, should actually be thoracic cavity. Note that Hyman defines the cavity as the space between the heart and the sac (but defines the sac as parietal) ZFA UMLS:C0225972 ncithesaurus:Pericardial_Cavity pericardial space Wikipedia:Pericardial_cavity cavitas pericardiaca Wikipedia:Pericardial_cavity Endocardium that is part of the cardiac ventricle. EMAPA:32747 FMA:12148 MA:0000079 SCTID:192172004 TAO:0002247 VHOG:0000607 ZFA:0001615 cardiac ventricle endocardium endocardium of cardiac ventricle endocardium of heart ventricle endocardium of lower chamber of heart endocardium of ventricle of heart heart ventricle endocardium lower chamber of heart endocardium ventricle endocardium ventricle of heart endocardium ventricular endocardium uberon ventricle endocardial tissue UBERON:0001081 endocardium of ventricle https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships Endocardium that is part of the cardiac ventricle. ZFIN:curator cardiac ventricle endocardium OBOL:automatic endocardium of cardiac ventricle OBOL:automatic endocardium of heart ventricle OBOL:automatic endocardium of lower chamber of heart OBOL:automatic endocardium of ventricle of heart OBOL:automatic heart ventricle endocardium OBOL:automatic lower chamber of heart endocardium OBOL:automatic ventricle of heart endocardium OBOL:automatic ventricle endocardial tissue VHOG:0000607 An epicardial layer that lines a cardiac ventricle The external layer of the ventricle bounding the ventricular myocardium. It is formed by a single layer of mesothelial cells supported by a basal lamina, and imbricated with collagen, fibroblasts, and vascular structures in the subepicardial space. Hu et al. 2001.[TAO] FMA:12150 TAO:0005058 ZFA:0005058 cardiac ventricle epicardium ventricular epicardium uberon UBERON:0001082 epicardium of ventricle An epicardial layer that lines a cardiac ventricle http://orcid.org/0000-0002-6601-2165 The external layer of the ventricle bounding the ventricular myocardium. It is formed by a single layer of mesothelial cells supported by a basal lamina, and imbricated with collagen, fibroblasts, and vascular structures in the subepicardial space. Hu et al. 2001.[TAO] 2012-08-14 TAO:0005058 TAO ZFIN:curator cardiac ventricle epicardium OBOL:automatic Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer. Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer Hu et al. 2001.[TAO] As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[uncertain][VHOG] EFO:0003088 EMAPA:32748 FMA:12151 MA:0000082 SCTID:192084000 TAO:0005061 VHOG:0000604 ZFA:0005061 ventricle myocardium ventricular myocardium uberon ventricle cardiac muscle UBERON:0001083 myocardium of ventricle https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer. ZFIN:curator Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer Hu et al. 2001.[TAO] 2012-08-14 TAO:0005061 TAO ZFIN:curator As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[uncertain][VHOG] 2012-09-17 VHOG:0000604 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481 http://bgee.unil.ch/ ventricle cardiac muscle VHOG:0000604 A zone of skin that is part of a head [Automatically generated definition]. TODO - distinguish between entire skin of region and arbitrary zone of skin on region FMA:12166 FMA:24756 MA:0000582 NCIT:C52757 SCTID:181484006 UMLS:C0205029 adult head zone of skin head skin head zone of skin zone of skin of adult head zone of skin of head uberon UBERON:0001084 skin of head A zone of skin that is part of a head [Automatically generated definition]. OBOL:automatic UMLS:C0205029 ncithesaurus:Head_Skin adult head zone of skin OBOL:automatic head zone of skin OBOL:automatic zone of skin of adult head OBOL:automatic zone of skin of head OBOL:automatic A zone of skin that is part of a trunk [Automatically generated definition]. TODO - distinguish between entire skin of region and arbitrary zone of skin on region EMAPA:37278 FMA:12167 FMA:23093 MA:0000517 NCIT:C12295 SCTID:181489001 UMLS:C0205031 torso zone of skin trunk skin trunk zone of skin zone of skin of torso zone of skin of trunk uberon UBERON:0001085 skin of trunk A zone of skin that is part of a trunk [Automatically generated definition]. OBOL:automatic EMAPA:37278 MA:th UMLS:C0205031 ncithesaurus:Skin_of_the_Trunk torso zone of skin OBOL:automatic trunk zone of skin OBOL:automatic zone of skin of torso OBOL:automatic zone of skin of trunk OBOL:automatic Transudate contained in the pleural cavity. BTO:0003080 FMA:12273 MA:0002532 MAT:0000500 Wikipedia:Pleural_fluid ncithesaurus:Pleural_Fluid uberon UBERON:0001087 pleural fluid Transudate contained in the pleural cavity. FMA:12273 Joint fluid is a transudate of plasma that is actively secreted by synovial cells. Portion of organism substance that is a clear fluid that occupies the space in synovial joints.[TAO] It provides nutrients and lubrication for articular cartilage The fluid contains hyaluronan secreted by fibroblast-like cells in the synovial membrane, lubricin (proteoglycan 4; PRG4) secreted by the surface chondrocytes of the articular cartilage and interstitial fluid filtered from the blood plasma BTO:0001339 CALOHA:TS-0996 ENVO:02000039 FMA:12277 GAID:265 MA:0002544 MESH:D013582 NCIT:C33718 TAO:0005154 UMLS:C0039097 Wikipedia:Synovial_fluid ZFA:0005154 galen:SynovialFluid joint fluid uberon UBERON:0001090 synovial fluid FMA Joint fluid is a transudate of plasma that is actively secreted by synovial cells. https://www.ncbi.nlm.nih.gov/books/NBK274/ Portion of organism substance that is a clear fluid that occupies the space in synovial joints.[TAO] 2012-08-14 TAO:0005154 TAO ZFIN:curator UMLS:C0039097 ncithesaurus:Synovial_Fluid joint fluid https://www.ncbi.nlm.nih.gov/books/NBK274/ Any vertebral bone that is part of the caudal region of the vertebral column (tail or coccyx). Vertebrae bearing a hemal arch and spine. The most posterior caudal vertebrae support the caudal fin and are referred to as preural vertebrae.[TAO] we deliberately merge the MA classes as we believe them equivalent UBERON:0006070 caudal vertebra EMAPA:18374 FMA:12527 MA:0000310 MA:0001420 NCIT:C32334 OpenCyc:Mx4rv9IEzZwpEbGdrcN5Y29ycA SCTID:361774004 TAO:0000326 UMLS:C0223616 Wikipedia:Caudal_vertebra XAO:0003079 ZFA:0000326 galen:CoccygealVertebra caudal vertebrae caudal vertebral bone caudal vertebral bone element coccygeal segment coccygeal vertebra fused tail vertebra uberon coccygea tail vertebra UBERON:0001095 Taxon notes In zebrafish, Vertebra bearing a hemal arch and spine. The most posterior caudal vertebrae support the caudal fin and are referred to as preural vertebrae caudal vertebra Any vertebral bone that is part of the caudal region of the vertebral column (tail or coccyx). http://orcid.org/0000-0002-6601-2165 Vertebrae bearing a hemal arch and spine. The most posterior caudal vertebrae support the caudal fin and are referred to as preural vertebrae.[TAO] 2012-08-14 TAO:0000326 TAO ZFIN:curator we deliberately merge the MA classes as we believe them equivalent MA caudal vertebra FMA:12527 UMLS:C0223616 ncithesaurus:Coccygeal_Vertebra caudal vertebrae coccygeal vertebra FMA:12527 fused tail vertebra https://orcid.org/0000-0002-6601-2165 coccygea MA:0001420 tail vertebra MA:0000310 An anatomical wall that is part of a esophagus [Automatically generated definition]. EMAPA:35326 FMA:12611 MA:0002691 anatomical wall of esophagus anatomical wall of gullet anatomical wall of oesophagus esophageal wall esophagus anatomical wall esophagus wall gullet anatomical wall gullet wall oesophagus anatomical wall oesophagus wall wall of gullet wall of oesophagus uberon UBERON:0001096 wall of esophagus An anatomical wall that is part of a esophagus [Automatically generated definition]. OBOL:automatic anatomical wall of esophagus OBOL:automatic anatomical wall of gullet OBOL:automatic anatomical wall of oesophagus OBOL:automatic esophagus anatomical wall OBOL:automatic gullet anatomical wall OBOL:automatic gullet wall OBOL:automatic oesophagus anatomical wall OBOL:automatic oesophagus wall OBOL:automatic wall of gullet OBOL:automatic wall of oesophagus OBOL:automatic A thin musculomebranous barrier that separates the abdominal and thoracic cavities. Often used for breathing control The diaphragm is a skeletal muscle that is responsible for contraction and expansion of the lungs[GO]. The mammals are characterized by a diaphragm, which separates the thoracic portion of the body cavity from the abdominal region and assists in drawing air into the lungs and forcing it out. Modern reptiles lack a muscular diaphragm and it is reasonable to suppose that the diaphragm developed as a new device that made possible a large degree of oxygen intake for active animals. The change may have taken place during the transition from reptile to mammal (...).[well established][VHOG] phrenic The existence of some membrane separating the pharynx from the stomach can be traced widely among the chordates. Thus amphioxus possesses an atrium by which water exits the pharynx, which has been argued (and disputed) to be homologous to structures in ascidians and hagfishes.[3] The urochordate epicardium separates digestive organs from the pharynx and heart, but the anus returns to the upper compartment to discharge wastes through an outgoing siphon (Thoracic_diaphragm#Comparative_anatomy_and_evolution) barrier between thoracic and abdominal cavities; stop gastric contents from refluxing into the oesophagus breathing control originate from the cervical somites, likely C3-C5[PMID:23586979] BTO:0000341 CALOHA:TS-0198 EFO:0000937 EHDAA2:0003495 EMAPA:17701 EV:0100376 FMA:13295 GAID:158 MA:0001904 MAT:0000502 MESH:D003964 NCIT:C12702 OpenCyc:Mx4rvVivz5wpEbGdrcN5Y29ycA SCTID:181614006 UMLS:C0011980 VHOG:0000713 Wikipedia:Thoracid_diaphragm diaphragm muscle diaphragm of thorax thoracic diaphragm uberon midriff phren UBERON:0001103 diaphragm PMID:23586979 definitional A thin musculomebranous barrier that separates the abdominal and thoracic cavities. Often used for breathing control MP:0002279 Wikipedia:Thoracic_diaphragm#Comparative_anatomy_and_evolution The diaphragm is a skeletal muscle that is responsible for contraction and expansion of the lungs[GO]. GO:0060539 The mammals are characterized by a diaphragm, which separates the thoracic portion of the body cavity from the abdominal region and assists in drawing air into the lungs and forcing it out. Modern reptiles lack a muscular diaphragm and it is reasonable to suppose that the diaphragm developed as a new device that made possible a large degree of oxygen intake for active animals. The change may have taken place during the transition from reptile to mammal (...).[well established][VHOG] 2012-09-17 VHOG:0000713 VHOG ISBN:978-0471384618 Colbert EH, Evolution of the vertebrates: a history of the backboned animals through time (2001) p.278 http://bgee.unil.ch/ UMLS:C0011980 ncithesaurus:Diaphragm diaphragm muscle BTO:0000341 midriff BTO:0000341 phren BTO:0000341 Subdivision of skeletal system that consists of all the vertebra and associated skeletal elements and joints in the body[modified from VSAO]. Note that in contrast to VSAO, this is a subset of the skeletal system, and thus includes intervertebral joints, cartilage and ligaments etc. Some ontologies such as AAO seem to purely refer to the skeleton Anatomical cluster that consists of all the vertebra in the body.[VSAO] The vertebral column consists of a series of vertebrae connected by ligaments. It provides a supporting axis for the body and protects the spinal cord. [TFD][VHOG] Vertebrata is characterized by three synapomorphies. First, vertebrates have a backbone composed of vertebrae (...).[well established][VHOG] spine AAO:0000699 AAO:0000734 BTO:0000818 EFO:0001369 EHDA:10119 EMAPA:35919 FMA:13478 GAID:106 MA:0002416 MESH:D013131 NCIT:C12998 NCIT:C33588 NIF_Subcellular:sao1145756102 OpenCyc:Mx4rv2j-CpwpEbGdrcN5Y29ycA OpenCyc:Mx4rv6GF55wpEbGdrcN5Y29ycA OpenCyc:Mx4rvVkFEpwpEbGdrcN5Y29ycA SCTID:44300000 TAO:0001559 UMLS:C0037949 UMLS:C1519455 VHOG:0001142 VSAO:0000185 Wikipedia:Vertebral_column XAO:0003074 ZFA:0001559 galen:SpinalColumn backbone vertebral column skeleton uberon columna vertebralis dorsal spine spinal column vertebral region UBERON:0001130 vertebral column cjm Subdivision of skeletal system that consists of all the vertebra and associated skeletal elements and joints in the body[modified from VSAO]. VSAO:0000185 https://orcid.org/0000-0002-6601-2165 https://sourceforge.net/tracker/?func=detail&aid=3530322&group_id=76834&atid=2257941 Anatomical cluster that consists of all the vertebra in the body.[VSAO] 2012-08-14 VSAO:0000185 VSAO VSAO:curator The vertebral column consists of a series of vertebrae connected by ligaments. It provides a supporting axis for the body and protects the spinal cord. [TFD][VHOG] 2012-09-17 VHOG:0001142 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/vertebral+column Vertebrata is characterized by three synapomorphies. First, vertebrates have a backbone composed of vertebrae (...).[well established][VHOG] 2012-09-17 VHOG:0001142 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.53 http://bgee.unil.ch/ spine FMA:13478 UMLS:C0037949 ncithesaurus:Vertebral_Column UMLS:C1519455 ncithesaurus:Spinal_Cord_Column backbone FMA:13478 vertebral column skeleton AAO:0000699 columna vertebralis BTO:0000818 dorsal spine BTO:0000818 spinal column MESH:A02.835.232.834 A foramen within a vertebral element through which the spinal cord runs. It is formed by the anterior segment, and the posterior part, the vertebral arch. Opening on the vertebra for a spinal nerve as it emerges from the spinal canal.[AAO] AAO:0000729 EMAPA:37803 FMA:13479 MA:0001454 OpenCyc:Mx4rv_EvQZwpEbGdrcN5Y29ycA SCTID:280734009 Wikipedia:Vertebral_foramen vertebra neural canal uberon foramen vertebrale UBERON:0001131 vertebral foramen http://upload.wikimedia.org/wikipedia/commons/1/10/Foramenvertebrale.png A foramen within a vertebral element through which the spinal cord runs. It is formed by the anterior segment, and the posterior part, the vertebral arch. Wikipedia:Vertebral_foramen http://orcid.org/0000-0002-6601-2165 Opening on the vertebra for a spinal nerve as it emerges from the spinal canal.[AAO] 2012-06-20 AAO:0000729 AAO AAO:LAP EMAPA:37803 MA:th foramen vertebrale Wikipedia:Vertebral_foramen Muscle tissue composed of cardiac muscle cells, forming the muscles of the heart[ZFA,modified]. check relationship with myocardium. part_of in MA - but we also have a more specific class 'cardiac muscle tissue of myocardium'. Check ncit UBERON:0007096 AAO:0010245 AEO:0000142 BILA:0000134 BTO:0000199 CALOHA:TS-0440 EHDAA2:0003142 EMAPA:32688 FMA:14068 TAO:0005280 Wikipedia:Cardiac_muscle ZFA:0005280 galen:CardiacMuscle galen:CardiacMuscleTissue ncithesaurus:Heart_Muscle cardiac muscle cardiac muscle muscle tissue cardiac muscle textus muscularis heart muscle muscle tissue heart muscle textus muscularis heart myocardium muscle tissue heart myocardium textus muscularis muscle of heart muscle tissue muscle of heart textus muscularis muscle tissue of cardiac muscle muscle tissue of heart muscle muscle tissue of heart myocardium muscle tissue of muscle of heart muscle tissue of myocardium myocardium muscle tissue myocardium textus muscularis textus muscularis of cardiac muscle textus muscularis of heart muscle textus muscularis of heart myocardium textus muscularis of muscle of heart textus muscularis of myocardium uberon cardiac musculature UBERON:0001133 cardiac muscle tissue ZFA Muscle tissue composed of cardiac muscle cells, forming the muscles of the heart[ZFA,modified]. ZFA:0005280 cardiac muscle muscle tissue OBOL:automatic cardiac muscle textus muscularis OBOL:automatic heart muscle muscle tissue OBOL:automatic heart muscle textus muscularis OBOL:automatic heart myocardium muscle tissue OBOL:automatic heart myocardium textus muscularis OBOL:automatic muscle of heart muscle tissue OBOL:automatic muscle of heart textus muscularis OBOL:automatic muscle tissue of cardiac muscle OBOL:automatic muscle tissue of heart muscle OBOL:automatic muscle tissue of heart myocardium OBOL:automatic muscle tissue of muscle of heart OBOL:automatic muscle tissue of myocardium OBOL:automatic myocardium muscle tissue OBOL:automatic myocardium textus muscularis OBOL:automatic textus muscularis of cardiac muscle OBOL:automatic textus muscularis of heart muscle OBOL:automatic textus muscularis of heart myocardium OBOL:automatic textus muscularis of muscle of heart OBOL:automatic textus muscularis of myocardium OBOL:automatic cardiac musculature BILA:0000134 Muscle tissue that consists primarily of skeletal muscle fibers. TODO - add skeletal muscle organ? See GO:0060538 skeletal muscle organ development. Todo - group FBbt:00005073 - somatic muscle. Muscle, composed of long cylindrical, multinucleated cells that attaches to the skeleton via tendons.[TAO] Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm[FMA] This result implies the following views in terms of evolutionary differentiation: (1) Arthropod striated muscle and vertebrate skeletal and cardiac muscles share a common ancestor. In other words, they did not evolve independently (...) (5) The divergence of vertebrate skeletal and cardiac muscles/vertebrate smooth muscle and nonmuscle is at least before that of vertebrates/arthropods. In other words, emergence of skeletal and cardiac musle type tissues preceded the vertebrate/arthropod divergence (ca. 700 MYA).[well established][VHOG] skeletal muscle EMAPA:32716 FMA:14069 MA:0002439 NCIT:C13050 SCTID:426215008 UMLS:C0242692 Wikipedia:Skeletal_striated_muscle uberon skeletal muscle system somatic muscle UBERON:0001134 skeletal muscle tissue Skeletal:muscle.jpg Muscle tissue that consists primarily of skeletal muscle fibers. https://github.com/obophenotype/uberon/issues/324 Muscle, composed of long cylindrical, multinucleated cells that attaches to the skeleton via tendons.[TAO] 2012-08-14 TAO:0005277 TAO ZFIN:curator Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm[FMA] FMA:14069 FMA This result implies the following views in terms of evolutionary differentiation: (1) Arthropod striated muscle and vertebrate skeletal and cardiac muscles share a common ancestor. In other words, they did not evolve independently (...) (5) The divergence of vertebrate skeletal and cardiac muscles/vertebrate smooth muscle and nonmuscle is at least before that of vertebrates/arthropods. In other words, emergence of skeletal and cardiac musle type tissues preceded the vertebrate/arthropod divergence (ca. 700 MYA).[well established][VHOG] 2012-09-17 VHOG:0000319 VHOG PMID:10368962 Oota S, Saitou N, Phylogenetic relationship of muscle tissues deduced from superimposition of gene trees. Mol Biol Evol (1999) http://bgee.unil.ch/ UMLS:C0242692 ncithesaurus:Skeletal_Muscle_Tissue skeletal muscle system BTO:0001103 somatic muscle BTO:0001103 Muscle tissue which is unstriated, composed primarily of smooth muscle fibers surrounded by a reticulum of collagen and elastic fibers. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length[GO]. A non-striated muscle that is composed of spindle-shaped cells. Smooth muscle usually is organized into sheets that line cavitated organs.[TAO] Involuntary muscle tissue consisting of uninucleate spindle-shaped fibers.[AAO] (...) the first bilateral animals possessed only smooth muscles with the molecular repertoire necessary to build a striated muscle. (...) it is more parsimonious to regard striated muscle cells as a sister cell type to the smooth muscle cells. In this scenario, striated and smooth muscles would have arisen in the stem lineage that led to the Nephrozoa (i.e. all Bilateria exclusive the acoelomorphs) (Hejnol et al., 2009), from an 'acoel-like' smooth muscle, by segregation and divergence of functions and through differential recruitment of additional genes[well established][VHOG] GO uses visceral and smooth interchangeably. However visceral can also be used in the sense of the viscera. Many fly annotations to smooth muscle terms. If we want to be inclusive of insects have to have a general definition of tissue that includes cells. AAO:0010244 AEO:0000141 BTO:0001260 CALOHA:TS-0943 EFO:0000889 EHDAA2:0003141 EMAPA:32717 EV:0100378 FBbt:00003525 FMA:14070 GAID:167 MA:0000166 MAT:0000303 MESH:D009130 MIAA:0000303 NCIT:C12437 OpenCyc:Mx4rvvSS3pwpEbGdrcN5Y29ycA TAO:0005274 UMLS:C1267092 VHOG:0001246 WBbt:0005781 Wikipedia:Smooth_muscle_tissue XAO:0000175 ZFA:0005274 galen:SmoothMuscle galen:SmoothMuscleTissue involuntary muscle non-striated muscle smooth muscle textus muscularis nonstriatus visceral muscle visceral muscle tissue uberon textus muscularis levis; textus muscularis nonstriatus UBERON:0001135 smooth muscle tissue Glatte:Muskelzellen.jpg Muscle tissue which is unstriated, composed primarily of smooth muscle fibers surrounded by a reticulum of collagen and elastic fibers. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length[GO]. GO:0006939 Wikipedia:Smooth_muscle_tissue A non-striated muscle that is composed of spindle-shaped cells. Smooth muscle usually is organized into sheets that line cavitated organs.[TAO] 2012-08-14 TAO:0005274 TAO ZFIN:curator Involuntary muscle tissue consisting of uninucleate spindle-shaped fibers.[AAO] 2012-06-20 AAO:0010244 AAO AAO:CAM (...) the first bilateral animals possessed only smooth muscles with the molecular repertoire necessary to build a striated muscle. (...) it is more parsimonious to regard striated muscle cells as a sister cell type to the smooth muscle cells. In this scenario, striated and smooth muscles would have arisen in the stem lineage that led to the Nephrozoa (i.e. all Bilateria exclusive the acoelomorphs) (Hejnol et al., 2009), from an 'acoel-like' smooth muscle, by segregation and divergence of functions and through differential recruitment of additional genes[well established][VHOG] 2012-09-17 VHOG:0001246 VHOG DOI:10.1002/jez.b.21416 Chiodin M, Achatz JG, Wanninger A, Martinez P, Molecular architecture of muscles in an acoel and its evolutionary implications. Journal of Experimental Zoology (2011) http://bgee.unil.ch/ UMLS:C1267092 ncithesaurus:Smooth_Muscle_Tissue textus muscularis nonstriatus FMA:14070 FMA:TA visceral muscle visceral muscle tissue textus muscularis levis; textus muscularis nonstriatus Wikipedia:Smooth_muscle_tissue Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. Wikipedia: The mesothelium is a membrane that forms the lining of several body cavities: the pleura (thoracal cavity), peritoneum (abdominal cavity including the mesentery) and pericardium (heart sac). Mesothelial tissue also surrounds the male internal reproductive organs (the tunica vaginalis testis) and covers the internal reproductive organs of women (the tunica serosa uteri). AEO:0000111 BTO:0002422 CALOHA:TS-1183 EHDAA2_RETIRED:0003111 EHDAA:2331 EHDAA:2349 EHDAA:295 EHDAA:6073 EHDAA:640 EHDAA:646 EMAPA:32856 FMA:14074 MA:0000565 NCIT:C33105 SCTID:361918002 UMLS:C0086610 Wikipedia:Mesothelium uberon UBERON:0001136 mesothelium http://upload.wikimedia.org/wikipedia/commons/2/25/Mesothelium_peritoneal_wash_high_mag.jpg FMA Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. Wikipedia: The mesothelium is a membrane that forms the lining of several body cavities: the pleura (thoracal cavity), peritoneum (abdominal cavity including the mesentery) and pericardium (heart sac). Mesothelial tissue also surrounds the male internal reproductive organs (the tunica vaginalis testis) and covers the internal reproductive organs of women (the tunica serosa uteri). FMA:14074 Wikipedia:Mesothelium UMLS:C0086610 ncithesaurus:Mesothelium A major subdivision of an organism that is the entire part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. In vertebrares this includes the vertebral column.. dorsal In humans, called the back, a large posterior area of the human body, rising from the top of the buttocks to the back of the neck and the shoulders. It is the surface opposite to the chest, its height being defined by the vertebral column (commonly referred to as the spine or backbone) and its breadth being supported by the ribcage and shoulders. The spinal canal runs through the spine and provides nerves to the rest of the body BTO:0001713 CALOHA:TS-2223 EFO:0001405 FMA:14181 GAID:30 MESH:A01.176 NCIT:C13062 OpenCyc:Mx4rvVkEU5wpEbGdrcN5Y29ycA SCTID:123961009 UMLS:C0004600 Wikipedia:Dorsum_(anatomy) galen:Back back back of body proper dorsal part of organism uberon UBERON:0001137 dorsum http://upload.wikimedia.org/wikipedia/commons/e/ee/432px-Gray-back.PNG A major subdivision of an organism that is the entire part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. In vertebrares this includes the vertebral column.. BSPO:0000063 UBERONREF:0000006 Wikipedia:Dorsum_(anatomy) UMLS:C0004600 ncithesaurus:Back back FMA:14181 back of body proper FMA:14181 A vein that carries deoxygenated blood from its corresponding ovary to inferior vena cava or one of its tributaries. EMAPA:18644 FMA:14346 MA:0002186 NCIT:C53058 OpenCyc:Mx4rvrST5ZwpEbGdrcN5Y29ycA SCTID:278193003 UMLS:C0226720 Wikipedia:Ovarian_vein female reproductive system gonad vein female reproductive system gonada vein gonad of female reproductive system vein gonada of female reproductive system vein ovary vein vein of female reproductive system gonad vein of female reproductive system gonada vein of gonad of female reproductive system vein of gonada of female reproductive system vein of ovary uberon vena ovarica dextra vena ovarica sinistra UBERON:0001145 ovarian vein http://upload.wikimedia.org/wikipedia/commons/c/cf/Ovarschaf.jpg A vein that carries deoxygenated blood from its corresponding ovary to inferior vena cava or one of its tributaries. Wikipedia:Ovarian_vein UMLS:C0226720 ncithesaurus:Ovarian_Vein female reproductive system gonad vein OBOL:automatic female reproductive system gonada vein OBOL:automatic gonad of female reproductive system vein OBOL:automatic gonada of female reproductive system vein OBOL:automatic ovary vein OBOL:automatic vein of female reproductive system gonad OBOL:automatic vein of female reproductive system gonada OBOL:automatic vein of gonad of female reproductive system OBOL:automatic vein of gonada of female reproductive system OBOL:automatic vein of ovary OBOL:automatic vena ovarica dextra Wikipedia:Ovarian_vein vena ovarica sinistra Wikipedia:Ovarian_vein A portion of the large intestine before it becomes the rectum. In mammals, the colon is the most part of the large intestine, excluding the vermiform appendix, the rectum and the anal canal. Some references do not consider the caecum to be part of the colon. TODO - abstract this such that it legitimately covers all vertebrates The last portion of the digestive system, it extracts water and salt from solid wastes before they are eliminated from the body.[AAO] The posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates. Wallace et al, 2005.[TAO] Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] colonic In mammals, the colon consists of four sections: the ascending colon, the transverse colon, the descending colon, and the sigmoid colon[WP] In zebrafish, the posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates[ZFIN] it extracts water and salt from solid wastes before they are eliminated from the body[WP] AAO:0010400 BTO:0000269 CALOHA:TS-0158 EFO:0000361 EMAPA:18939 EV:0100079 FMA:14543 GAID:309 MA:0000335 MAP:0000001 MAT:0000526 MESH:A03.492.411.495.356 NCIT:C12382 OpenCyc:Mx4rvgLEM5wpEbGdrcN5Y29ycA SCTID:302508007 TAO:0000706 UMLS:C0009368 VHOG:0000648 Wikipedia:Colon_(anatomy) XAO:0000243 ZFA:0000706 galen:Colon large bowel posterior intestine uberon hindgut UBERON:0001155 colon 3 cjm FMA A portion of the large intestine before it becomes the rectum. In mammals, the colon is the most part of the large intestine, excluding the vermiform appendix, the rectum and the anal canal. Wikipedia:Colon_(anatomy) ZFIN:curator http://orcid.org/0000-0002-2825-0621 http://orcid.org/0000-0002-6601-2165 Some references do not consider the caecum to be part of the colon. http://orcid.org/0000-0002-1572-1316 The last portion of the digestive system, it extracts water and salt from solid wastes before they are eliminated from the body.[AAO] 2012-06-20 AAO:0010400 AAO UBERON:0001155 The posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates. Wallace et al, 2005.[TAO] 2012-08-14 TAO:0000706 TAO ZFIN:curator Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] 2012-09-17 VHOG:0000648 VHOG ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 http://bgee.unil.ch/ UMLS:C0009368 ncithesaurus:Colon The part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about 40 cm. in length, and normally lies within the pelvis, but on account of its freedom of movement it is liable to be displaced into the abdominal cavity. BTO:0000645 CALOHA:TS-2044 EFO:0000846 EMAPA:36391 FMA:14548 MAT:0000314 MESH:A03.492.411.495.356.668 MIAA:0000314 NCIT:C12384 NCIT:C33550 OpenCyc:Mx4rwHX_-5wpEbGdrcN5Y29ycA SCTID:362166007 UMLS:C0227391 UMLS:C0682612 Wikipedia:Sigmoid_colon galen:SigmoidColon uberon colon sigmoideum pelvic colon sigmoid colon sigmoid flexure UBERON:0001159 sigmoid colon http://upload.wikimedia.org/wikipedia/commons/3/3b/Dickdarm-Schema.svg FMA Wikipedia The part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about 40 cm. in length, and normally lies within the pelvis, but on account of its freedom of movement it is liable to be displaced into the abdominal cavity. Wikipedia:Sigmoid_colon UMLS:C0227391 ncithesaurus:Sigmoid_Colon UMLS:C0682612 ncithesaurus:Sigmoid_Flexure colon sigmoideum Wikipedia:Sigmoid_colon the layered structure that makes up the stomach, typiclly consists of a serous coat, a muscular coat, a mucous membrane, and other tissue layers in between EMAPA:35826 FMA:14582 MA:0002692 SCTID:279995000 galen:WallOfStomach anatomical wall of stomach anatomical wall of ventriculus gastric wall stomach anatomical wall stomach wall ventriculus anatomical wall ventriculus wall wall of ventriculus uberon UBERON:0001167 wall of stomach the layered structure that makes up the stomach, typiclly consists of a serous coat, a muscular coat, a mucous membrane, and other tissue layers in between MGI:csmith MP:0010783 anatomical wall of stomach OBOL:automatic anatomical wall of ventriculus OBOL:automatic stomach anatomical wall OBOL:automatic ventriculus anatomical wall OBOL:automatic ventriculus wall OBOL:automatic wall of ventriculus OBOL:automatic An anatomical wall that is part of a large intestine [Automatically generated definition]. EMAPA:35470 FMA:14619 MA:0002695 anatomical wall of large intestine large intestinal wall large intestine anatomical wall large intestine wall uberon UBERON:0001169 wall of large intestine An anatomical wall that is part of a large intestine [Automatically generated definition]. OBOL:automatic anatomical wall of large intestine OBOL:automatic large intestine anatomical wall OBOL:automatic The inner layer of peritoneum that is wrapped around organs located inside the intraperitoneal space. EMAPA:16592 FMA:14703 SCTID:362702003 TAO:0005132 VHOG:0001528 Wikipedia:Visceral_peritoneum ZFA:0005132 visceral serous membrane of peritoneum uberon UBERON:0001178 visceral peritoneum http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray1040.png The inner layer of peritoneum that is wrapped around organs located inside the intraperitoneal space. Wikipedia:Peritoneum#Types http://orcid.org/0000-0002-6601-2165 visceral serous membrane of peritoneum UBERON:cjm Anatomical cavity bounded by visceral and parietal peritoneum The potential space between the parietal and visceral layers of the peritoneum, which are normally in contact. The peritoneal cavity is divided into the greater and lesser sac. The greater sac is the peritoneal cavity, and the lesser sac is the omental bursa. [TFD][VHOG] In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart [of other tetrapods] is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes) Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG] BTO:0001782 EHDAA2:0001446 EMAPA:16138 FMA:14704 GAID:24 MA:0000054 MESH:A01.047.025.600.678 NCIT:C12769 SCTID:181616008 UMLS:C1704247 VHOG:0000852 Wikipedia:Peritoneal_cavity uberon cavitas peritonealis saccus serosus peritonei UBERON:0001179 peritoneal cavity Wikipedia Anatomical cavity bounded by visceral and parietal peritoneum Wikipedia:Peritoneal_cavity http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/86 The potential space between the parietal and visceral layers of the peritoneum, which are normally in contact. The peritoneal cavity is divided into the greater and lesser sac. The greater sac is the peritoneal cavity, and the lesser sac is the omental bursa. [TFD][VHOG] 2012-09-17 VHOG:0000852 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/peritoneal+cavity In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart [of other tetrapods] is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes) Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG] 2012-09-17 VHOG:0000852 VHOG ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206 http://bgee.unil.ch/ UMLS:C1704247 ncithesaurus:Peritoneal_Cavity cavitas peritonealis BTO:0001782 cavitas peritonealis Wikipedia:Peritoneal_cavity saccus serosus peritonei Wikipedia:Peritoneal_cavity An artery that supplies an ovary. In human anatomy, the ovarian artery is a blood vessel that supplies oxygenated blood to the ovary. It arises from the abdominal aorta below the renal artery, and does not pass out of the abdomiproperty_value external_definitioncavity. It can be found in the suspensory ligament of the ovary. [WP]. EMAPA:18620 FMA:14761 MA:0002012 NCIT:C33242 OpenCyc:Mx4rwOa9PZwpEbGdrcN5Y29ycA SCTID:244280002 UMLS:C0226411 Wikipedia:Ovarian_artery ovarian arterial tree uberon arteria ovarica UBERON:0001190 ovarian artery http://upload.wikimedia.org/wikipedia/commons/a/ae/Gray1170.png An artery that supplies an ovary. OBOL:automatic In human anatomy, the ovarian artery is a blood vessel that supplies oxygenated blood to the ovary. It arises from the abdominal aorta below the renal artery, and does not pass out of the abdomiproperty_value external_definitioncavity. It can be found in the suspensory ligament of the ovary. [WP]. Wikipedia:Ovarian_artery UMLS:C0226411 ncithesaurus:Ovarian_Artery arteria ovarica Wikipedia:Ovarian_artery The mucosal layer that lines the stomach. The gastric mucosa is the mucous membrane layer of the stomach which contains the glands and the gastric pits. In men it is about 1 mm thick and its surface is smooth, soft, and velvety. It consists of epithelium, lamina propria, and the muscularis mucosae. In its fresh state, it is of a pinkish tinge at the pyloric end and of a red or reddish-brown color over the rest of its surface. In infancy it is of a brighter hue, the vascular redness being more marked. It is thin at the cardiac extremity, but thicker toward the pylorus. During the contracted state of the organ it is thrown into numerous plaits or rugae, which, for the most part, have a longitudinal direction, and are most marked toward the pyloric end of the stomach, and along the greater curvature. These folds are entirely obliterated when the organ becomes distended. When examined with a lens, the inner surface of the mucous membrane presents a peculiar honeycomb appearance from being covered with funnel-like depressions or foveolae of a polygonal or hexagonal form, which vary from 0.12 to 0.25 mm. in diameter. These are the ducts of the gastric glands, and at the bottom of each may be seen one or more minute orifices, the openings of the gland tubes. Gastric glands are simple or branched tubular glands that emerge on the deeper part of the gastric foveola, inside the gastric areas and outlined by the folds of the mucosa. There are three types of glands: cardiac glands (in the proximal part of the stomach), oxyntic glands (the dominating type of gland), and pyloric glands. The cardiac glands mainly contain mucus producing cells. The bottom part of the oxyntic glands is dominated by zymogen (chief) cells that produce pepsinogen (an inactive precursor of the pepsin enzyme). Parietal cells, which secrete hydrochloric acid are scattered in the glands, with most of them in the middle part. The upper part of the glands consist of mucous neck cells; in this part the dividing cells are seen. The pyloric glands contain mucus-secreting cells. Several types of endocrine cells are found in all regions of the gastric mucosa. In the pyloric glands contain gastrin producing cells (G cells); this hormone stimulates acid production from the parietal cells. ECL (enterochromaffine-like) cells, found in the oxyntic glands release histamine, which also is a powerful stimulant of the acid secretion. The A cells produce glucagon, which mobilizes the hepatic glycogen, and the enterochromaffin cells that produce serotonin, which stimulates the contraction of the smooth muscles. The surface of the mucous membrane is covered by a single layer of columnar epithelium . This epithelium commences very abruptly at the cardiac orifice, where there is a sudden transition from the stratified epithelium of the esophagus. The epithelial lining of the gland ducts is of the same character and is continuous with the general lining of the stomach. [WP,unvetted][Wikipedia:Gastric_mucosa]. BTO:0001308 CALOHA:TS-0404 EMAPA:35817 FMA:14907 GAID:321 MA:0002683 MESH:A03.492.766.440 NCIT:C32656 OpenCyc:Mx8NhB4rvcD6KJwpEbGdrcN5Y29ycB4rvmKNOpwpEbGdrcN5Y29ycB4rvVj5FpwpEbGdrcN5Y29ycB4rvVjlqpwpEbGdrcN5Y29ycA SCTID:362131005 UMLS:C0017136 Wikipedia:Gastric_mucosa galen:GastricMucosa gastric mucosa gastric mucous membrane mucosa of organ of stomach mucosa of organ of ventriculus mucosa of ventriculus mucous membrane of stomach mucous membrane of ventriculus organ mucosa of stomach organ mucosa of ventriculus stomach mucosa stomach mucosa of organ stomach mucous membrane stomach organ mucosa tunica mucosa (gaster) tunica mucosa gastricae ventriculus mucosa ventriculus mucosa of organ ventriculus mucous membrane ventriculus organ mucosa uberon Magenschleimhaut tunica mucosa gastris UBERON:0001199 mucosa of stomach Wikipedia:File:Normal_gastric_mucosa_intermed_mag.jpg The mucosal layer that lines the stomach. http://orcid.org/0000-0002-6601-2165 The gastric mucosa is the mucous membrane layer of the stomach which contains the glands and the gastric pits. In men it is about 1 mm thick and its surface is smooth, soft, and velvety. It consists of epithelium, lamina propria, and the muscularis mucosae. In its fresh state, it is of a pinkish tinge at the pyloric end and of a red or reddish-brown color over the rest of its surface. In infancy it is of a brighter hue, the vascular redness being more marked. It is thin at the cardiac extremity, but thicker toward the pylorus. During the contracted state of the organ it is thrown into numerous plaits or rugae, which, for the most part, have a longitudinal direction, and are most marked toward the pyloric end of the stomach, and along the greater curvature. These folds are entirely obliterated when the organ becomes distended. When examined with a lens, the inner surface of the mucous membrane presents a peculiar honeycomb appearance from being covered with funnel-like depressions or foveolae of a polygonal or hexagonal form, which vary from 0.12 to 0.25 mm. in diameter. These are the ducts of the gastric glands, and at the bottom of each may be seen one or more minute orifices, the openings of the gland tubes. Gastric glands are simple or branched tubular glands that emerge on the deeper part of the gastric foveola, inside the gastric areas and outlined by the folds of the mucosa. There are three types of glands: cardiac glands (in the proximal part of the stomach), oxyntic glands (the dominating type of gland), and pyloric glands. The cardiac glands mainly contain mucus producing cells. The bottom part of the oxyntic glands is dominated by zymogen (chief) cells that produce pepsinogen (an inactive precursor of the pepsin enzyme). Parietal cells, which secrete hydrochloric acid are scattered in the glands, with most of them in the middle part. The upper part of the glands consist of mucous neck cells; in this part the dividing cells are seen. The pyloric glands contain mucus-secreting cells. Several types of endocrine cells are found in all regions of the gastric mucosa. In the pyloric glands contain gastrin producing cells (G cells); this hormone stimulates acid production from the parietal cells. ECL (enterochromaffine-like) cells, found in the oxyntic glands release histamine, which also is a powerful stimulant of the acid secretion. The A cells produce glucagon, which mobilizes the hepatic glycogen, and the enterochromaffin cells that produce serotonin, which stimulates the contraction of the smooth muscles. The surface of the mucous membrane is covered by a single layer of columnar epithelium . This epithelium commences very abruptly at the cardiac orifice, where there is a sudden transition from the stratified epithelium of the esophagus. The epithelial lining of the gland ducts is of the same character and is continuous with the general lining of the stomach. [WP,unvetted][Wikipedia:Gastric_mucosa]. Wikipedia:Gastric_mucosa UMLS:C0017136 ncithesaurus:Gastric_Mucosa mucosa of organ of stomach OBOL:automatic mucosa of organ of ventriculus OBOL:automatic mucosa of ventriculus OBOL:automatic mucous membrane of ventriculus OBOL:automatic organ mucosa of stomach OBOL:automatic organ mucosa of ventriculus OBOL:automatic stomach mucosa of organ OBOL:automatic stomach mucous membrane OBOL:automatic stomach organ mucosa OBOL:automatic tunica mucosa gastricae FMA:14907 FMA:TA ventriculus mucosa OBOL:automatic ventriculus mucosa of organ OBOL:automatic ventriculus mucous membrane OBOL:automatic ventriculus organ mucosa OBOL:automatic Magenschleimhaut BTO:0001308 tunica mucosa gastris BTO:0001308 tunica mucosa gastris Wikipedia:Gastric_mucosa the fibrous connective tissue layer beneath the stomach mucosa BTO:0002110 EMAPA:35825 FMA:14908 MA:0002685 NCIT:C32663 SCTID:52459002 UMLS:C0227211 gastric submucosa stomach submucosa submucosa of ventriculus tela submucosa (gaster) tela submucosa gastricae ventriculus submucosa uberon submucous layer of stomach tela submucosa ventriculi UBERON:0001200 submucosa of stomach the fibrous connective tissue layer beneath the stomach mucosa MGI:csmith MP:0010794 UMLS:C0227211 ncithesaurus:Gastric_Submucosa submucosa of ventriculus OBOL:automatic tela submucosa gastricae FMA:14908 FMA:TA ventriculus submucosa OBOL:automatic submucous layer of stomach BTO:0002110 tela submucosa ventriculi BTO:0002110 the outermost layer of the stomach wall, consisting of layers of connective tissue continuous with the peritoneum TODO - check serosa/peritoneum EMAPA:35822 FMA:14914 MA:0001626 NCIT:C32662 SCTID:1353004 UMLS:C1517453 anatomical wall of stomach serosa anatomical wall of stomach serous membrane anatomical wall of ventriculus serosa anatomical wall of ventriculus serous membrane gastric wall serosa gastric wall serous membrane serosa of anatomical wall of stomach serosa of anatomical wall of ventriculus serosa of gastric wall serosa of stomach anatomical wall serosa of stomach wall serosa of ventriculus anatomical wall serosa of ventriculus wall serosa of wall of stomach serosa of wall of ventriculus serous coat of stomach serous membrane of anatomical wall of stomach serous membrane of anatomical wall of ventriculus serous membrane of gastric wall serous membrane of stomach anatomical wall serous membrane of stomach wall serous membrane of ventriculus anatomical wall serous membrane of ventriculus wall serous membrane of wall of stomach serous membrane of wall of ventriculus stomach anatomical wall serosa stomach anatomical wall serous membrane stomach serosa stomach wall serosa stomach wall serous membrane tunica serosa (gaster) tunica serosa gastricae ventriculus anatomical wall serosa ventriculus anatomical wall serous membrane ventriculus wall serosa ventriculus wall serous membrane visceral peritoneum of stomach wall of stomach serosa wall of stomach serous membrane wall of ventriculus serosa wall of ventriculus serous membrane uberon gastric serosa UBERON:0001201 serosa of stomach the outermost layer of the stomach wall, consisting of layers of connective tissue continuous with the peritoneum MGI:csmith MP:0010793 UMLS:C1517453 ncithesaurus:Gastric_Serosal_Surface anatomical wall of stomach serosa OBOL:automatic anatomical wall of stomach serous membrane OBOL:automatic anatomical wall of ventriculus serosa OBOL:automatic anatomical wall of ventriculus serous membrane OBOL:automatic gastric wall serosa OBOL:automatic gastric wall serous membrane OBOL:automatic serosa of anatomical wall of stomach OBOL:automatic serosa of anatomical wall of ventriculus OBOL:automatic serosa of gastric wall OBOL:automatic serosa of stomach anatomical wall OBOL:automatic serosa of stomach wall OBOL:automatic serosa of ventriculus anatomical wall OBOL:automatic serosa of ventriculus wall OBOL:automatic serosa of wall of stomach OBOL:automatic serosa of wall of ventriculus OBOL:automatic serous membrane of anatomical wall of stomach OBOL:automatic serous membrane of anatomical wall of ventriculus OBOL:automatic serous membrane of gastric wall OBOL:automatic serous membrane of stomach anatomical wall OBOL:automatic serous membrane of stomach wall OBOL:automatic serous membrane of ventriculus anatomical wall OBOL:automatic serous membrane of ventriculus wall OBOL:automatic serous membrane of wall of stomach OBOL:automatic serous membrane of wall of ventriculus OBOL:automatic stomach anatomical wall serosa OBOL:automatic stomach anatomical wall serous membrane OBOL:automatic stomach wall serosa OBOL:automatic stomach wall serous membrane OBOL:automatic tunica serosa gastricae FMA:14914 FMA:TA ventriculus anatomical wall serosa OBOL:automatic ventriculus anatomical wall serous membrane OBOL:automatic ventriculus wall serosa OBOL:automatic ventriculus wall serous membrane OBOL:automatic wall of stomach serosa OBOL:automatic wall of stomach serous membrane OBOL:automatic wall of ventriculus serosa OBOL:automatic wall of ventriculus serous membrane OBOL:automatic A mucosa that is part of a large intestine [Automatically generated definition]. CALOHA:TS-2106 EMAPA:35467 FMA:14969 MA:0002688 NCIT:C32926 UMLS:C0734203 large intestinal mucosa large intestine mucosa large intestine mucosa of organ large intestine mucous membrane large intestine organ mucosa mucosa of organ of large intestine mucous membrane of large intestine organ mucosa of large intestine tunica mucosa intestini crassi uberon UBERON:0001207 mucosa of large intestine A mucosa that is part of a large intestine [Automatically generated definition]. OBOL:automatic UMLS:C0734203 ncithesaurus:Large_Intestinal_Mucosa large intestine mucosa of organ OBOL:automatic large intestine mucous membrane OBOL:automatic large intestine organ mucosa OBOL:automatic mucosa of organ of large intestine OBOL:automatic organ mucosa of large intestine OBOL:automatic tunica mucosa intestini crassi FMA:14969 FMA:TA A submucosa that is part of a large intestine [Automatically generated definition]. BTO:0002111 EMAPA:37560 FMA:14970 MA:0002690 NCIT:C32930 UMLS:C0734204 large intestinal submucosa large intestine submucosa tela submucosa intestini crassi uberon submucous layer of large intestine UBERON:0001208 submucosa of large intestine A submucosa that is part of a large intestine [Automatically generated definition]. OBOL:automatic EMAPA:37560 MA:th UMLS:C0734204 ncithesaurus:Large_Intestinal_Submucosa tela submucosa intestini crassi FMA:14970 FMA:TA submucous layer of large intestine BTO:0002111 A serous membrane that is part of a large intestine [Automatically generated definition]. TODO - check serosa/peritoneum EMAPA:37557 FMA:14975 MA:0001546 NCIT:C32929 UMLS:C1517727 large intestinal serosa large intestine serosa large intestine serous membrane serous coat of large intestine serous membrane of large intestine tunica serosa intestini crassi visceral peritoneum of large intestine uberon UBERON:0001209 serosa of large intestine A serous membrane that is part of a large intestine [Automatically generated definition]. OBOL:automatic EMAPA:37557 MA:th UMLS:C1517727 ncithesaurus:Large_Intestinal_Serosal_Surface large intestine serous membrane OBOL:automatic serous membrane of large intestine OBOL:automatic tunica serosa intestini crassi FMA:14975 FMA:TA A blood vessel that drains blood from the large intestine that usually terminates when reaching the splenic vein, which goes on to form the portal vein with the superior mesenteric vein (SMV). Anatomical variations include the IMV draining into the confluence of the SMV and splenic vein and the IMV draining in the SMV. The IMV lies to the right of the similarly name artery, the inferior mesenteric artery, which originates from the abdominal aorta. [WP,unvetted]. BTO:0002782 EHDAA2:0000819 EHDAA:8712 EMAPA:18642 FMA:15391 MA:0002178 NCIT:C32782 OpenCyc:Mx4rvcV53ZwpEbGdrcN5Y29ycA SCTID:281055007 UMLS:C0226754 VHOG:0001118 Wikipedia:Inferior_mesenteric_vein uberon lower mesenteric vein vena mesenterica inferior UBERON:0001215 inferior mesenteric vein http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png FMA/obol A blood vessel that drains blood from the large intestine that usually terminates when reaching the splenic vein, which goes on to form the portal vein with the superior mesenteric vein (SMV). Anatomical variations include the IMV draining into the confluence of the SMV and splenic vein and the IMV draining in the SMV. The IMV lies to the right of the similarly name artery, the inferior mesenteric artery, which originates from the abdominal aorta. [WP,unvetted]. Wikipedia:Inferior_mesenteric_vein UMLS:C0226754 ncithesaurus:Inferior_Mesenteric_Vein lower mesenteric vein BTO:0002782 vena mesenterica inferior Wikipedia:Inferior_mesenteric_vein Mucosal layer that lines the intestine. BTO:0000642 EMAPA:35440 FMA:15695 GAID:296 MA:0001537 MESH:A03.492.411.369 NCIT:C49241 SCTID:362080002 UMLS:C0021839 bowel mucosa bowel mucosa of organ bowel mucous membrane bowel organ mucosa intestine mucosa intestine mucosa of organ intestine mucous membrane intestine organ mucosa mucosa of bowel mucosa of intestine mucosa of organ of bowel mucosa of organ of intestine mucous membrane of bowel mucous membrane of intestine organ mucosa of bowel organ mucosa of intestine tunica mucosa intestini uberon UBERON:0001242 intestinal mucosa Mucosal layer that lines the intestine. UBERON:cjm UMLS:C0021839 ncithesaurus:Intestinal_Mucosa bowel mucosa OBOL:automatic bowel mucosa of organ OBOL:automatic bowel mucous membrane OBOL:automatic bowel organ mucosa OBOL:automatic intestine mucosa of organ OBOL:automatic intestine mucous membrane OBOL:automatic intestine organ mucosa OBOL:automatic mucosa of bowel OBOL:automatic mucosa of organ of bowel OBOL:automatic mucosa of organ of intestine OBOL:automatic mucous membrane of bowel OBOL:automatic mucous membrane of intestine OBOL:automatic organ mucosa of bowel OBOL:automatic organ mucosa of intestine OBOL:automatic A serous membrane that is part of a wall of intestine [Automatically generated definition]. TODO - check serosa/peritoneum EMAPA:37619 FMA:15701 MA:0001538 anatomical wall of bowel serosa anatomical wall of bowel serous membrane anatomical wall of intestine serosa anatomical wall of intestine serous membrane bowel anatomical wall serosa bowel anatomical wall serous membrane bowel wall serosa bowel wall serous membrane intestinal serosa intestinal wall serosa intestinal wall serous membrane intestine anatomical wall serosa intestine anatomical wall serous membrane intestine serosa intestine wall serosa intestine wall serous membrane serosa of anatomical wall of bowel serosa of anatomical wall of intestine serosa of bowel anatomical wall serosa of bowel wall serosa of intestinal wall serosa of intestine anatomical wall serosa of intestine wall serosa of wall of bowel serosa of wall of intestine serous membrane of anatomical wall of bowel serous membrane of anatomical wall of intestine serous membrane of bowel anatomical wall serous membrane of bowel wall serous membrane of intestinal wall serous membrane of intestine anatomical wall serous membrane of intestine wall serous membrane of wall of bowel serous membrane of wall of intestine visceral peritoneum of intestine wall of bowel serosa wall of bowel serous membrane wall of intestine serosa wall of intestine serous membrane uberon UBERON:0001243 serosa of intestine A serous membrane that is part of a wall of intestine [Automatically generated definition]. OBOL:automatic EMAPA:37619 MA:th anatomical wall of bowel serosa OBOL:automatic anatomical wall of bowel serous membrane OBOL:automatic anatomical wall of intestine serosa OBOL:automatic anatomical wall of intestine serous membrane OBOL:automatic bowel anatomical wall serosa OBOL:automatic bowel anatomical wall serous membrane OBOL:automatic bowel wall serosa OBOL:automatic bowel wall serous membrane OBOL:automatic intestinal wall serosa OBOL:automatic intestinal wall serous membrane OBOL:automatic intestine anatomical wall serosa OBOL:automatic intestine anatomical wall serous membrane OBOL:automatic intestine wall serosa OBOL:automatic intestine wall serous membrane OBOL:automatic serosa of anatomical wall of bowel OBOL:automatic serosa of anatomical wall of intestine OBOL:automatic serosa of bowel anatomical wall OBOL:automatic serosa of bowel wall OBOL:automatic serosa of intestinal wall OBOL:automatic serosa of intestine anatomical wall OBOL:automatic serosa of intestine wall OBOL:automatic serosa of wall of bowel OBOL:automatic serosa of wall of intestine OBOL:automatic serous membrane of anatomical wall of bowel OBOL:automatic serous membrane of anatomical wall of intestine OBOL:automatic serous membrane of bowel anatomical wall OBOL:automatic serous membrane of bowel wall OBOL:automatic serous membrane of intestinal wall OBOL:automatic serous membrane of intestine anatomical wall OBOL:automatic serous membrane of intestine wall OBOL:automatic serous membrane of wall of bowel OBOL:automatic serous membrane of wall of intestine OBOL:automatic wall of bowel serosa OBOL:automatic wall of bowel serous membrane OBOL:automatic wall of intestine serosa OBOL:automatic wall of intestine serous membrane OBOL:automatic Orifice at the opposite end of an animal's digestive tract from the mouth. Its function is to expel feces, unwanted semi-solid matter produced during digestion, which, depending on the type of animal, may be one or more of: matter which the animal cannot digest, such as bones; food material after all the nutrients have been extracted, for example cellulose or lignin; ingested matter which would be toxic if it remained in the digestive tract; and dead or excess gut bacteria and other endosymbionts. anal In the lungfish, sharks and rays the rectum opens into the cloaca which also receives wastes (urine) from the kidneys and material from the reproductive organs. In bony fish the rectum reaches the outside environment through the anus, which is normally situated just in front the urinary and reproductive openings. However in some fish the digestive tract may be curled back on itself, and in the Electric Eel (Electrophorus electricus) the anus is situated in the fish's throat. -- http://www.earthlife.net/fish/digestion.html BTO:0001680 CALOHA:TS-2005 EV:0100082 FBbt:00003148 FMA:15711 GAID:312 MA:0000331 MESH:A03.492.411.495.767.288 NCIT:C43362 OpenCyc:Mx4rvVjaEZwpEbGdrcN5Y29ycA SCTID:181262009 TADS:0000066 TGMA:0001279 UMLS:C0003461 WBbt:0005364 Wikipedia:Anus galen:Anus anal opening anal orifice opening of terminal part of digestive tract uberon proctodeum UBERON:0001245 anus http://upload.wikimedia.org/wikipedia/commons/6/65/Protovsdeuterostomes.svg http://upload.wikimedia.org/wikipedia/commons/7/75/Anorectum.gif Orifice at the opposite end of an animal's digestive tract from the mouth. Its function is to expel feces, unwanted semi-solid matter produced during digestion, which, depending on the type of animal, may be one or more of: matter which the animal cannot digest, such as bones; food material after all the nutrients have been extracted, for example cellulose or lignin; ingested matter which would be toxic if it remained in the digestive tract; and dead or excess gut bacteria and other endosymbionts. Wikipedia:Anus ZFIN:curator UMLS:C0003461 ncithesaurus:Anus An anatomical wall that is part of a intestine [Automatically generated definition]. we place two MA classes here due to the official ncit2ma mapping to intestinal wall tissue; not clear how bowel and intestine are different BTO:0000647 EMAPA:35444 FMA:15949 MA:0001525 MA:0002693 NCIT:C49478 UMLS:C1708548 anatomical wall of bowel anatomical wall of intestine bowel anatomical wall bowel wall intestinal wall intestine anatomical wall intestine wall wall of bowel uberon bowel wall UBERON:0001262 wall of intestine An anatomical wall that is part of a intestine [Automatically generated definition]. OBOL:automatic UMLS:C1708548 ncithesaurus:Intestinal_Wall_Tissue anatomical wall of bowel OBOL:automatic anatomical wall of intestine OBOL:automatic bowel anatomical wall OBOL:automatic bowel wall OBOL:automatic intestine anatomical wall OBOL:automatic wall of bowel OBOL:automatic bowel wall MA:0001525 Transudate contained in the peritoneal cavity. BTO:0001031 EMAPA:35683 FMA:16515 MA:0002531 Wikipedia:Peritoneal_fluid ncithesaurus:Peritoneal_Fluid uberon UBERON:0001268 peritoneal fluid FMA Transudate contained in the peritoneal cavity. FMA:16515 The organism subdivision that includes the pelvic girdle skeleton and associated soft tissue. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Examples: There are only two instances in an organism, right and left pectoral girdle regions. this class describes the subdivision of the limb/fin, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831). See also comments on obo-anatomy mail list. Note that even though the class includes soft tissue it is more restrictive than 'pelvis' which also includes structures in cavities etc. TODO this needs to be better documented Subdivision of lower limb or fin which links the limb/fin to the body[FMA,modified]. There is only one instance of the pelvic girdle region per organism.[VSAO] EMAPA:37862 FMA:16581 NCIT:C33291 SCTID:360010001 UMLS:C0684083 VSAO:0000304 uberon girdle - pelvic pelvic girdle UBERON:0001271 pelvic girdle region The organism subdivision that includes the pelvic girdle skeleton and associated soft tissue. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Examples: There are only two instances in an organism, right and left pectoral girdle regions. DOI:10.1002/dvdy.22617 FMA:16581 FMA:23217 UBERONREF:0000003 https://groups.google.com/d/topic/obo-anatomy/h4R4xKmINrw/discussion https://orcid.org/0000-0002-6601-2165 Subdivision of lower limb or fin which links the limb/fin to the body[FMA,modified]. There is only one instance of the pelvic girdle region per organism.[VSAO] 2012-08-14 VSAO:0000304 VSAO https://orcid.org/0000-0002-6601-2165 EMAPA:37862 MA:th UMLS:C0684083 ncithesaurus:Pelvic_Girdle pelvic girdle The epithelial layer of the stomach . in FMA this is classified as simple columnar, MA divides this into squamous and glandular BTO:0000500 CALOHA:TS-2068 EHDAA2:0001918 EMAPA:17023 FMA:17091 MA:0001610 SCTID:64977002 VHOG:0001433 epithelial tissue of stomach epithelial tissue of ventriculus epithelium of ventriculus stomach epithelial tissue stomach epithelium ventriculus epithelial tissue ventriculus epithelium uberon gastric epithelium UBERON:0001276 epithelium of stomach The epithelial layer of the stomach . MP:0000471 in FMA this is classified as simple columnar, MA divides this into squamous and glandular FMA epithelial tissue of stomach OBOL:automatic epithelial tissue of ventriculus OBOL:automatic epithelium of ventriculus OBOL:automatic stomach epithelial tissue OBOL:automatic stomach epithelium OBOL:automatic ventriculus epithelial tissue OBOL:automatic ventriculus epithelium OBOL:automatic gastric epithelium BTO:0000500 Epithelial layer that lines the intestine. Simple columnar epithelium that lines the intestine, sometimes pseudostratified, with absorptive brush-border cells and mucous goblet cells clearly visible. Crosnier et al. 2005[TAO] BTO:0000781 EMAPA:32873 FMA:17229 MA:0001536 NCIT:C49240 SCTID:266135004 TAO:0005124 UMLS:C0226890 Wikipedia:Intestinal_epithelium ZFA:0005124 bowel epithelial tissue bowel epithelium epithelial tissue of bowel epithelial tissue of intestine epithelium of bowel epithelium of intestine intestine epithelial tissue villous epithelium uberon intestine epithelium UBERON:0001277 intestinal epithelium Epithelial layer that lines the intestine. UBERON:cjm Simple columnar epithelium that lines the intestine, sometimes pseudostratified, with absorptive brush-border cells and mucous goblet cells clearly visible. Crosnier et al. 2005[TAO] 2012-08-14 TAO:0005124 TAO ZFIN:curator UMLS:C0226890 ncithesaurus:Intestinal_Epithelium bowel epithelial tissue OBOL:automatic bowel epithelium OBOL:automatic epithelial tissue of bowel OBOL:automatic epithelial tissue of intestine OBOL:automatic epithelium of bowel OBOL:automatic epithelium of intestine OBOL:automatic intestine epithelial tissue OBOL:automatic villous epithelium ZFA:0005124 An epithelium that is part of a large intestine [Automatically generated definition]. CALOHA:TS-2105 EMAPA:35466 FMA:17301 MA:0001545 epithelial tissue of large intestine large intestinal epithelium large intestine epithelial tissue large intestine epithelium uberon UBERON:0001278 epithelium of large intestine An epithelium that is part of a large intestine [Automatically generated definition]. OBOL:automatic epithelial tissue of large intestine OBOL:automatic large intestine epithelial tissue OBOL:automatic Muscle (organ) which is a part of the pelvis. Examples: levator ani, EMAPA:18184 EMAPA:37481 FMA:19086 MA:0000534 muscle organ of pelvis pelvic muscle pelvis muscle pelvis muscle organ uberon UBERON:0001325 muscle of pelvis FMAdef MA Muscle (organ) which is a part of the pelvis. Examples: levator ani, FMA:19086 EMAPA:37481 MA:th muscle organ of pelvis OBOL:automatic pelvic muscle FMA:19086 pelvis muscle organ OBOL:automatic The anus and surrounding regions. Encompasses both internal and external regions, where present Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] EFO:0000847 EHDAA2:0000122 EHDAA:2931 EMAPA:16831 MA:0000329 MAT:0000042 MIAA:0000042 NCIT:C32069 SCTID:362680001 UMLS:C0230120 VHOG:0000395 WBbt:0006919 uberon posterior posterior end of organism UBERON:0001353 anal region https://github.com/obophenotype/uberon/issues/507 http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray408.png cjm The anus and surrounding regions. Encompasses both internal and external regions, where present https://orcid.org/0000-0002-6601-2165 Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] 2012-09-17 VHOG:0000395 VHOG ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 http://bgee.unil.ch/ UMLS:C0230120 ncithesaurus:Anal_Region The outer layer of peritoneum that is attached to the abdominal and pelvic walls. Peritoneum attached to the abdominal wall.[AAO] UBERON:0004459 AAO:0010816 EMAPA:16591 FMA:21451 SCTID:362700006 TAO:0005131 VHOG:0001527 Wikipedia:Parietal_peritoneum ZFA:0005131 parietal serous membrane of peritoneum uberon peritoneal cavity lining UBERON:0001366 parietal peritoneum http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray1040.png The outer layer of peritoneum that is attached to the abdominal and pelvic walls. Wikipedia:Peritoneum#Types http://orcid.org/0000-0002-6601-2165 Peritoneum attached to the abdominal wall.[AAO] 2012-06-20 AAO:0010816 AAO AAO:JMG parietal serous membrane of peritoneum UBERON:cjm A zone of skin that is part of a pelvis [Automatically generated definition]. EMAPA:37282 FMA:22984 MA:0000546 SCTID:181517009 pelvic skin pelvis skin pelvis zone of skin zone of skin of pelvis uberon UBERON:0001415 skin of pelvis A zone of skin that is part of a pelvis [Automatically generated definition]. OBOL:automatic EMAPA:37282 MA:th pelvis zone of skin OBOL:automatic zone of skin of pelvis OBOL:automatic A zone of skin that is part of an abdomen [Automatically generated definition]. EFO:0000214 FMA:22988 FMA:23000 MA:0000523 NCIT:C52758 SCTID:361707007 UMLS:C0222166 abdomen skin abdomen zone of skin abdominal skin skin of abdomen proper zone of skin of abdomen uberon UBERON:0001416 skin of abdomen A zone of skin that is part of an abdomen [Automatically generated definition]. OBOL:automatic UMLS:C0222166 ncithesaurus:Abdominal_Skin abdomen zone of skin OBOL:automatic skin of abdomen proper FMA:22988 zone of skin of abdomen OBOL:automatic A zone of skin that is part of a neck [Automatically generated definition]. EMAPA:37277 FMA:23021 FMA:23022 MA:0000590 NCIT:C52756 SCTID:361705004 UMLS:C0205030 neck (volume) zone of skin neck skin neck zone of skin zone of skin of neck zone of skin of neck (volume) uberon UBERON:0001417 skin of neck A zone of skin that is part of a neck [Automatically generated definition]. OBOL:automatic EMAPA:37277 MA:th UMLS:C0205030 ncithesaurus:Neck_Skin neck (volume) zone of skin OBOL:automatic neck zone of skin OBOL:automatic zone of skin of neck OBOL:automatic zone of skin of neck (volume) OBOL:automatic A zone of skin that is part of a thorax [Automatically generated definition]. EMAPA:37765 FMA:23028 FMA:23029 MA:0000564 SCTID:281723000 thoracic skin thorax skin thorax zone of skin zone of skin of thorax uberon upper body skin UBERON:0001418 skin of thorax A zone of skin that is part of a thorax [Automatically generated definition]. OBOL:automatic EMAPA:37765 MA:th thorax zone of skin OBOL:automatic zone of skin of thorax OBOL:automatic Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system. Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO] Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO] System that provides physical support to the organism.[AAO] By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG] skeletal GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates AAO:0000566 BTO:0001486 CALOHA:TS-1320 EFO:0000806 EHDAA2:0003168 EMAPA:35773 FMA:23881 MA:0000018 NCIT:C12788 OpenCyc:Mx4rvVi1rpwpEbGdrcN5Y29ycA TAO:0000434 UMLS:C0037253 VHOG:0001254 VSAO:0000027 XAO:0003060 ZFA:0000434 skeleton system set of all bones and joints uberon Skelettsystem UBERON:0001434 skeletal system https://github.com/obophenotype/uberon/wiki/The-skeletal-system Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system. GO_REF:0000034 VSAO:0000027 http://dx.plos.org/10.1371/journal.pone.0051070 Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO] 2012-08-14 TAO:0000434 TAO TAO:wd Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO] 2012-08-14 VSAO:0000027 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 PSPUB:0000170 System that provides physical support to the organism.[AAO] 2012-06-20 AAO:0000566 AAO AAO:LAP By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG] 2012-09-17 VHOG:0001254 VHOG DOI:10.1159/000324245 Donoghue PCJ, Sansom IJ, Origin and early evolution of vertebrate skeletonization. Microscopy research and technique (2002) http://bgee.unil.ch/ GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates GO UMLS:C0037253 ncithesaurus:Skeletal_System set of all bones and joints Skelettsystem BTO:0001486 FMA:24218 SCTID:123852005 XAO:0000040 head subdivision uberon head region region of head UBERON:0001444 subdivision of head A subdivision of the head that has as parts the layers deep to the surface of the anterior surface, including the mouth, eyes, and nose (when present). In vertebrates, this includes the facial skeleton and structures superficial to the facial skeleton (cheeks, mouth, eyeballs, skin of face, etc). Subdivision of head which consists of the viscerocranium and all layers superficial to it. Examples: There is only one face. The area that extends from the median ocellus to the oral foramen[HAO]. facial The face develops from outward growth of tissue located rostral to the cranium & pharynx. The lower jaw and most of the upper jaw are formed by growth of the first pharyngeal (branchial) arch. The upper incisor region and the nose and forehead (frontal region) are formed from tissue located rostral to the neural tube (frontonasal prominence) BTO:0003369 CALOHA:TS-2216 EMAPA:32763 FMA:24728 GAID:64 HAO:0000316 MA:0002473 MESH:D005145 NCIT:C13071 OpenCyc:Mx4rvVi5GZwpEbGdrcN5Y29ycA SCTID:302549007 UMLS:C0015450 Wikipedia:Face galen:Face uberon facia/facies visage UBERON:0001456 face http://upload.wikimedia.org/wikipedia/commons/5/55/Mona_Lisa_headcrop.jpg A subdivision of the head that has as parts the layers deep to the surface of the anterior surface, including the mouth, eyes, and nose (when present). In vertebrates, this includes the facial skeleton and structures superficial to the facial skeleton (cheeks, mouth, eyeballs, skin of face, etc). http://orcid.org/0000-0002-6601-2165 Subdivision of head which consists of the viscerocranium and all layers superficial to it. Examples: There is only one face. FMA:24728 The area that extends from the median ocellus to the oral foramen[HAO]. HAO:0000316 http://api.hymao.org/api/ref/67791 NCBITaxon:7399 The face develops from outward growth of tissue located rostral to the cranium & pharynx. The lower jaw and most of the upper jaw are formed by growth of the first pharyngeal (branchial) arch. The upper incisor region and the nose and forehead (frontal region) are formed from tissue located rostral to the neural tube (frontonasal prominence) vanat.cvm.umn.edu/TFFlectPDFs/LectFaceDevelop.pdf UMLS:C0015450 ncithesaurus:Face facia/facies Wikipedia:Face visage BTO:0003369 A zone of skin that is part of a lip [Automatically generated definition]. EMAPA:37643 FMA:24764 MA:0001579 NCIT:C12291 SCTID:244092005 UMLS:C0222101 lip skin lip zone of skin zone of skin of lip uberon skin of lips UBERON:0001458 skin of lip A zone of skin that is part of a lip [Automatically generated definition]. OBOL:automatic EMAPA:37643 MA:th UMLS:C0222101 ncithesaurus:Skin_of_the_Lip lip zone of skin OBOL:automatic zone of skin of lip OBOL:automatic skin of lips Skeletal element that is composed of bone tissue. Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO] Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO] Skeletal element that is composed of bone tissue.[VSAO] relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG] AAO:0000047 AEO:0000082 BTO:0000140 CALOHA:TS-0088 EFO:0000298 EHDAA2:0003082 EMAPA:32782 ENVO:00002039 EV:0100140 FMA:30317 FMA:5018 GAID:92 MA:0001459 MAT:0000299 MIAA:0000299 NCIT:C12366 OpenCyc:Mx4rvViDlpwpEbGdrcN5Y29ycA OpenCyc:Mx4rvVkCG5wpEbGdrcN5Y29ycA SCTID:90780006 TAO:0001514 UMLS:C0262950 VHOG:0001190 VSAO:0000057 Wikipedia:Bone XAO:0000169 ZFA:0001514 galen:Bone bone organ uberon bone bones UBERON:0001474 bone element VSAO-modified Skeletal element that is composed of bone tissue. GO_REF:0000034 PSPUB:0000170 VSAO:0000057 http://dx.plos.org/10.1371/journal.pone.0051070 https://github.com/obophenotype/uberon/issues/277 Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO] 2012-06-20 AAO:0000047 AAO AAO:LAP Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO] 2012-08-14 TAO:0001514 TAO ZFIN:curator Skeletal element that is composed of bone tissue.[VSAO] 2012-08-14 VSAO:0000057 VSAO PSPUB:0000170 relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] 2012-06-20 AAO:0000047 AAO The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG] 2012-09-17 VHOG:0001190 VHOG DOI:10.1159/000324245 Murdock DJ, Donoghue PC, Evolutionary Origins of Animal Skeletal Biomineralization. Cells Tissues Organs (2011) http://bgee.unil.ch/ UMLS:C0262950 ncithesaurus:Bone bone organ FMA:5018 bone AEO:0000082 BTO:0000140 MA:0001459 VHOG:0001190 bones ZFA:0001514 An articular capsule (or joint capsule) is an envelope surrounding a synovial joint. [WP,unvetted]. check ncita EMAPA:37621 FMA:34836 GAID:263 MA:0001519 MESH:D017746 NCIT:C32259 NCIT:C84388 SCTID:182238002 UMLS:C0206207 Wikipedia:Articular_capsule galen:JointCapsule capsula articularis fibrous capsule of joint joint capsule joint fibrous capsule uberon capsulae articulares UBERON:0001484 articular capsule http://upload.wikimedia.org/wikipedia/commons/1/19/Joint.png http://upload.wikimedia.org/wikipedia/commons/4/4a/Gray299.png An articular capsule (or joint capsule) is an envelope surrounding a synovial joint. [WP,unvetted]. Wikipedia:Articular_capsule check ncita ncit EMAPA:37621 MA:th UMLS:C0206207 ncithesaurus:Joint_Capsule capsula articularis FMA:34836 FMA:TA capsulae articulares Wikipedia:Articular_capsule Any muscle organ that is part of a pelvic girdle [Automatically generated definition]. Note that in MA, this is a subclass of pelvis muscle; in FMA this is a hindlimb muscle, but recall in FMA hindlimb includes the girdle. UBERON:0003271 EHDAA:8326 EMAPA:18184 EMAPA:18185 FMA:37367 MA:0000537 RETIRED_EHDAA2:0001430 girdle-pelvic muscle organ muscle organ of girdle-pelvic muscle organ of pelvic girdle muscle organ of pelvic girdle bone pelvic girdle muscle pelvic girdle muscle organ pelvic girdle skeletal muscle uberon UBERON:0001497 muscle of pelvic girdle https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships Any muscle organ that is part of a pelvic girdle [Automatically generated definition]. OBOL:automatic Note that in MA, this is a subclass of pelvis muscle; in FMA this is a hindlimb muscle, but recall in FMA hindlimb includes the girdle. MA girdle-pelvic muscle organ OBOL:automatic muscle organ of girdle-pelvic OBOL:automatic muscle organ of pelvic girdle OBOL:automatic muscle organ of pelvic girdle bone OBOL:automatic pelvic girdle muscle organ OBOL:automatic pelvic girdle skeletal muscle EMAPA:18185 the convex portion of the aorta between the ascending and descending parts of the aorta; branches from it include the brachiocephalic trunk, the left common carotid artery, and the left subclavian artery; the brachiocephalic trunk further splits to form the right subclavian artery and the right common carotid artery Do not confuse with aortic arch The curving portion between the ascending aorta and the descending aorta, giving rise to the brachiocephalic trunk, the left common carotid artery, and the left subclavian artery. [TFD][VHOG] The double systemic arch arches (left and right) present in amphibians and reptiles become reduced to a single systemic arch - the right in birds, the left in mammals.[well established][VHOG] birds have right aortic arch, mammals left. BTO:0000157 EFO:0002526 EHDAA2:0000132 EMAPA:17613 FMA:3768 GAID:471 MA:0000475 SCTID:181300001 VHOG:0001196 Wikipedia:Arch_of_aorta arcus aortae uberon aortic arch thoracic aorta UBERON:0001508 arch of aorta http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg left arch 4 in human embryology.ch the convex portion of the aorta between the ascending and descending parts of the aorta; branches from it include the brachiocephalic trunk, the left common carotid artery, and the left subclavian artery; the brachiocephalic trunk further splits to form the right subclavian artery and the right common carotid artery ISBN:0-683-40008-8 MP:0004113 The curving portion between the ascending aorta and the descending aorta, giving rise to the brachiocephalic trunk, the left common carotid artery, and the left subclavian artery. [TFD][VHOG] 2012-09-17 VHOG:0001196 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/arch+of+aorta The double systemic arch arches (left and right) present in amphibians and reptiles become reduced to a single systemic arch - the right in birds, the left in mammals.[well established][VHOG] 2012-09-17 VHOG:0001196 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.460 and p.461 Figure 12.20 http://bgee.unil.ch/ arcus aortae FMA:3768 FMA:TA aortic arch FMA:3768 thoracic aorta GAID:471 The descending aorta is the portion of the aorta in a two-pass circulatory system from the arch of aorta to the point where it divides into the common iliac arteries[GO]. The descending aorta is part of the aorta, the largest artery in the body. The descending aorta is the part of the aorta beginning at the aortic arch that runs down through the chest and abdomen. The descending aorta is divided into two portions, the thoracic and abdominal, in correspondence with the two great cavities of the trunk in which it is situated. Within the abdomen, the descending aorta branches into the two common iliac arteries which serve the legs. [WP,unvetted]. results from fusion of left and right dorsal aortae EMAPA:18606 FMA:3784 MA:0002571 NCIT:C32455 OpenCyc:Mx4rv4EE35wpEbGdrcN5Y29ycA SCTID:261399002 UMLS:C0011666 Wikipedia:Descending_aorta pars descendens aortae uberon aorta descendens pars descendens aortae UBERON:0001514 descending aorta http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg FMA Wikipedia The descending aorta is the portion of the aorta in a two-pass circulatory system from the arch of aorta to the point where it divides into the common iliac arteries[GO]. The descending aorta is part of the aorta, the largest artery in the body. The descending aorta is the part of the aorta beginning at the aortic arch that runs down through the chest and abdomen. The descending aorta is divided into two portions, the thoracic and abdominal, in correspondence with the two great cavities of the trunk in which it is situated. Within the abdomen, the descending aorta branches into the two common iliac arteries which serve the legs. [WP,unvetted]. GO:0035906 Wikipedia:Descending_aorta UMLS:C0011666 ncithesaurus:Descending_Aorta pars descendens aortae FMA:3784 aorta descendens Wikipedia:Descending_aorta aorta descendens Wikipedia:Descending_aorta pars descendens aortae Wikipedia:Descending_aorta the part of the aorta that extends from the origin at the heart to the diaphragm, and from which arises numerous branches that supply oxygenated blood to the chest cage and the organs within the chest BTO:0000157 EFO:0002525 EMAPA:18603 FMA:3786 GAID:471 MA:0002569 MESH:D001013 NCIT:C33766 OpenCyc:Mx4rveb9TpwpEbGdrcN5Y29ycA SCTID:302510009 UMLS:C1522460 Wikipedia:Thoracic_aorta galen:ThoracicAorta aorta thoracica thoracic part of aorta uberon aorta thoracalis pars thoracica aortae UBERON:0001515 thoracic aorta http://upload.wikimedia.org/wikipedia/commons/7/75/Gray530.png FMA the part of the aorta that extends from the origin at the heart to the diaphragm, and from which arises numerous branches that supply oxygenated blood to the chest cage and the organs within the chest MP:0010468 http://www.medterms.com UMLS:C1522460 ncithesaurus:Thoracic_Aorta aorta thoracica FMA:3786 FMA:TA aorta thoracalis Wikipedia:Thoracic_aorta pars thoracica aortae Wikipedia:Thoracic_aorta Abdominal part of aorta: the distal part of the descending aorta, which is the continuation of the thoracic part and gives rise to the inferior phrenic, lumbar, median sacral, superior and inferior mesenteric, middle suprarenal, renal, and testicular or ovarian arteries, and celiac trunk[BTO]. The abdominal aorta is the largest artery in the abdominal cavity. As part of the aorta, it is a direct continuation of descending aorta(of the thorax). [WP,unvetted]. Many of the branches of the abdominal aorta in mammals may be branches of the dorsal aorta in other vertebrates BTO:0002976 EFO:0002524 EMAPA:17856 FMA:3789 GAID:470 MA:0000474 MESH:D001012 NCIT:C32038 OpenCyc:Mx4rvYhWCZwpEbGdrcN5Y29ycA SCTID:244231007 UMLS:C0003484 Wikipedia:Abdominal_aorta galen:AbdominalAorta abdominal part of aorta descending abdominal aorta pars abdominalis aortae uberon abdominal part of aorta aorta abdominalis pars abdominalis aortae UBERON:0001516 abdominal aorta http://upload.wikimedia.org/wikipedia/commons/a/af/Gray531.png FMA Abdominal part of aorta: the distal part of the descending aorta, which is the continuation of the thoracic part and gives rise to the inferior phrenic, lumbar, median sacral, superior and inferior mesenteric, middle suprarenal, renal, and testicular or ovarian arteries, and celiac trunk[BTO]. The abdominal aorta is the largest artery in the abdominal cavity. As part of the aorta, it is a direct continuation of descending aorta(of the thorax). [WP,unvetted]. BTO:0002976 Wikipedia:Abdominal_aorta UMLS:C0003484 ncithesaurus:Abdominal_Aorta abdominal part of aorta FMA:3789 descending abdominal aorta FMA:3789 pars abdominalis aortae FMA:3789 abdominal part of aorta BTO:0002976 aorta abdominalis BTO:0002976 aorta abdominalis Wikipedia:Abdominal_aorta pars abdominalis aortae BTO:0002976 pars abdominalis aortae Wikipedia:Abdominal_aorta the short first aortic arch branch and divides into the right subclavian artery and the right common carotid artery innominate EFO:0002550 EHDAA2:0000835 EMAPA:17615 FMA:3932 GAID:476 MA:0001922 MESH:D016122 NCIT:C32814 OpenCyc:Mx4rv9mMTpwpEbGdrcN5Y29ycA SCTID:244244002 UMLS:C0006094 Wikipedia:Brachiocephalic_artery galen:BrachioCephalicArtery brachiocephalic trunk innominate artery truncus brachiocephalicus uberon truncus brachiocephalicus UBERON:0001529 brachiocephalic artery http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg the short first aortic arch branch and divides into the right subclavian artery and the right common carotid artery MGI:csmith MP:0010663 innominate Wikipedia:Brachiocephalic_artery UMLS:C0006094 ncithesaurus:Innominate_Artery brachiocephalic trunk MA:0001922 innominate artery Wikipedia:Brachiocephalic_artery truncus brachiocephalicus FMA:3932 FMA:TA truncus brachiocephalicus Wikipedia:Brachiocephalic_artery A bilaterally paired branched artery that originates from the aortic arches and divides into and includes as parts the internal and external carotid arteries[cjm]. we follow the FMA and treat the artery as a tree-structure - here we include the internal and external as parts. For the part that excludes the branches, see 'trunk of common carotid artery' This class represents the adult and developing structures' in birds and reptiles, develops from arch III and parts of ventral and dorsal aortae carotid artery CALOHA:TS-0116 EHDAA2:0000217 EHDAA:7331 EMAPA:17855 FMA:3939 GAID:479 MA:0001926 MESH:D017536 NCIT:C32352 SCTID:362041005 UMLS:C0162859 VHOG:0000272 Wikipedia:Common_carotid_artery carotid artery system common carotid artery trunk of common carotid tree uberon a. carotis communis UBERON:0001530 common carotid artery plus branches http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg FMA Wikipedia A bilaterally paired branched artery that originates from the aortic arches and divides into and includes as parts the internal and external carotid arteries[cjm]. Wikipedia:Common_carotid_artery carotid artery FMA:3939 UMLS:C0162859 ncithesaurus:Common_Carotid_Artery carotid artery system EHDAA2:0000217 common carotid artery FMA:3939 trunk of common carotid tree FMA:3939 a. carotis communis Wikipedia:Common_carotid_artery The rightmost of the two common carotid arteries, originating from in the neck from the brachiocephalic trunk. placement of the MA class here is not strictly correct, as the MA class does not include the branches EMAPA:35749 FMA:3941 MA:0001928 NCIT:C33473 OpenCyc:Mx4rtW9-AqgEEdudWQACs5b6Bw OpenCyc:Mx8Ngh4rvgHsHZwpEbGdrcN5Y29ycB4rvg7rcJwpEbGdrcN5Y29ycA SCTID:362042003 UMLS:C0226086 Wikipedia:Right_common_carotid_artery right common carotid artery trunk of right common carotid tree uberon right common carotid artery UBERON:0001531 right common carotid artery plus branches http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg FMA The rightmost of the two common carotid arteries, originating from in the neck from the brachiocephalic trunk. UBERON:cjm UMLS:C0226086 ncithesaurus:Right_Common_Carotid_Artery right common carotid artery MA:0001928 trunk of right common carotid tree FMA:3941 right common carotid artery FMA:3941 A terminal branch of the left or right common carotid artery which supplies oxygenated blood to the brain and eyes[MP] Each of two arteries starting at the bifurcation of the common carotid arteries through which blood circulates to many structures and organs in the head. [TFD][VHOG] One of the major arteries of the head, it is the as the cranial continuation of the aortic arches and the dorsal aorta. It curves ventrally before resuming a dorsal course as it enters the head proper, and it lies ventral to the internal jugular vein. The internal carotid artery gives off palatine, ophthalmic, and cerebral branches by stage NF stage 41.[AAO] AAO:0010219 AAO:0011054 BTO:0004697 EFO:0001952 EHDAA2:0000873 EHDAA:408 EHDAA:6389 EMAPA:16328 FMA:3947 GAID:481 MA:0001930 MESH:D002343 NCIT:C32836 OpenCyc:Mx4rvYx8KZwpEbGdrcN5Y29ycA SCTID:362045001 TAO:0005081 UMLS:C0007276 VHOG:0000267 Wikipedia:Internal_carotid_artery XAO:0000366 ZFA:0005081 cranial carotid artery internal carotid uberon ICA arteria carotis interna UBERON:0001532 internal carotid artery http://upload.wikimedia.org/wikipedia/commons/9/9c/Gray513.png MA cjm FMA A terminal branch of the left or right common carotid artery which supplies oxygenated blood to the brain and eyes[MP] MGI:anna Each of two arteries starting at the bifurcation of the common carotid arteries through which blood circulates to many structures and organs in the head. [TFD][VHOG] 2012-09-17 VHOG:0000267 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/Internal+carotid+artery One of the major arteries of the head, it is the as the cranial continuation of the aortic arches and the dorsal aorta. It curves ventrally before resuming a dorsal course as it enters the head proper, and it lies ventral to the internal jugular vein. The internal carotid artery gives off palatine, ophthalmic, and cerebral branches by stage NF stage 41.[AAO] 2012-06-20 AAO:0011054 AAO PMID:12606281 UMLS:C0007276 ncithesaurus:Internal_Carotid_Artery cranial carotid artery ZFA:0005081 internal carotid AAO:0010219 ICA arteria carotis interna Wikipedia:Internal_carotid_artery The leftmost of the two common carotid arteries, originating from the aortic arch in the thorax. placement of the MA class here is not strictly correct, as the MA class does not include the branches EMAPA:35491 FMA:4058 MA:0001927 NCIT:C32956 OpenCyc:Mx4rdz4xcLVIEduAAAAOpmP6tw OpenCyc:Mx8Ngh4rvgIFoJwpEbGdrcN5Y29ycB4rvg7rcJwpEbGdrcN5Y29ycA SCTID:362043008 UMLS:C0226087 Wikipedia:Left_common_carotid_artery left common carotid artery trunk of left common carotid tree uberon left common carotid artery UBERON:0001536 left common carotid artery plus branches http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg FMA The leftmost of the two common carotid arteries, originating from the aortic arch in the thorax. UBERON:cjm UMLS:C0226087 ncithesaurus:Left_Common_Carotid_Artery left common carotid artery MA:0001927 trunk of left common carotid tree FMA:4058 left common carotid artery FMA:4058 A tube extending from the mouth to the anus. The alimentary or digestive tract, and associated organs.[TAO] The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] FMA also has a term 'gastrointestinal tract', but this includes the liver. we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509 we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this gut AAO:0010023 BILA:0000083 BTO:0000511 BTO:0000545 EHDAA2:0000726 EHDAA:518 EMAPA:16247 FBbt:00003125 FMA:45615 MA:0000917 NCIT:C34082 OpenCyc:Mx4rvVi0GpwpEbGdrcN5Y29ycA TAO:0000112 TGMA:0001819 UMLS:C0017189 VHOG:0000309 WBbt:0005743 ZFA:0000112 galen:AlimentaryTract digestive tube enteric tract alimentary canal alimentary tract uberon digestive canal gut tube UBERON:0001555 digestive tract NCBIBook:NBK10107 A tube extending from the mouth to the anus. Wikipedia:Talk:Human_gastrointestinal_tract https://github.com/geneontology/go-ontology/issues/7549 Wikipedia:Acoelomorpha DOI:10.1371/journal.pone.0016309 The alimentary or digestive tract, and associated organs.[TAO] 2012-08-14 TAO:0000112 TAO ZFIN:curator The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000309 VHOG ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 http://bgee.unil.ch/ FMA also has a term 'gastrointestinal tract', but this includes the liver. FMA we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509 MA UMLS:C0017189 ncithesaurus:Gastrointestinal_Tract enteric tract ZFA:0000112 digestive canal BTO:0000058 The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified] EHDAA2:0001036 EMAPA:16738 FMA:45662 MA:0000435 OpenCyc:Mx4rQRqjUgAKEdyHxgDggVfs8g SCTID:281488008 VHOG:0000382 Wikipedia:Lower_respiratory_tract lower respiratory system uberon UBERON:0001558 lower respiratory tract http://upload.wikimedia.org/wikipedia/commons/9/9f/Illu_conducting_passages.svg http://upload.wikimedia.org/wikipedia/commons/c/c3/Illu_conducting_passages.jpg The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified] Wikipedia:Lower_respiratory_tract http://orcid.org/0000-0002-6601-2165 The muscles associated with the larynx. BTO:0001626 EMAPA:35473 FMA:46562 GAID:144 MA:0001768 MESH:D007821 NCIT:C32934 SCTID:181744001 UMLS:C0023054 Wikipedia:Muscles_of_larynx laryngeal muscle larynx muscle larynx muscle organ muscle organ of larynx musculi laryngeales uberon UBERON:0001568 muscle of larynx prolog The muscles associated with the larynx. MP:0002263 UMLS:C0023054 ncithesaurus:Laryngeal_Muscle larynx muscle organ OBOL:automatic muscle organ of larynx OBOL:automatic One of two jugular veins that collect the blood from the brain, the superficial parts of the face, and the neck. [WP,unvetted]. Vein which receives many veins draining the palate, brain, and the orbital, nasal, and auditory regions.[AAO] AAO:0010236 EHDAA2:0000877 EHDAA:5407 EMAPA:17620 FMA:4724 MA:0002157 NCIT:C32849 OpenCyc:Mx4rvqdb95wpEbGdrcN5Y29ycA RETIRED_EHDAA2:0000878 SCTID:181372005 UMLS:C0226550 Wikipedia:Internal_jugular_vein XAO:0000382 galen:InternalJugularVein internal jugular internal jugular venous tree uberon vena jugularis interna UBERON:0001586 internal jugular vein http://upload.wikimedia.org/wikipedia/commons/e/e9/Gray562.png One of two jugular veins that collect the blood from the brain, the superficial parts of the face, and the neck. [WP,unvetted]. Wikipedia:Internal_jugular_vein Vein which receives many veins draining the palate, brain, and the orbital, nasal, and auditory regions.[AAO] 2012-06-20 AAO:0010236 AAO AAO:BJB UMLS:C0226550 ncithesaurus:Internal_Jugular_Vein internal jugular EHDAA2:0000877 vena jugularis interna Wikipedia:Internal_jugular_vein The ciliary muscle is a ring of smooth muscle in the middle layer of the eye that controls the eye's accommodation for viewing objects at varying distances and regulates the flow of aqueous humour through Schlemm's canal. [WP,unvetted]. BTO:0000654 EMAPA:35240 FMA:49151 MA:0001269 NCIT:C32315 SCTID:280862009 UMLS:C0559230 Wikipedia:Ciliary_muscle musculus ciliarus uberon Bowman`s muscles ciliaris musculus ciliaris UBERON:0001605 ciliary muscle http://upload.wikimedia.org/wikipedia/commons/2/28/Gray872.png MA FMA FMA The ciliary muscle is a ring of smooth muscle in the middle layer of the eye that controls the eye's accommodation for viewing objects at varying distances and regulates the flow of aqueous humour through Schlemm's canal. [WP,unvetted]. Wikipedia:Ciliary_muscle UMLS:C0559230 ncithesaurus:Ciliary_Muscle musculus ciliarus BTO:0000654 Bowman`s muscles BTO:0000654 ciliaris Wikipedia:Ciliary_muscle musculus ciliaris Wikipedia:Ciliary_muscle . revisit this, see issue #331 The muscle cells of the iris are smooth muscle in mammals and amphibians, but are striated muscle in birds and reptiles. Many fish have neither, and, as a result, their irides are unable to dilate and contract, so that the pupil always remains of a fixed size[Romer, via WP] in aves, stromal mesenchymal cells may migrate to the iris and become skeletal EMAPA:35448 FMA:49154 MA:0001287 SCTID:280888007 Wikipedia:Iris_muscle iris muscle iris muscle organ muscle organ of iris uberon UBERON:0001606 muscle of iris FMA . Wikipedia:Iris_muscle iris muscle organ OBOL:automatic muscle organ of iris OBOL:automatic A branch of the external carotid artery that supplies structures of the face. [WP,unvetted]. EMAPA:19213 FMA:49549 MA:0001950 NCIT:C32578 OpenCyc:Mx4rwCt95ZwpEbGdrcN5Y29ycA SCTID:181328007 UMLS:C0226109 Wikipedia:Facial_artery uberon arteria maxillaris externa external maxillary artery UBERON:0001612 facial artery http://upload.wikimedia.org/wikipedia/commons/7/7b/Gray508.png A branch of the external carotid artery that supplies structures of the face. [WP,unvetted]. Wikipedia:Facial_artery UMLS:C0226109 ncithesaurus:Facial_Artery arteria maxillaris externa Wikipedia:Facial_artery An artery that supplies deep structures of the face. It comes just out behind the neck of the mandible. [WP,unvetted]. ...1st pair undergoes partial regression, the remnants of which becomes part of the maxillary arteries EHDAA2:0001069 EHDAA:7357 EMAPA:17311 FMA:49675 GAID:498 MA:0001919 MESH:D008438 NCIT:C34205 OpenCyc:Mx4rwDDJ45wpEbGdrcN5Y29ycA SCTID:181326006 UMLS:C0024949 Wikipedia:Maxillary_artery uberon arteria maxillaris internal maxillary artery UBERON:0001616 maxillary artery http://upload.wikimedia.org/wikipedia/commons/3/39/Gray510.png An artery that supplies deep structures of the face. It comes just out behind the neck of the mandible. [WP,unvetted]. Wikipedia:Maxillary_artery ...1st pair undergoes partial regression, the remnants of which becomes part of the maxillary arteries http://download.videohelp.com/vitualis/med/Vascular_Devt.html UMLS:C0024949 ncithesaurus:Maxillary_Artery arteria maxillaris Wikipedia:Maxillary_artery One of a pair of right-sided and left-sided blood vessels in the circle of Willis. It connects the three cerebral arteries of the same side. Anteriorly, it is one portion of the terminal trifurcation of the internal carotid artery. The anterior cerebral artery and the middle cerebral artery are the other two branches of the trifurcation. Posteriorly, it communicates with the posterior cerebral artery. An artery that connects caudal division of the internal carotid artery and the basal communicating artery to the basilar artery. Isogai et al. 2001.[TAO] todo - verify ZFA link: An artery that connects caudal division of the internal carotid artery and the basal communicating artery to the basilar artery EHDAA2:0004518 EHDAA:3352 EMAPA:18600 FMA:50084 MA:0002023 NCIT:C33357 OpenCyc:Mx4rwDDlqpwpEbGdrcN5Y29ycA RETIRED_EHDAA2:0001487 SCTID:181314001 TAO:0005001 UMLS:C0149559 Wikipedia:Posterior_communicating_artery ZFA:0005001 caudal communicating segment posterior communicating segment of the basilar artery uberon PCA PCS arteria cerebri communicans posterior UBERON:0001628 posterior communicating artery http://upload.wikimedia.org/wikipedia/commons/2/2e/Circle_of_Willis_en.svg FMA-abduced-lr FMA ZFA One of a pair of right-sided and left-sided blood vessels in the circle of Willis. It connects the three cerebral arteries of the same side. Anteriorly, it is one portion of the terminal trifurcation of the internal carotid artery. The anterior cerebral artery and the middle cerebral artery are the other two branches of the trifurcation. Posteriorly, it communicates with the posterior cerebral artery. Wikipedia:Posterior_communicating_artery An artery that connects caudal division of the internal carotid artery and the basal communicating artery to the basilar artery. Isogai et al. 2001.[TAO] 2012-08-14 TAO:0005001 TAO ZFIN:curator UMLS:C0149559 ncithesaurus:Posterior_Communicating_Artery caudal communicating segment ZFA:0005001 posterior communicating segment of the basilar artery ZFA:0005001 arteria cerebri communicans posterior Wikipedia:Posterior_communicating_artery Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO]. Portion of tissue composed of contractile fibers.[TAO] It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG] muscular muscle AAO:0011066 EMAPA:32715 EMAPA:37474 EV:0100146 FMA:5022 GAID:131 MA:0000015 OpenCyc:Mx4rv2kf-5wpEbGdrcN5Y29ycA SCTID:71616004 TAO:0005145 VHOG:0001245 XAO:0000172 ZFA:0005145 galen:Muscle uberon UBERON:0001630 muscle organ Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO]. GO:0007517 Portion of tissue composed of contractile fibers.[TAO] 2012-08-14 TAO:0005145 TAO ZFIN:curator It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG] 2012-09-17 VHOG:0001245 VHOG ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.75 http://bgee.unil.ch/ muscle ZFA:0005145 EMAPA:37474 MA:th An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition]. Note that in FMA an artery is a tree, whereas AEO/JB defines it as a tube; FMA includes a separate class for what it calls the trunk. Classification in this ontology may currently (Jan 2012) represent a mix of both schemes, although we are gradually revising in the direction of the AEO scheme. Part of the circulatory system composed of blood vessels which carry oxygenated blood away from the heart to the rest of the body.[AAO] The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] arterial AAO:0010211 AEO:0000208 BTO:0000573 CALOHA:TS-0054 EFO:0000814 EHDAA2:0000143 EHDAA2:0003253 EMAPA:35147 EV:0100026 FMA:50720 GAID:468 MA:0000064 MAT:0000034 MESH:D001158 MIAA:0000034 NCIT:C12372 OpenCyc:Mx4rvVjknZwpEbGdrcN5Y29ycA SCTID:362877004 TAO:0000005 UMLS:C0003842 VHOG:0001251 Wikipedia:Artery XAO:0000114 ZFA:0000005 galen:Artery arterial subtree arterial tree organ part arteries uberon arterial system arterial vessel UBERON:0001637 artery An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition]. AEO:JB Part of the circulatory system composed of blood vessels which carry oxygenated blood away from the heart to the rest of the body.[AAO] 2012-06-20 AAO:0010211 AAO AAO:BJB The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] 2012-09-17 VHOG:0001251 VHOG DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006) http://bgee.unil.ch/ UMLS:C0003842 ncithesaurus:Artery arteries TAO:0000005 Any of the tubular branching vessels that carry blood from the capillaries toward the heart. TODO - check with MA - vein vs venous blood vessel Part of the circulatory system composed of blood vessels which carry blood from other organs, tissues, and cells to the heart.[AAO] The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] venous venous subtree venous vessel AAO:0010212 AEO:0000209 BTO:0000234 CALOHA:TS-1108 EFO:0000816 EHDAA2:0003254 EMAPA:35906 EV:0100031 FMA:50723 GAID:492 MA:0000067 MAT:0000037 MESH:D014680 MIAA:0000037 NCIT:C12814 OpenCyc:Mx4rvVjkWpwpEbGdrcN5Y29ycA SCTID:181367001 TAO:0000082 UMLS:C0042449 VHOG:0001743 Wikipedia:Vein XAO:0000115 ZFA:0000082 galen:Vein venous tree organ part uberon vascular element vena venae UBERON:0001638 vein http://upload.wikimedia.org/wikipedia/commons/c/c2/Venous_system_en.svg Any of the tubular branching vessels that carry blood from the capillaries toward the heart. Wikipedia:Vein Part of the circulatory system composed of blood vessels which carry blood from other organs, tissues, and cells to the heart.[AAO] 2012-06-20 AAO:0010212 AAO AAO:BJB The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] 2012-09-17 VHOG:0001743 VHOG DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006) http://bgee.unil.ch/ UMLS:C0042449 ncithesaurus:Vein vascular element EMAPA:th vena Wikipedia:Vein venae VHOG:0001743 Cranial nerve that has three branches - the ophthalmic (supplying the skin of the nose and upper jaw), the maxillary and the mandibular (supplying the lower jaw). Nerve consists of motor and sensory components. Ganglion cells of the sensory component form the proximal part of the trigeminal (Gasserian) ganglion. From the ganglion 3 major rami innervate jaws, snout, and buccal roof.[AAO] We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG] the ophthalmic usually usually merges with the other two. In some vertebrates, the ophthalmic emerges from the brain separately[Kardong] The trigeminal nerve has 3 branches in mammals - similar branches are present in nonmammalian vertebrates, but in some a separate profundus nerve that corresponds to opthalmic branch in mammls 5n AAO:0010470 BAMS:5n BAMS:Vn BAMS:nV BIRNLEX:869 BM:VN BTO:0001072 EFO:0001402 EHDAA2:0002084 EHDAA:3738 EMAPA:17576 FMA:50866 GAID:726 HBA:9322 MA:0001100 MBA:901 MESH:D014276 MFMO:0000093 NCIT:C12806 OpenCyc:Mx4rwMF8CJwpEbGdrcN5Y29ycA SCTID:362459002 TAO:0000697 UMLS:C0040996 VHOG:0000704 Wikipedia:Trigeminal_nerve XAO:0003092 ZFA:0000697 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=549 fifth cranial nerve nervus trigeminus nervus trigeminus [v] trigeminal V trigeminal nerve [V] trigeminal nerve tree trigeminal v nerve uberon CN-V cranial nerve V nerve V nervus trigeminus trigeminus UBERON:0001645 trigeminal nerve Gray778:Trigeminal.png Wikipedia Cranial nerve that has three branches - the ophthalmic (supplying the skin of the nose and upper jaw), the maxillary and the mandibular (supplying the lower jaw). ISBN:0471209627 Wikipedia:Trigeminal_nerve Nerve consists of motor and sensory components. Ganglion cells of the sensory component form the proximal part of the trigeminal (Gasserian) ganglion. From the ganglion 3 major rami innervate jaws, snout, and buccal roof.[AAO] 2012-06-20 AAO:0010470 AAO AAO:EJS We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000704 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625 http://bgee.unil.ch/ the ophthalmic usually usually merges with the other two. In some vertebrates, the ophthalmic emerges from the brain separately[Kardong] The trigeminal nerve has 3 branches in mammals - similar branches are present in nonmammalian vertebrates, but in some a separate profundus nerve that corresponds to opthalmic branch in mammls ISBN:0471888893 5n BIRNLEX:869 NIFSTD:NeuroNames_abbrevSource UMLS:C0040996 BIRNLEX:869 UMLS:C0040996 ncithesaurus:Trigeminal_Nerve http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=549 BIRNLEX:869 nervus trigeminus Wikipedia:Trigeminal_nerve nervus trigeminus [v] FMA:50866 FMA:TA trigeminal V EHDAA2:0002084 nerve V NeuroNames:549 nervus trigeminus BTO:0001072 trigeminus BTO:0001072 Cranial nerve that branches into the ramus communicans (to the skin), the pretrematic (to the walls of the pharynx and mouth, viscero-sensory fibers), and the larval post-trematic branch (lost in the adult). Small nerve consisting of branchiomotor and visceral efferent and afferent fibers which innervate the m. subarculais rectus I, dorsal buccal mucosa, and the tongue.[AAO] We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG] 9n AAO:0010474 BAMS:9n BAMS:IXn BIRNLEX:899 BTO:0004979 EHDAA2:0000709 EHDAA:3733 EMAPA:17268 FMA:50870 GAID:827 HBA:9334 MA:0001093 MBA:808 MESH:D005930 NCIT:C12723 OpenCyc:Mx4rwIr5X5wpEbGdrcN5Y29ycA SCTID:362465002 TAO:0000668 UMLS:C0017679 UMLS:C1305752 VHOG:0000701 Wikipedia:Glossopharyngeal_nerve XAO:0003096 ZFA:0000668 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=701 glossopharyngeal IX glossopharyngeal IX nerve glossopharyngeal nerve [IX] glossopharyngeal nerve tree nervus glossopharyngeus nervus glossopharyngeus [ix] ninth cranial nerve uberon CN-IX cranial nerve IX nerve IX nervus glossopharyngeus UBERON:0001649 glossopharyngeal nerve http://upload.wikimedia.org/wikipedia/commons/5/5e/Gray791.png motor Wikipedia Cranial nerve that branches into the ramus communicans (to the skin), the pretrematic (to the walls of the pharynx and mouth, viscero-sensory fibers), and the larval post-trematic branch (lost in the adult). ISBN:0471209627 Wikipedia:Glossopharyngeal_nerve Small nerve consisting of branchiomotor and visceral efferent and afferent fibers which innervate the m. subarculais rectus I, dorsal buccal mucosa, and the tongue.[AAO] 2012-06-20 AAO:0010474 AAO AAO:EJS We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000701 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625 http://bgee.unil.ch/ 9n BIRNLEX:899 NIFSTD:NeuroNames_abbrevSource UMLS:C0017679 BIRNLEX:899 UMLS:C0017679 ncithesaurus:Glossopharyngeal_Nerve UMLS:C1305752 BIRNLEX:899 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=701 BIRNLEX:899 glossopharyngeal IX EHDAA2:0000709 nervus glossopharyngeus ZFA:0000668 nervus glossopharyngeus [ix] FMA:50870 FMA:TA CN-IX nerve IX NeuroNames:701 nervus glossopharyngeus Wikipedia:Glossopharyngeal_nerve The pulmonary artery that supplies the right lung. TODO - add class 'pulmonary artery tree organ' EMAPA:37378 FMA:50872 MA:0002500 NCIT:C33489 SCTID:244235003 UMLS:C0923924 Wikipedia:Right_pulmonary_artery galen:RightPulmonaryArtery right main pulmonary artery right pulmonary arterial tree uberon arteria pulmonalis dextra UBERON:0001651 right pulmonary artery Alveoli:diagram.png http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray504.png The pulmonary artery that supplies the right lung. UBERON:cjm EMAPA:37378 MA:th UMLS:C0923924 ncithesaurus:Right_Pulmonary_Artery arteria pulmonalis dextra Wikipedia:Right_pulmonary_artery The pulmonary artery that supplies the left lung. TODO - add class 'pulmonary artery tree organ' EMAPA:37097 FMA:50873 MA:0002032 NCIT:C32971 SCTID:244234004 UMLS:C0923925 Wikipedia:Left_pulmonary_artery galen:LeftPulmonaryArtery left main pulmonary artery left pulmonary arterial tree uberon arteria pulmonalis sinistra UBERON:0001652 left pulmonary artery Alveoli:diagram.png http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray504.png The pulmonary artery that supplies the left lung. UBERON:cjm EMAPA:37097 MA:th UMLS:C0923925 ncithesaurus:Left_Pulmonary_Artery arteria pulmonalis sinistra Wikipedia:Left_pulmonary_artery The anterior facial vein (facial vein) commences at the side of the root of the nose, and is a direct continuation of the angular vein where it also receives a small nasal branch. It lies behind the facial artery and follows a less tortuous course. It receives blood from the external palatine vein before it either joins the anterior branch of the retromandibular vein to form the common facial vein, or drains directly into the internal jugular vein. [WP,unvetted]. Vein which collects blood from muscles of the head and drains into the external jugular vein.[AAO] MA and NCITA also has 'anterior facial vein' AAO:0010513 EMAPA:19220 FMA:50874 MA:0002115 NCIT:C32579 OpenCyc:Mx4rvziz3JwpEbGdrcN5Y29ycA SCTID:181374006 UMLS:C0226532 Wikipedia:Facial_vein face vein vein of face uberon anterior facial vein vena facialis anterior UBERON:0001653 facial vein http://upload.wikimedia.org/wikipedia/commons/8/8c/Gray557.png FMA The anterior facial vein (facial vein) commences at the side of the root of the nose, and is a direct continuation of the angular vein where it also receives a small nasal branch. It lies behind the facial artery and follows a less tortuous course. It receives blood from the external palatine vein before it either joins the anterior branch of the retromandibular vein to form the common facial vein, or drains directly into the internal jugular vein. [WP,unvetted]. Wikipedia:Facial_vein Vein which collects blood from muscles of the head and drains into the external jugular vein.[AAO] 2012-06-20 AAO:0010513 AAO AAO:BJB MA and NCITA also has 'anterior facial vein' MA UMLS:C0226532 ncithesaurus:Facial_Vein face vein OBOL:automatic vein of face OBOL:automatic anterior facial vein Wikipedia:Facial_vein vena facialis anterior Wikipedia:Facial_vein The cerebral veins are divisible into external and internal groups according to the outer surfaces or the inner parts of the hemispheres they drain into. The external veins are the superior cerebral veins, inferior cerebral veins, and middle cerebral vein. [WP,unvetted]. EMAPA:37140 FMA:50981 GAID:530 MA:0002096 MESH:D002550 NCIT:C53037 SCTID:244392000 UMLS:C0007797 Wikipedia:Cerebral_veins XAO:0004160 uberon venae cerebri venae encephali UBERON:0001663 cerebral vein http://upload.wikimedia.org/wikipedia/commons/9/9f/Gray568.png The cerebral veins are divisible into external and internal groups according to the outer surfaces or the inner parts of the hemispheres they drain into. The external veins are the superior cerebral veins, inferior cerebral veins, and middle cerebral vein. [WP,unvetted]. Wikipedia:Cerebral_veins EMAPA:37140 MA:th UMLS:C0007797 ncithesaurus:Cerebral_Vein venae cerebri Wikipedia:Cerebral_veins venae encephali Wikipedia:Cerebral_veins The cranial ganglion that is associated with and extends fibers into the trigeminal nerve. consider renaming this 'trigeminal ganglion complex'. The complex may be fused (amniotes) partially fused (xenopus) or separate (sharks) A prominent collection of touch-sensory neurons of the trigeminal or fifth cranial nerve, positioned beside the brain between the eye and the ear. Kimmel et al, 1995.[TAO] In Xenopus, the profundal and the trigeminal ganglia are separate distally but fused at their proximal end as they condense around NF stage 24. AAO:0011107 BAMS:5Gn BAMS:GV BTO:0001231 EFO:0000903 EHDAA2:0002085 EHDAA:2113 EMAPA:16797 FMA:52618 GAID:725 MA:0001080 MAT:0000511 MESH:D012668 NCIT:C62642 SCTID:244449009 TAO:0000295 UMLS:C0040995 VHOG:0000694 Wikipedia:Trigeminal_ganglion XAO:0000427 XAO:0000428 ZFA:0000295 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1402 5th ganglion Gasserian ganglion fifth ganglion ganglion of trigeminal complex semilunar ganglion trigeminal V ganglion fused trigeminal ganglion uberon Gasser's ganglion Gasserian ganglia gV ganglion of trigeminal nerve ganglion semilunare ganglion trigeminale trigeminal ganglia trigeminus ganglion UBERON:0001675 trigeminal ganglion http://upload.wikimedia.org/wikipedia/commons/6/69/Gray776.png ncithesaurus Bgee:AN The cranial ganglion that is associated with and extends fibers into the trigeminal nerve. http://orcid.org/0000-0002-6601-2165 http://www.ncbi.nlm.nih.gov/books/NBK53171 https://github.com/obophenotype/uberon/issues/693 A prominent collection of touch-sensory neurons of the trigeminal or fifth cranial nerve, positioned beside the brain between the eye and the ear. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000295 TAO ZFIN:curator In Xenopus, the profundal and the trigeminal ganglia are separate distally but fused at their proximal end as they condense around NF stage 24. PMID:21452441 XAO:0004093 UMLS:C0040995 ncithesaurus:Trigeminal_Ganglion 5th ganglion ZFA:0000295 Gasserian ganglion Wikipedia:Trigeminal_ganglion fifth ganglion ZFA:0000295 ganglion of trigeminal complex http://orcid.org/0000-0002-6601-2165 semilunar ganglion ISBN:0471888893 trigeminal V ganglion MA:0001080 fused trigeminal ganglion NCBITaxon:32524 Gasser's ganglion BTO:0001231 Gasserian ganglia Wikipedia:Trigeminal_ganglion ganglion of trigeminal nerve BTO:0001231 ganglion semilunare Wikipedia:Trigeminal_ganglion ganglion trigeminale BTO:0001231 ganglion trigeminale Wikipedia:Trigeminal_ganglion trigeminal ganglia the bone at the lower, posterior part of the skull formed from the sclerotome of the occipital somites. It is not present in living or fossil agnathans or cartilaginous fishes, but appears to have arisen in parallel in many bony fishes. Incorporation of the occipital ver- tebrae into the skull was associated with the annexation of the upper part of the spinal cord into the brain, together with the first 2 spinal nerves as cranial nerves XI and XII fusion of basi-, exo- and supra-occipitals (and maybe tabular) EMAPA:25112 FMA:52735 GAID:227 MA:0001468 MESH:D009777 NCIT:C12757 OpenCyc:Mx4rwQtsiZwpEbGdrcN5Y29ycA SCTID:181796003 UMLS:C0028784 Wikipedia:Occipital_bone uberon occipital complex occipital squama os occipitale UBERON:0001676 occipital bone http://upload.wikimedia.org/wikipedia/commons/2/27/Gray194.png FMA FMA basi paired exo and supra occipital bones MA-modified interparietal (postparietal) WP PMID:11523816 the bone at the lower, posterior part of the skull ISBN:0-683-40008-8 MP:0005269 formed from the sclerotome of the occipital somites. It is not present in living or fossil agnathans or cartilaginous fishes, but appears to have arisen in parallel in many bony fishes. Incorporation of the occipital ver- tebrae into the skull was associated with the annexation of the upper part of the spinal cord into the brain, together with the first 2 spinal nerves as cranial nerves XI and XII PMID:11523816 fusion of basi-, exo- and supra-occipitals (and maybe tabular) Kardong UMLS:C0028784 ncithesaurus:Occipital_Bone occipital complex http://palaeos.com/vertebrates/bones/braincase/occiput.html os occipitale Wikipedia:Occipital_bone the large, irregular bone located at the base and side of the skull; consists of three parts at birth: squamous, tympanic, and petrous In many mammals, as in humans, the petrosal, ectotympanic and squamosal bones synostose to form the temporal bone + styloid process fusion of squamosal + angular (tympanic annulus) [derm.] + petrosal (prootic + opisthotic) The temporal bone consists of four parts: * Squama temporalis * Mastoid portion * Petrous portion (Petrosal ridge) * Tympanic part[WP]. Note the Temporal bone is not explicitly categorized to a part of the cranium in FMA EHDAA:6035 EMAPA:17682 FMA:52737 GAID:232 MA:0001476 MESH:D013701 NCIT:C12797 OpenCyc:Mx4rvbkAk5wpEbGdrcN5Y29ycA SCTID:181795004 UMLS:C0039484 VHOG:0000800 Wikipedia:Temporal_bone uberon os temporale UBERON:0001678 temporal bone http://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cranial_bones2.jpg FMA petrosal squamosal plus angular temporal series styloid process the large, irregular bone located at the base and side of the skull; consists of three parts at birth: squamous, tympanic, and petrous ISBN:0-683-40008-8 MP:0005272 fusion of squamosal + angular (tympanic annulus) [derm.] + petrosal (prootic + opisthotic) chond. The temporal bone consists of four parts: * Squama temporalis * Mastoid portion * Petrous portion (Petrosal ridge) * Tympanic part[WP]. [WP] Note the Temporal bone is not explicitly categorized to a part of the cranium in FMA FMA UMLS:C0039484 ncithesaurus:Temporal_Bone os temporale Wikipedia:Temporal_bone The group of neuron cell bodies associated with the ninth cranial nerve. These (the epibranchial placodes) are focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches in all vertebrates, and they produce the neuroblasts which migrate and condense to form the distal cranial ganglia: the geniculate, petrosal and nodose ganglia. (...) The one substantial difference between the vertebrate pharyngeal arches and those of the protochordates is the presence of the epibranchial placodes but the evolution of these structures was undoubtedly driven by the endoderm.[well established][VHOG] EHDAA2:0000710 EHDAA:2838 EMAPA:16795 FMA:53471 MA:0001077 SCTID:244451008 TAO:0001301 VHOG:0000702 ZFA:0001301 ganglion of glossopharyngeal nerve ganglion of glosspharyngeal nerve glossopharyngeal IX ganglion petrosal ganglion uberon gIX UBERON:0001701 glossopharyngeal ganglion ZFA dorsal EHDAA2 ISBN:0471888893 ZFA ventrolateral EHDAA2 ISBN:0471888893 ZFA The group of neuron cell bodies associated with the ninth cranial nerve. MP:0001096 These (the epibranchial placodes) are focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches in all vertebrates, and they produce the neuroblasts which migrate and condense to form the distal cranial ganglia: the geniculate, petrosal and nodose ganglia. (...) The one substantial difference between the vertebrate pharyngeal arches and those of the protochordates is the presence of the epibranchial placodes but the evolution of these structures was undoubtedly driven by the endoderm.[well established][VHOG] 2012-09-17 VHOG:0000702 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) http://bgee.unil.ch/ ganglion of glosspharyngeal nerve FMA:53471 glossopharyngeal IX ganglion MA:0001077 petrosal ganglion ZFA:0001301 Subdivision of skeletal system that surrounds and protects the brain. Includes the skull base, sensory capsules and the central part of the skull roof. Anatomical cluster that consists of the cartilages and bones that surround the brain.[TAO] neurocranial It includes the following bones: Ethmoid bone, Frontal bone, Occipital bone, Parietal bone, Sphenoid bone, Temporal bone. The term cranium can be ambiguous, in that it can refer to the neurocranium, or the neurocranium and the Facial skeleton The cartilaginous parts of the neurocranium undergo endochondral ossification in most species; ossification has been lost in cartilaginous fishes, but the cartilaginous condition of the skull of lampreys is considered to be primitive (Kardong, 1995)[PMID:11523816]. The neurocranium arises from paraxial mesoderm in the head (first five somites and the unsegmented somitomeres rostral to the first somite) and from ectoderm via the neural crest. In Chondrichthyes and other cartilaginous vertebrates this portion of the cranium does not ossify; it is not replaced via endochondral ossification[WP]. It seems MA uses 'neurocranium' as a synonym for chondrocranium. Note there are currently some structures part of both viscero and neurocranium - ethmoid, zyogomatic, ... AAO:0010153 EHDAA2:0000243 EMAPA:17681 FMA:53672 MA:0000317 SCTID:361731002 TAO:0001580 Wikipedia:Neuroranium XAO:0003170 ZFA:0001580 brain box uberon brain case brain pan braincase UBERON:0001703 neurocranium FMA Subdivision of skeletal system that surrounds and protects the brain. Includes the skull base, sensory capsules and the central part of the skull roof. PMID:11523816 TAO:MAH Wikipedia:Neuroranium ZFA:0001580 Anatomical cluster that consists of the cartilages and bones that surround the brain.[TAO] 2012-08-14 TAO:0001580 TAO TAO:MAH The cartilaginous parts of the neurocranium undergo endochondral ossification in most species; ossification has been lost in cartilaginous fishes, but the cartilaginous condition of the skull of lampreys is considered to be primitive (Kardong, 1995)[PMID:11523816]. The neurocranium arises from paraxial mesoderm in the head (first five somites and the unsegmented somitomeres rostral to the first somite) and from ectoderm via the neural crest. In Chondrichthyes and other cartilaginous vertebrates this portion of the cranium does not ossify; it is not replaced via endochondral ossification[WP]. WP It seems MA uses 'neurocranium' as a synonym for chondrocranium. Note there are currently some structures part of both viscero and neurocranium - ethmoid, zyogomatic, ... MA brain case ZFA:0001580 brain pan http://www.thefreedictionary.com/braincase braincase ZFA:0001580 Subdivision of skeleton which includes upper and lower jaw skeletons. TODO - move ZFA:0001227 (it is the entire jaw skeleton). Skeletal and cartilage elements of the first pharyngeal arch.[TAO] There are cellular contributions from all three embryonic germ layers: pharyngeal mesoderm, endoderm and neural crest that migrates out of the ectoderm (Noden, 1983). in FMA, the jaw is an organism subdivision cluster, and includes mucosal tissue such as the gingiva as parts. It appears to be skeletal in MA (and has teeth as parts). It is reasonable to assume that ZFA and XAO consider the upper and lower jaws to be skeletal elements or clusters. EHDAA2 also considers these clusters. TODO - follow EHDAA2 model. These arbitrary differences in terminology and classification have to be reconciled with the genuine well-known biological differences in the skeletal elements across vertebrates AAO:0000988 BTO:0001749 EMAPA:35455 FMA:54396 GAID:214 MA:0001905 MESH:D007568 NCIT:C48821 OpenCyc:Mx4rvVjjEZwpEbGdrcN5Y29ycA SCTID:181811001 TAO:0001227 UMLS:C0022359 Wikipedia:Jaw ZFA:0001227 galen:Jaw jaw jaw cartilage mandibular arch skeleton uberon anterior splanchnocranium jaws mandibular arch oral jaw skeleton pharyngeal arch 1 skeleton visceral arch 1 UBERON:0001708 jaw skeleton cjm Subdivision of skeleton which includes upper and lower jaw skeletons. Wikipedia:Jaw https://orcid.org/0000-0002-6601-2165 Skeletal and cartilage elements of the first pharyngeal arch.[TAO] 2012-08-14 TAO:0001227 TAO ZFIN:curator in FMA, the jaw is an organism subdivision cluster, and includes mucosal tissue such as the gingiva as parts. It appears to be skeletal in MA (and has teeth as parts). It is reasonable to assume that ZFA and XAO consider the upper and lower jaws to be skeletal elements or clusters. EHDAA2 also considers these clusters. TODO - follow EHDAA2 model. These arbitrary differences in terminology and classification have to be reconciled with the genuine well-known biological differences in the skeletal elements across vertebrates FMA UMLS:C0022359 ncithesaurus:Jaw jaw MA:0001905 jaw cartilage ZFA:0001227 mandibular arch skeleton ZFA:0001227 mandibular arch TAO:0001227 Subdivision of head that consists of the lower jaw skeletal elements plus associated soft tissue (skin, lips, muscle)[cjm]. Inferior mandibular arch located on the anterior and lateral sides of the skull.[AAO] Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG] Note isa/partof difference MA/FMA AAO:0000272 EFO:0003660 EHDAA2:0001018 EHDAA:7995 EMAPA:17906 FMA:59398 MESH:D008334 SCTID:362637005 VHOG:0000453 Wikipedia:Lower_jaw ncithesaurus:Lower_Jaw mandibular part of mouth uberon lower part of mouth mandibular series UBERON:0001710 See notes for jaw w.r.t skeletal element vs subdivision of head lower jaw region http://upload.wikimedia.org/wikipedia/commons/6/64/Gray176.png Wikipedia:Mandibular_prominence Subdivision of head that consists of the lower jaw skeletal elements plus associated soft tissue (skin, lips, muscle)[cjm]. Wikipedia:Lower_jaw Inferior mandibular arch located on the anterior and lateral sides of the skull.[AAO] 2012-06-20 AAO:0000272 AAO AAO:LAP Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG] 2012-09-17 VHOG:0000453 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) http://bgee.unil.ch/ Note isa/partof difference MA/FMA MA mandibular part of mouth FMA:59398 the groups of nerve cell bodies associated with the twelve cranial nerves Ganglion which is located in the head.[TAO] UBERON:0003213 UBERON:0026601 BIRNLEX:2597 BTO:0000106 EFO:0000902 EMAPA:16659 FMA:54502 MA:0000213 MA:0000214 MAT:0000200 MIAA:0000200 SCTID:244448001 TAO:0000013 VHOG:0000076 Wikipedia:Cranial_nerve_ganglion XAO:0000027 ZFA:0000013 cranial ganglion cranial ganglion part of peripheral nervous system cranial ganglion/nerve cranial nerve ganglion cranial neural ganglion cranial neural tree organ ganglion ganglion of cranial nerve ganglion of cranial neural tree organ uberon cranial ganglia head ganglion presumptive cranial ganglia UBERON:0001714 cranial ganglion the groups of nerve cell bodies associated with the twelve cranial nerves ISBN:0-683-40008-8 MGI:csmith MP:0001081 PMID:9362461 Ganglion which is located in the head.[TAO] 2012-08-14 TAO:0000013 TAO ZFIN:curator cranial ganglion part of peripheral nervous system BIRNLEX:2597 cranial neural tree organ ganglion OBOL:automatic ganglion of cranial nerve FMA:54502 ganglion of cranial neural tree organ OBOL:automatic presumptive cranial ganglia ZFA:0000013 A specialized receptor organ that is a collection of cells spanning the gustatory epithelium. A chemoreceptive organ.[AAO] One of a number of receptor cell nests located in the epithelium of the papillae of the tongue and in the soft palate, epiglottis, and pharynx that mediate the sense of taste. [TFD][VHOG] Experients in amphibia have shown that an intrinsic feature of the pharyngeal endoderm is its ability to generate taste buds and this capacity must have been acquired by the endoderm at the origin of the vertebrates.[well established][VHOG] In humans, saste buds may be found on the tongue, soft palatte, epiglottis and upper pharynx. In other species they may be found in more unusual places, such as the trunk, or on the barbels or fins of fish. arise by inductive interactions between epithelial cells and invading gustatory cells from chorda tympani (facial), glossophrayngeal and vagues nerves ISBN:1607950324 (todo - request cell terms from CL) AAO:0010573 BIRNLEX:4101 BTO:0000989 CALOHA:TS-1015 EMAPA:35850 FMA:54825 GAID:815 MA:0001591 MESH:A08.800.550.700.120.800 NCIT:C96518 OpenCyc:Mx4rvVjan5wpEbGdrcN5Y29ycA SCTID:362099006 TAO:0001074 UMLS:C0039337 VHOG:0000130 Wikipedia:Taste_bud XAO:0000445 ZFA:0001074 http://uri.neuinfo.org/nif/nifstd/nifext_14 tastebud uberon caliculus gustatorius taste buds taste-bud tastebuds UBERON:0001727 taste bud http://upload.wikimedia.org/wikipedia/commons/5/5a/Gray1018.png NIF FMA http://dev.biologists.org/content/128/22/4573.full A specialized receptor organ that is a collection of cells spanning the gustatory epithelium. http://periowiki.wikispot.org/Taste_bud_histology A chemoreceptive organ.[AAO] 2012-06-20 AAO:0010573 AAO AAO:EJS One of a number of receptor cell nests located in the epithelium of the papillae of the tongue and in the soft palate, epiglottis, and pharynx that mediate the sense of taste. [TFD][VHOG] 2012-09-17 VHOG:0000130 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/taste+bud Experients in amphibia have shown that an intrinsic feature of the pharyngeal endoderm is its ability to generate taste buds and this capacity must have been acquired by the endoderm at the origin of the vertebrates.[well established][VHOG] 2012-09-17 VHOG:0000130 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) http://bgee.unil.ch/ UMLS:C0039337 BIRNLEX:4101 UMLS:C0039337 ncithesaurus:Taste_Bud tastebud Wikipedia:Taste_bud caliculus gustatorius Wikipedia:Taste_bud caliculus gustatorius Wikipedia:Taste_bud taste buds Wikipedia:Taste_bud taste-bud Wikipedia:Taste_bud tastebuds Wikipedia:Taste_bud A anatomical space that is enclosed by a pharynx. See notes for pharynx - as a grouping class this is probably too bad. We exclude WBbt:0005790 (pharyngeal lumen) because of the developmental relationship TOODO check AAO:0010435 BSA:0000113 BTO:0002097 EMAPA:18381 FMA:54935 SCTID:180543003 XAO:0000105 lumen of pharynx pharyngeal cavity uberon cavitas pharyngealis cavitas pharyngis UBERON:0001731 cavity of pharynx XAO A anatomical space that is enclosed by a pharynx. OBOL:automatic cavitas pharyngealis cavitas pharyngis BTO:0002097 A continuation of the pharynx that is involved in breathing, sound production, and protecting the trachea against food aspiration. An anatomical cluster consisting of the epiglottus, the arytenoid cartilages, the thyroid cartilage, the cricoid cartilage and the muscles, membranes, and ligaments connecting them, and also of the mucosal covering these structures.[FEED] Anatomical structure consisting of a narrowly triangular chamber supported by a series of semicircular cartilages in which part of the sound-production system is located.[AAO] (In anura) a dorsal pair of arytenoid cartilages (...), which support vocal cords, and a ventral pair (often fused) of cricoid cartilage (...). These cartilages are regarded as derivatives of posterior visceral arches of ancestors. Together they constitute the larynx, a structure characteristic of tetrapods. (...) (In mammals) Paired arytenoid cartilages help support and control the vocal cords. The cricoid cartilage is single. Two additional cartilages are present that are lacking in other vertebrates: a large ventral thyroid cartilage (...) and a cartilage in the epiglottis.[well established][VHOG] laryngeal AAO:0000268 BTO:0001208 CALOHA:TS-0532 EFO:0000838 EHDAA2:0004063 EMAPA:18333 EV:0100039 FMA:55097 GAID:108 MA:0000414 MAT:0000187 MESH:D007830 MIAA:0000187 NCIT:C12420 OpenCyc:Mx4rvViOnZwpEbGdrcN5Y29ycA SCTID:181212004 UMLS:C0023078 VHOG:0001279 Wikipedia:Larynx XAO:0003081 galen:Larynx uberon UBERON:0001737 larynx http://upload.wikimedia.org/wikipedia/commons/8/8a/Larynx_external_en.svg EHDAA2 A continuation of the pharynx that is involved in breathing, sound production, and protecting the trachea against food aspiration. Wikipedia:Larynx http://orcid.org/0000-0002-6601-2165 An anatomical cluster consisting of the epiglottus, the arytenoid cartilages, the thyroid cartilage, the cricoid cartilage and the muscles, membranes, and ligaments connecting them, and also of the mucosal covering these structures.[FEED] 2012-07-02 FEED http://www.feedexp.org Anatomical structure consisting of a narrowly triangular chamber supported by a series of semicircular cartilages in which part of the sound-production system is located.[AAO] 2012-06-20 AAO:0000268 AAO AAO:BJB (In anura) a dorsal pair of arytenoid cartilages (...), which support vocal cords, and a ventral pair (often fused) of cricoid cartilage (...). These cartilages are regarded as derivatives of posterior visceral arches of ancestors. Together they constitute the larynx, a structure characteristic of tetrapods. (...) (In mammals) Paired arytenoid cartilages help support and control the vocal cords. The cricoid cartilage is single. Two additional cartilages are present that are lacking in other vertebrates: a large ventral thyroid cartilage (...) and a cartilage in the epiglottis.[well established][VHOG] 2012-09-17 VHOG:0001279 VHOG ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.239-241 http://bgee.unil.ch/ UMLS:C0023078 ncithesaurus:Larynx The cartilaginous structures that support the larynx. (In anura) a dorsal pair of arytenoid cartilages (...), which support vocal cords, and a ventral pair (often fused) of cricoid cartilage (...). These cartilages are regarded as derivatives of posterior visceral arches of ancestors. Together they constitute the larynx, a structure characteristic of tetrapods. (...) (In mammals) Paired arytenoid cartilages help support and control the vocal cords. The cricoid cartilage is single. Two additional cartilages are present that are lacking in other vertebrates: a large ventral thyroid cartilage (...) and a cartilage in the epiglottis.[well established][VHOG] BTO:0003660 EHDAA:8157 EMAPA:18697 FMA:55108 GAID:107 MA:0001758 MESH:A02.165.507 NCIT:C12281 SCTID:263482005 UMLS:C0023050 VHOG:0001550 cartilage of larynx cartilagines laryngeales larynx cartilage uberon UBERON:0001739 laryngeal cartilage The cartilaginous structures that support the larynx. MP:0002256 (In anura) a dorsal pair of arytenoid cartilages (...), which support vocal cords, and a ventral pair (often fused) of cricoid cartilage (...). These cartilages are regarded as derivatives of posterior visceral arches of ancestors. Together they constitute the larynx, a structure characteristic of tetrapods. (...) (In mammals) Paired arytenoid cartilages help support and control the vocal cords. The cricoid cartilage is single. Two additional cartilages are present that are lacking in other vertebrates: a large ventral thyroid cartilage (...) and a cartilage in the epiglottis.[well established][VHOG] 2012-09-17 VHOG:0001550 VHOG ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.239-241 http://bgee.unil.ch/ UMLS:C0023050 ncithesaurus:Laryngeal_Cartilage cartilage of larynx FMA:55108 cartilagines laryngeales larynx cartilage VHOG:0001550 Cranial nerve that branches into the lateral (to body sense organs) and the intestino-accessorial (to the skin, muscles of shoulder, hyoid, larynx, gut, lungs, and heart). Nerve consisting of branchiomotor and visceral efferent fibers which branch and innervate the smooth muscles and glands of the heart, lungs, esophagus, and stomach as well as some throat muscles. Sensory fibers supply mucosa of the mouth and pharynx.[AAO] We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG] 10n AAO:0010475 BAMS:10n BAMS:Xn BIRNLEX:801 BTO:0003472 EFO:0002549 EMAPA:37797 FMA:5731 GAID:721 HBA:9337 MA:0001106 MBA:917 MESH:D014630 NCIT:C12812 OpenCyc:Mx4rviHk2ZwpEbGdrcN5Y29ycA SCTID:362466001 TAO:0000453 UMLS:C0042276 UMLS:C1305910 VHOG:0000737 Wikipedia:Vagus_nerve XAO:0003097 ZFA:0000453 galen:VagusNerve http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=702 nervus vagus [x] tenth cranial nerve vagus vagus X nerve vagus nerve [X] vagus nerve tree uberon CN-X cranial nerve X nerve X nervus vagus pneuomgastric nerve vagal nerve vagus nerve or its root UBERON:0001759 vagus nerve http://upload.wikimedia.org/wikipedia/commons/5/5e/Gray791.png motor Wikipedia Cranial nerve that branches into the lateral (to body sense organs) and the intestino-accessorial (to the skin, muscles of shoulder, hyoid, larynx, gut, lungs, and heart). ISBN:0471209627 Wikipedia:Vagus_nerve Nerve consisting of branchiomotor and visceral efferent fibers which branch and innervate the smooth muscles and glands of the heart, lungs, esophagus, and stomach as well as some throat muscles. Sensory fibers supply mucosa of the mouth and pharynx.[AAO] 2012-06-20 AAO:0010475 AAO AAO:EJS We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000737 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625 http://bgee.unil.ch/ 10n BIRNLEX:801 NIFSTD:NeuroNames_abbrevSource EMAPA:37797 MA:th UMLS:C0042276 BIRNLEX:801 UMLS:C0042276 ncithesaurus:Vagus_Nerve UMLS:C1305910 BIRNLEX:801 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=702 BIRNLEX:801 nervus vagus [x] FMA:5731 FMA:TA vagus X nerve MA:0001106 nerve X NeuroNames:702 nervus vagus BTO:0003472 nervus vagus Wikipedia:Vagus_nerve pneuomgastric nerve BTO:0003472 vagus nerve or its root BAMS:10n the space in the eye, filled with aqueous humor, and bounded anteriorly by the cornea and a small portion of the sclera and posteriorly by a small portion of the ciliary body, the iris, and part of the crystalline lens The part of the eyeball between the cornea and the iris, filled with aqueous humor. [TFD][VHOG] space in EHDAA2 - consider adding Cavity of anterior chamber of eyeball BTO:0002084 EHDAA2:0000129 EHDAA:9033 EMAPA:18231 FMA:58078 GAID:889 MA:0000262 MESH:D000867 NCIT:C12667 SCTID:181160009 UMLS:C0003151 VHOG:0001431 Wikipedia:Anterior_chamber_of_eyeball anterior chamber anterior chamber of eye camera anterior eye anterior chamber uberon camera anterior bulbi camera anterior bulbi oculi camera oculi anterior UBERON:0001766 anterior chamber of eyeball http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg FMA the space in the eye, filled with aqueous humor, and bounded anteriorly by the cornea and a small portion of the sclera and posteriorly by a small portion of the ciliary body, the iris, and part of the crystalline lens MESH:A09.371.060.067 MP:0005205 The part of the eyeball between the cornea and the iris, filled with aqueous humor. [TFD][VHOG] 2012-09-17 VHOG:0001431 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/anterior+chamber space in EHDAA2 - consider adding Cavity of anterior chamber of eyeball EHDAA2 UMLS:C0003151 ncithesaurus:Anterior_Chamber_of_the_Eye anterior chamber HP:0000593 MP:0010709 camera anterior bulbi BTO:0002084 camera anterior bulbi oculi Wikipedia:Anterior_chamber_of_eyeball camera oculi anterior BTO:0002084 the pigmented middle of the three concentric layers that make up an eye, consisting of the iris, ciliary body and choroid[WP,edited]. TODO - check child terms, isa vs partof. See also MA:0001284 ! tunica vasculosa plexus uveal CALOHA:TS-2228 EMAPA:35901 FMA:58103 GAID:912 MA:0002480 MESH:D014602 NCIT:C12811 SCTID:280648000 UMLS:C0042160 Wikipedia:Uvea tunica vasculosa of eyeball uvea uveal tract uberon pars iridica retinae tunica vasculatis oculi tunica vasculosa bulbi vascular layer of eyeball UBERON:0001768 uvea http://upload.wikimedia.org/wikipedia/commons/e/eb/Gray869.png FMA the pigmented middle of the three concentric layers that make up an eye, consisting of the iris, ciliary body and choroid[WP,edited]. MP:0005197 Wikipedia:Uvea DOI:10.1177/0192623311409597 UMLS:C0042160 ncithesaurus:Uvea tunica vasculosa of eyeball FMA:58103 uvea FMA:58103 uveal tract FMA:58103 pars iridica retinae Wikipedia:Uvea tunica vasculatis oculi Wikipedia:Uvea tunica vasculosa bulbi Wikipedia:Uvea vascular layer of eyeball FMA:58103 the adjustable membrane, composed of the stroma and pigmented epithelium, located just in front of the crystalline lens within the eye The opaque muscular contractile diaphragm suspended in the aqueous humour in front of the lens of the eye. The organ is perforated by the pupil and continues peripherally with the ciliary body. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] iridial The avian iris and ciliary body undergoes a transition from smooth-to-striated muscle during embryonic development [DOI:dx.doi.org/10.1006/dbio.1998.9019] AAO:0010347 BTO:0000653 CALOHA:TS-0491 EFO:0004245 EMAPA:19154 EV:0100345 FMA:58235 GAID:917 MA:0000273 MESH:D007498 NCIT:C12737 OpenCyc:Mx4rvVjbppwpEbGdrcN5Y29ycA SCTID:181164000 TAO:0001238 UMLS:C0022077 VHOG:0000101 Wikipedia:Iris_(anatomy) XAO:0000185 ZFA:0001238 uberon anterior uvea irides irises UBERON:0001769 iris XAO the adjustable membrane, composed of the stroma and pigmented epithelium, located just in front of the crystalline lens within the eye ISBN:0-683-40008-8 MP:0001322 The opaque muscular contractile diaphragm suspended in the aqueous humour in front of the lens of the eye. The organ is perforated by the pupil and continues peripherally with the ciliary body. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000101 VHOG http://bgee.unil.ch/ The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] 2012-09-17 VHOG:0000101 VHOG DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007) http://bgee.unil.ch/ UMLS:C0022077 ncithesaurus:Iris irides irises VHOG:0000101 the smooth stratified squamous epithelium that covers the outer surface of the cornea Portion of tissue comprised of four to six layers of nonkeratinized, stratified squamous cells and represents approximately 60% of the thickness of the cornea.[TAO] In Humans: It consists of several layers of cells. The cells of the deepest layer are columnar; then follow two or three layers of polyhedral cells, the majority of which are prickle cells similar to those found in the stratum mucosum of the cuticle. Lastly, there are three or four layers of squamous cells, with flattened nuclei In zebrafish: nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals BTO:0000287 CALOHA:TS-0173 EFO:0001917 EHDAA2:0000319 EMAPA:17162 FMA:58263 GAID:895 MA:0001243 MESH:D019573 NCIT:C12928 SCTID:368825001 TAO:0002187 UMLS:C0459875 Wikipedia:Corneal_epithelium ZFA:0001683 anterior corneal epithelium cornea epithelial tissue cornea epithelium epithelial tissue of cornea epithelium anterius (cornea) epithelium anterius corneae epithelium corneæ anterior layer epithelium of cornea external epithelium of cornea uberon anterior endothelium of cornea e. anterius corneae endothelium anterius corneae endothelium camerae anterioris bulbi endothelium corneale epithelium posterius corneae UBERON:0001772 corneal epithelium http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png ISBN:0781772214 the smooth stratified squamous epithelium that covers the outer surface of the cornea MESH:A09.371.060.217.325 MGI:smb MP:0006000 Portion of tissue comprised of four to six layers of nonkeratinized, stratified squamous cells and represents approximately 60% of the thickness of the cornea.[TAO] 2012-08-14 TAO:0002187 TAO ZFIN:ZDB-PUB-061010-3 UMLS:C0459875 ncithesaurus:Corneal_Epithelium cornea epithelial tissue OBOL:automatic cornea epithelium OBOL:automatic epithelial tissue of cornea OBOL:automatic epithelium anterius corneae FMA:58263 FMA:TA anterior endothelium of cornea BTO:0000287 e. anterius corneae Wikipedia:Corneal_epithelium endothelium anterius corneae BTO:0000287 endothelium camerae anterioris bulbi BTO:0000287 endothelium corneale BTO:0000287 epithelium posterius corneae BTO:0000287 Opaque fibrous outer layer of the eyeball[ZFA,Kardong,WP]. The sclera, also known as the white part of the eye, is the opaque (usually white, though certain animals, such as horses and lizards, can have black sclera), fibrous, protective, outer layer of the eye containing collagen and elastic fiber. It is derived from the neural crest. In children, it is thinner and shows some of the underlying pigment, appearing slightly blue. In the elderly, however, fatty deposits on the sclera can make it appear slightly yellow. The sclera forms the posterior five sixths of the connective tissue coat of the globe. It is continuous with the dura mater and the cornea, and maintains the shape of the globe, offering resistance to internal and external forces, and provides an attachment for the extraocular muscle insertions. The sclera is perforated by plenty of nerves and vessels passing through the posterior scleral foramen, the hole that is formed by the optic nerve. At the optic disk the outer two-thirds of the sclera continues with the dura mater (outer coat of the brain) via the dural sheath of the optic nerve. The inner third joins with some choroidal tissue to form a plate (lamina cribrosa) across the optic nerve with perforations through which the optic fibers (fasciculi). The thickness of the sclera varies from 1mm at the posterior pole to 0.3 mm just behind the rectus muscle insertions. The sclera's blood vessels are mainly on the surface, and together with the conjunctiva (which lies on top) This is a thin layer covering the sclera. Along with the vessels of the conjunctiva, those of the sclera renders the inflamed eye bright red. [WP,unvetted][Wikipedia:Sclera]. The tough, usually white, outer coat of the eyeball, covering all the posterior surface and continuous anteriorly with the cornea. [TFD][VHOG] scleral in fish, reptiles and monotremes the connective tissue of the sclera is skeletal continuous with the dura mater and the cornea; The sclera forms the posterior five-sixths of the connective tissue coat of the globe. Majority derives from NC that surrounds optic cup of neurectoderm; a small temporal portion develops from the mesoderm that contributes to striated extra-ocular muscles and vascular endothelia[Rada&Johnson]. Seko et al demonstrate chondrogenic potential and identify this as connective tissue[DOI:10.1371/journal.pone.0003709]. AAO:0010354 BTO:0001606 EMAPA:19027 EV:0100342 FMA:58269 GAID:911 MA:0000280 MESH:D012590 NCIT:C12784 OpenCyc:Mx4rv7yR55wpEbGdrcN5Y29ycA SCTID:181163006 UMLS:C0036410 VHOG:0001274 Wikipedia:Sclera XAO:0000183 ZFA:0005563 uberon scleral capsule UBERON:0001773 Disease notes: implicated in rheumatoid arthritis. sclera http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg FMA ZFA ISBN:0781772214 Opaque fibrous outer layer of the eyeball[ZFA,Kardong,WP]. Wikipedia:Sclera ZFIN:ZDB-PUB-050701-15 The sclera, also known as the white part of the eye, is the opaque (usually white, though certain animals, such as horses and lizards, can have black sclera), fibrous, protective, outer layer of the eye containing collagen and elastic fiber. It is derived from the neural crest. In children, it is thinner and shows some of the underlying pigment, appearing slightly blue. In the elderly, however, fatty deposits on the sclera can make it appear slightly yellow. The sclera forms the posterior five sixths of the connective tissue coat of the globe. It is continuous with the dura mater and the cornea, and maintains the shape of the globe, offering resistance to internal and external forces, and provides an attachment for the extraocular muscle insertions. The sclera is perforated by plenty of nerves and vessels passing through the posterior scleral foramen, the hole that is formed by the optic nerve. At the optic disk the outer two-thirds of the sclera continues with the dura mater (outer coat of the brain) via the dural sheath of the optic nerve. The inner third joins with some choroidal tissue to form a plate (lamina cribrosa) across the optic nerve with perforations through which the optic fibers (fasciculi). The thickness of the sclera varies from 1mm at the posterior pole to 0.3 mm just behind the rectus muscle insertions. The sclera's blood vessels are mainly on the surface, and together with the conjunctiva (which lies on top) This is a thin layer covering the sclera. Along with the vessels of the conjunctiva, those of the sclera renders the inflamed eye bright red. [WP,unvetted][Wikipedia:Sclera]. Wikipedia:Sclera The tough, usually white, outer coat of the eyeball, covering all the posterior surface and continuous anteriorly with the cornea. [TFD][VHOG] 2012-09-17 VHOG:0001274 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/sclera UMLS:C0036410 ncithesaurus:Sclera A skeletal muscle organ that is part of the trunk region. Note that this class excludes smooth muscle elements in the trunk region, such as the internal anal sphincter. This appears to be consistent with other ontologies such as FMA and ZFA which appear to only include skeletal muscles here. In fact the MA class 'trunk muscle' is classified as a 'set of skeletal muscles'. Many ontologies do not appear to have a coherent distinction between an individual muscle and the musculature (i.e. the set of muscles in a region), so we group all together here. AAO:0000611 EMAPA:35888 FMA:58274 MA:0000514 TAO:0000473 XAO:0003230 ZFA:0000473 body musculature muscle of trunk muscle organ of torso muscle organ of trunk torso muscle organ trunk muscle trunk muscle organ trunk musculature uberon UBERON:0001774 skeletal muscle of trunk prolog A skeletal muscle organ that is part of the trunk region. http://orcid.org/0000-0002-6601-2165 body musculature ZFA:0000473 muscle of trunk FMA:58274 muscle organ of torso OBOL:automatic muscle organ of trunk OBOL:automatic torso muscle organ OBOL:automatic trunk muscle organ OBOL:automatic the thickened portion of the vascular tunic, which lies between the choroid and the iris, composed of ciliary muscle and ciliary processes The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] AAO:0010341 BTO:0000260 CALOHA:TS-0694 EMAPA:19065 EV:0100346 FMA:58295 GAID:916 MA:0000264 MESH:D002924 NCIT:C12345 SCTID:263340007 UMLS:C0008779 VHOG:0000102 Wikipedia:Ciliary_body XAO:0000186 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1571 ocular ciliary body uberon anterior uvea ciliary bodies corpus ciliare UBERON:0001775 ciliary body http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg ISBN:0781772214 the thickened portion of the vascular tunic, which lies between the choroid and the iris, composed of ciliary muscle and ciliary processes ISBN:0-683-40008-8 MP:0005099 Wikipedia:Ciliary_body The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] 2012-09-17 VHOG:0000102 VHOG DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007) http://bgee.unil.ch/ UMLS:C0008779 ncithesaurus:Ciliary_Body ciliary bodies VHOG:0000102 corpus ciliare Wikipedia:Ciliary_body corpus ciliare Wikipedia:Ciliary_body vascular layer containing connective tissue, of the eye lying between the retina and the sclera. The choroid provides oxygen and nourishment to the outer layers of the retina. Along with the ciliary body and iris, the choroid forms the uveal tract[WP]. check choroid vs choroid layer; check ZFA/TAO placement - no homology assertion in VHOG. Note this is entirely in the posterior region of eyeball in ZFA choroidal MP treats posterior uvea and optic choroid as distinct BTO:0001829 CALOHA:TS-2054 EMAPA:19077 EV:0100347 FMA:58298 GAID:913 MA:0000263 MESH:D002829 NCIT:C12344 SCTID:181172003 TAO:0005229 UMLS:C0008520 VHOG:0001568 Wikipedia:Choroid ZFA:0005229 choroid choroid coat choroidea eye choroid posterior uvea uberon chorioid choroidea optic choroid UBERON:0001776 optic choroid http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg MA Wikipedia lexical vascular layer containing connective tissue, of the eye lying between the retina and the sclera. The choroid provides oxygen and nourishment to the outer layers of the retina. Along with the ciliary body and iris, the choroid forms the uveal tract[WP]. Wikipedia:Choroid MP treats posterior uvea and optic choroid as distinct MP UMLS:C0008520 ncithesaurus:Choroid choroid MA:0000263 choroid coat Wikipedia:Choroid choroidea Wikipedia:Choroid eye choroid VHOG:0001568 posterior uvea Wikipedia:Uvea#Regions chorioid BTO:0001829 choroidea Wikipedia:Choroid optic choroid ZFA:0005229 the lamellated connective tissue of the cornea between the Bowman and Descemet membranes Portion of tissue that is located basal to Bowman's layer and distal to Descemet's membrane and is comprised largely of connective tissue.[TAO] relationship type change: subclass tissue (CARO:0000043) CHANGED TO: develops_from tissue (UBERON:0000479)[TAO] relationship type change: subclass tissue (CARO:0000043) CHANGED TO: has_developmental_contribution_from tissue (UBERON:0000479)[TAO] substantia propria CALOHA:TS-1138 EFO:0002514 EMAPA:17602 FMA:58306 GAID:893 MA:0001245 MESH:D003319 NCIT:C12699 SCTID:362511000 TAO:0002189 UMLS:C0010040 Wikipedia:Corneal_stroma ZFA:0001685 corneal stroma stroma of cornea substantia propria corneae uberon UBERON:0001777 substantia propria of cornea http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png cjm ISBN:0781772214 Wikipedia the lamellated connective tissue of the cornea between the Bowman and Descemet membranes ISBN:0-683-40008-8 MESH:A09.371.060.217.228 MP:0005300 Portion of tissue that is located basal to Bowman's layer and distal to Descemet's membrane and is comprised largely of connective tissue.[TAO] 2012-08-14 TAO:0002189 TAO ZFIN:ZDB-PUB-061010-3 relationship type change: subclass tissue (CARO:0000043) CHANGED TO: develops_from tissue (UBERON:0000479)[TAO] 2012-08-14 TAO:0002189 TAO relationship type change: subclass tissue (CARO:0000043) CHANGED TO: has_developmental_contribution_from tissue (UBERON:0000479)[TAO] 2012-08-14 TAO:0002189 TAO UMLS:C0010040 ncithesaurus:Corneal_Stroma corneal stroma MA:0001245 substantia propria corneae FMA:58306 FMA:TA A double layer covering the ciliary body that produces aqueous humor. BTO:0001770 CALOHA:TS-0695 EMAPA:35239 FMA:58464 MA:0001238 NCIT:C32314 SCTID:280870004 UMLS:C0459736 Wikipedia:Ciliary_body#Ciliary_epithelium ciliary body epithelium epithelium of ciliary body ocular ciliary epithelium uberon UBERON:0001778 ciliary epithelium FMA MA MP Wikipedia A double layer covering the ciliary body that produces aqueous humor. Wikipedia:Ciliary_body#Ciliary_epithelium UMLS:C0459736 ncithesaurus:Ciliary_Epithelium ciliary body epithelium FMA:58464 epithelium of ciliary body FMA:58464 The delicate vascular connective tissue that lies between the anterior surface of the iris and the pars iridica retinae. EMAPA:35451 FMA:58526 MA:0002777 SCTID:280882008 Wikipedia:Iris_stroma ZFA:0005569 iridial stroma stroma of iris uberon UBERON:0001779 iris stroma http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png The delicate vascular connective tissue that lies between the anterior surface of the iris and the pars iridica retinae. Wikipedia:Iris_stroma http://www.drugs.com/dict/stroma-of-iris.html the any of the paired peripheral nerves formed by the union of the dorsal and ventral spinal roots from each spinal cord segment[MP,modified] Any of the paired nerves emerging from the spinal cord, each attached to the cord by two roots: ventral and dorsal, and passing out between the vertebrae. [TFD][VHOG] AAO:0011101 BAMS:spin BTO:0000870 EHDAA2:0001898 EMAPA:16989 FMA:5858 GAID:841 MA:0000233 MESH:D013127 NCIT:C12792 OpenCyc:Mx4rwK_iFJwpEbGdrcN5Y29ycA SCTID:361099009 UMLS:C0037941 VHOG:0000824 Wikipedia:Spinal_nerve XAO:0003101 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1228 backbone nerve nerve of backbone nerve of spinal column nerve of spine nerve of vertebral column spinal column nerve spinal nerve tree spine nerve vertebral column nerve uberon nervi spinales spinal nerves UBERON:0001780 spinal nerve Spinal:nerve.svg the any of the paired peripheral nerves formed by the union of the dorsal and ventral spinal roots from each spinal cord segment[MP,modified] MESH:A08.800.800.720 MP:0001077 Any of the paired nerves emerging from the spinal cord, each attached to the cord by two roots: ventral and dorsal, and passing out between the vertebrae. [TFD][VHOG] 2012-09-17 VHOG:0000824 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/spinal+nerve UMLS:C0037941 ncithesaurus:Spinal_Nerve backbone nerve OBOL:automatic nerve of backbone OBOL:automatic nerve of spinal column OBOL:automatic nerve of spine OBOL:automatic nerve of vertebral column OBOL:automatic spinal column nerve OBOL:automatic spine nerve OBOL:automatic vertebral column nerve OBOL:automatic nervi spinales Wikipedia:Spinal_nerve spinal nerves BAMS:spin Any of the layers that make up the retina[MP]. MA does not treat internal/external limiting memranes as layers - these are classified as laminae. Here we follow other ontologies in grouping with other layers. MA also treats retinal pigment epithelium and neural retina epithelium as distinct from the layers. We follow ontologies such as FMA and ZFA in first dividing into pigmented and neural layers - these are also classified as layers, giving us over the usual 10 layers AAO:0010353 EMAPA:35742 FMA:58617 MA:0001319 NCIT:C49328 SCTID:280657006 UMLS:C0459649 XAO:0000266 retina layer retina neuronal layer retinal layer retinal neuronal layer uberon UBERON:0001781 layer of retina Any of the layers that make up the retina[MP]. MP:0003727 MA does not treat internal/external limiting memranes as layers - these are classified as laminae. Here we follow other ontologies in grouping with other layers. MA also treats retinal pigment epithelium and neural retina epithelium as distinct from the layers. We follow ontologies such as FMA and ZFA in first dividing into pigmented and neural layers - these are also classified as layers, giving us over the usual 10 layers MA UMLS:C0459649 ncithesaurus:Retina_Layer retina neuronal layer MP:0006069 retinal neuronal layer MP:0006069 Cranial nerves are nerves that emerge directly from the brain, in contrast to spinal nerves, which emerge from segments of the spinal cord. classified as neural tree organ, not nerve in FMA. CN II poses a challenge here as it is not strictly a nerve, yet is expected to be classified under CN. Twelve pairs of cranial nerves exit/enter the cranium through openings in the skull. The nerves contain efferent axons with motor and glandular functions, as well as afferent axons from cranial ganglia with sensory functions. The nerves are numbered in a rostral to caudal sequence, with the exception of the lateral line nerves.[TAO] We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...).[well established][VHOG] See https://github.com/obophenotype/mouse-anatomy-ontology/issues/6 AAO:0000108 BAMS:cran BIRNLEX:1623 BTO:0001104 EHDAA2:0000323 EMAPA:17264 FMA:5865 GAID:802 HBA:9299 MA:0000215 MBA:967 MESH:D003391 NCIT:C12700 OpenCyc:Mx4rvWvJVpwpEbGdrcN5Y29ycA SCTID:244447006 TAO:0000641 UMLS:C0010268 UMLS:C1269897 VHOG:0000279 Wikipedia:Cranial_nerve XAO:0000429 XAO:0003089 ZFA:0000641 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1227 cranial neural tree organ uberon cranial nerves nervus cranialis UBERON:0001785 cranial nerve http://upload.wikimedia.org/wikipedia/commons/1/18/Brain_human_normal_inferior_view_with_labels_en-2.svg http://upload.wikimedia.org/wikipedia/commons/8/84/Brain_human_normal_inferior_view_with_labels_en.svg Cranial nerves are nerves that emerge directly from the brain, in contrast to spinal nerves, which emerge from segments of the spinal cord. Wikipedia:Cranial_nerve Twelve pairs of cranial nerves exit/enter the cranium through openings in the skull. The nerves contain efferent axons with motor and glandular functions, as well as afferent axons from cranial ganglia with sensory functions. The nerves are numbered in a rostral to caudal sequence, with the exception of the lateral line nerves.[TAO] 2012-08-14 TAO:0000641 TAO ZFIN:curator We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...).[well established][VHOG] 2012-09-17 VHOG:0000279 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 http://bgee.unil.ch/ UMLS:C0010268 BIRNLEX:1623 UMLS:C0010268 ncithesaurus:Cranial_Nerve UMLS:C1269897 BIRNLEX:1623 nervus cranialis Wikipedia:Cranial_nerve A thick watery refractive medium that fills the space between the lens and the cornea[WP]. The fluid produced by the ciliary process in the eye and occupying the anterior and posterior chambers. It provides nourishment for the lens and cornea and maintains the ocular pressure, and hence the optical integrity of the eyeball. [TFD][VHOG] (...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG] FMA says A+P chambers, and MA states A chamber. ZFA states A chamber and tha it is produced primarily by dorsal ciliary epithelial cells.To be investigated across taxa. EHDAA2:0000139 EHDAA:10196 EMAPA:18232 ENVO:02000024 FMA:58819 GAID:890 MA:0001236 MESH:D001082 NCIT:C13190 OpenCyc:Mx4rvdGd-5wpEbGdrcN5Y29ycA SCTID:280587006 UMLS:C0003662 VHOG:0000548 Wikipedia:Aqueous_humor ZFA:0005564 aqueous humor aqueous humour humor aquosus uberon UBERON:0001796 aqueous humor of eyeball http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg FMA def states A and P located_in in EHDAA2 VHOG A thick watery refractive medium that fills the space between the lens and the cornea[WP]. Wikipedia:Aqueous_humor The fluid produced by the ciliary process in the eye and occupying the anterior and posterior chambers. It provides nourishment for the lens and cornea and maintains the ocular pressure, and hence the optical integrity of the eyeball. [TFD][VHOG] 2012-09-17 VHOG:0000548 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/aqueous+humour (...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000548 VHOG DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.424 and p.426 and p.429 and Figure 12-24 http://bgee.unil.ch/ FMA says A+P chambers, and MA states A chamber. ZFA states A chamber and tha it is produced primarily by dorsal ciliary epithelial cells.To be investigated across taxa. FMA UMLS:C0003662 ncithesaurus:Aqueous_Humor aqueous humour EHDAA2:0000139 humor aquosus FMA:58819 FMA:TA The clusters of neurons in the somatic peripheral nervous system which contain the cell bodies of sensory nerve axons, interneurons and non-neuronal supporting cells. AEO:0001000 BTO:0005630 EMAPA:36596 FMA:5885 MA:0002566 MESH:D017950 NCIT:C13060 UMLS:C0206429 ganglion sensorium uberon UBERON:0001800 sensory ganglion The clusters of neurons in the somatic peripheral nervous system which contain the cell bodies of sensory nerve axons, interneurons and non-neuronal supporting cells. MP:0000960 UMLS:C0206429 ncithesaurus:Sensory_Ganglion ganglion sensorium any of the parts of the eye that lie in front of, or ventral to, the lens (inclusive) EMAPA:36594 FMA:58865 MA:0002484 MESH:D000869 NCIT:C12668 SCTID:280658001 UMLS:C0003153 Wikipedia:Anterior_segment_of_eyeball ZFA:0005566 anterior eye segment anterior segment eye anterior segment of eye anterior segment of the eye eye anterior segment segmentum anterius (bulbus oculi) uberon segmentum anterius bulbi oculi UBERON:0001801 anterior segment of eyeball http://upload.wikimedia.org/wikipedia/commons/b/ba/Cataract_in_human_eye.png FMA cjm lexical any of the parts of the eye that lie in front of, or ventral to, the lens (inclusive) ISBN:0-683-40008-8 MESH:A09.371.060 MP:0005193 UMLS:C0003153 ncithesaurus:Anterior_Eye_Segment anterior segment eye ZFA:0005566 segmentum anterius bulbi oculi Wikipedia:Anterior_segment_of_eyeball any of the parts of the eye that lie in back of, or dorsal to, the lens (but not inclusive) EMAPA:36595 FMA:58868 MA:0002485 NCIT:C12906 SCTID:280659009 UMLS:C0278450 Wikipedia:Posterior_segment_of_eyeball ZFA:0005567 eye posterior segment posterior eye segment posterior segment eye posterior segment of eye posterior segment of the eye segmentum posterius (bulbus oculi) uberon segmentum posterius bulbi oculi UBERON:0001802 posterior segment of eyeball http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg FMA cjm lexical any of the parts of the eye that lie in back of, or dorsal to, the lens (but not inclusive) ISBN:0-683-40008-8 MP:0005195 UMLS:C0278450 ncithesaurus:Posterior_Eye_Segment posterior segment eye ZFA:0005567 segmentum posterius bulbi oculi Wikipedia:Posterior_segment_of_eyeball A layer of epithelial cells that is part of the eye. this class is the superclass of the anterior epithelium and equatorial epithlium, although the term 'lens epithelium' may refer specifically to the former BTO:0001873 CALOHA:TS-0543 EMAPA:32871 FMA:58871 MA:0001301 SCTID:362523006 TAO:0001326 Wikipedia:Lens_(anatomy)#Lens_Epithelium XAO:0004094 ZFA:0001326 epithelial tissue of eye lens epithelial tissue of lens epithelium lentis epithelium of eye lens eye lens epithelial tissue eye lens epithelium lens epithelial tissue lens epithelium uberon UBERON:0001803 epithelium of lens A layer of epithelial cells that is part of the eye. http://orcid.org/0000-0002-6601-2165 epithelial tissue of eye lens OBOL:automatic epithelial tissue of lens OBOL:automatic epithelium lentis FMA:58871 FMA:TA epithelium of eye lens OBOL:automatic eye lens epithelial tissue OBOL:automatic eye lens epithelium OBOL:automatic lens epithelial tissue OBOL:automatic the elastic, clear, membrane-like structure, that is outer most layer of the lens The transparent membrane which surrounds the lens of the eye. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] (...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG] synthesized by the lens epithelium and its main components are Type IV collagen and sulfated glycosaminoglycans (GAGs). [Wikipedia:Capsule_of_lens FMA classifies this is a capsule and hence an organ part. In contrast we classify this as acellular EHDAA2:0000977 EMAPA:18237 FMA:58881 MA:0001300 NCIT:C32975 SCTID:244500004 UMLS:C0229232 VHOG:0000550 Wikipedia:Lens_(anatomy)#Lens_capsule ZFA:0005574 capsula lentis lens capsule uberon UBERON:0001804 capsule of lens http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png EHDAA2 the elastic, clear, membrane-like structure, that is outer most layer of the lens MGI:smb MP:0003236 PMID:15483628 The transparent membrane which surrounds the lens of the eye. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000550 VHOG http://bgee.unil.ch/ (...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000550 VHOG DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.424 and p.426 and p.429 and Figure 12-24 http://bgee.unil.ch/ FMA classifies this is a capsule and hence an organ part. In contrast we classify this as acellular FMA UMLS:C0229232 ncithesaurus:Lens_Capsule capsula lentis ganglion that has dendrites that form a junction between autonomic nerves originating from the central nervous system and autonomic nerves innervating their target organs in the periphery. There are two subtypes, sympathetic ganglion and parasympathetic ganglion. AEO:0001001 CALOHA:TS-2340 EMAPA:17157 EMAPA:18221 FMA:5889 MA:0000220 MESH:D005725 NCIT:C12720 UMLS:C0017068 Wikipedia:Autonomic_ganglion autonomic nervous system ganglion ganglion of autonomic nervous system ganglion of visceral nervous system visceral nervous system ganglion uberon ganglion autonomicum UBERON:0001805 autonomic ganglion http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png ganglion that has dendrites that form a junction between autonomic nerves originating from the central nervous system and autonomic nerves innervating their target organs in the periphery. There are two subtypes, sympathetic ganglion and parasympathetic ganglion. Wikipedia:Autonomic_ganglion UMLS:C0017068 ncithesaurus:Autonomic_Ganglion autonomic nervous system ganglion OBOL:automatic ganglion of autonomic nervous system OBOL:automatic ganglion of visceral nervous system OBOL:automatic visceral nervous system ganglion OBOL:automatic ganglion autonomicum Wikipedia:Autonomic_ganglion A ganglion of the sympathetic nervous system. Examples: paravertebral and the prevertebral ganglia, which include the sympathetic chain ganglia, the superior, middle, and inferior cervical ganglia, and the aorticorenal, celiac, and stellate ganglia AAO:0010773 BTO:0001333 CALOHA:TS-0994 EHDAA2:0001969 EMAPA:17157 FMA:5890 MA:0000226 NCIT:C12467 SCTID:362485003 UMLS:C0017071 Wikipedia:Sympathetic_ganglion ganglion of sympathetic nervous system ganglion of sympathetic part of autonomic division of nervous system ganglion sympatheticum sympathetic nervous system ganglion sympathetic part of autonomic division of nervous system ganglion uberon ganglion sympathicum UBERON:0001806 sympathetic ganglion http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png DOI:10.1101/gr.157586.113 ISBN:0073040584 A ganglion of the sympathetic nervous system. Examples: paravertebral and the prevertebral ganglia, which include the sympathetic chain ganglia, the superior, middle, and inferior cervical ganglia, and the aorticorenal, celiac, and stellate ganglia MP:0001008 http://orcid.org/0000-0002-6601-2165 UMLS:C0017071 ncithesaurus:Sympathetic_Ganglion ganglion of sympathetic nervous system OBOL:automatic ganglion of sympathetic part of autonomic division of nervous system OBOL:automatic sympathetic nervous system ganglion OBOL:automatic sympathetic part of autonomic division of nervous system ganglion OBOL:automatic ganglion sympathicum BTO:0001333 ganglion sympathicum Wikipedia:Sympathetic_ganglion The mucous lining of the larynx, which is composed of squamous epithelium in the upper larynx and ciliated columnar epithelium in the lower larynx. EMAPA:18334 FMA:59662 GAID:301 MA:0001766 MESH:D007820 NCIT:C49246 SCTID:361940006 UMLS:C0023053 laryngeal mucosa larynx mucosa larynx mucosa of organ larynx mucous membrane larynx organ mucosa mucosa of organ of larynx mucous membrane of larynx organ mucosa of larynx tunica mucosa laryngis uberon laryngeal mucous membrane UBERON:0001824 mucosa of larynx The mucous lining of the larynx, which is composed of squamous epithelium in the upper larynx and ciliated columnar epithelium in the lower larynx. MP:0002261 UMLS:C0023053 ncithesaurus:Laryngeal_Mucosa larynx mucosa of organ OBOL:automatic larynx mucous membrane OBOL:automatic larynx organ mucosa OBOL:automatic mucosa of organ of larynx OBOL:automatic organ mucosa of larynx OBOL:automatic tunica mucosa laryngis FMA:59662 FMA:TA laryngeal mucous membrane EMAPA:18334 One of the two fleshy folds which surround the opening of the mouth. Surface structure that is one of the two fleshy folds surrounding the opening of the mouth.[TAO] labial BTO:0001647 CALOHA:TS-0558 EMAPA:32839 FMA:59816 GAID:76 MA:0000343 MESH:D008046 NCIT:C12220 OpenCyc:Mx4rvVi4U5wpEbGdrcN5Y29ycA SCTID:181221003 TAO:0007006 UMLS:C0023759 VHOG:0000677 Wikipedia:Lip ZFA:0007006 galen:Lip uberon labia oris lips UBERON:0001833 lip http://upload.wikimedia.org/wikipedia/commons/9/90/Lips.JPG http://upload.wikimedia.org/wikipedia/commons/9/99/Mouth.jpg ZFA BTO FMA-implicit VHOG ZFA cjm One of the two fleshy folds which surround the opening of the mouth. Wikipedia:Lip http://www.medterms.com/script/main/art.asp?articlekey=9458 Surface structure that is one of the two fleshy folds surrounding the opening of the mouth.[TAO] 2012-08-14 TAO:0007006 TAO ZFIN:curator http//:www.medterms.com/script/main/art.asp?articlekey=9458 UMLS:C0023759 ncithesaurus:Lip labia oris Wikipedia:Lip Lip that covers the lower portion of the mouth.[TAO]. Lip that covers the lower portion of the mouth.[TAO] UBERON:0003392 EHDAA2:0001020 EMAPA:17909 FMA:59818 MA:0000921 NCIT:C94572 OpenCyc:Mx4rv842UpwpEbGdrcN5Y29ycA SCTID:245777007 TAO:0002060 UMLS:C0458583 Wikipedia:Lower_lip ZFA:0005225 lower jaw lip uberon labium inferius oris UBERON:0001835 lower lip http://upload.wikimedia.org/wikipedia/commons/9/99/Mouth.jpg Lip that covers the lower portion of the mouth.[TAO]. TAO:0002060 Wikipedia:Lower_lip Lip that covers the lower portion of the mouth.[TAO] 2012-08-14 TAO:0002060 TAO TAO:wd UMLS:C0458583 ncithesaurus:Lower_Lip lower jaw lip https://orcid.org/0000-0002-6601-2165 labium inferius oris Wikipedia:Lower_lip One of two bilateral, largely symmetrical organ subdivisions within the telencephalon which contain the cerebral cortex and cerebral white matter.[FMA] Part of the telencephalon consisting of either of the two smooth, elongated halves of the cerebrum.[AAO] The presence of paired evaginated hemispheres and olfactory bulbs in both agnathan and gnathostome radiations suggests that such hemispheres were also present in the common ancestor.[well established][VHOG] AAO:0010480 BAMS:HEM BIRNLEX:1042 BTO:0000231 CALOHA:TS-2007 DMBA:15739 EFO:0002521 EMAPA:16653 FMA:61817 MA:0000133 MBA:403 NCIT:C12351 OpenCyc:Mx4rvigx5ZwpEbGdrcN5Y29ycA SCTID:278251007 UMLS:C0228174 UMLS:C0242202 VHOG:0001639 Wikipedia:Cerebral_hemisphere galen:CerebralHemisphere http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=241 uberon cerebrum hemisphere hemispheric regions hemispherium cerebri medial amygdalar nucleus nucleus amygdaloideus medialis nucleus medialis amygdalae UBERON:0001869 cerebral hemisphere http://upload.wikimedia.org/wikipedia/commons/9/92/Hemispheres.png FMA-abduced-lr One of two bilateral, largely symmetrical organ subdivisions within the telencephalon which contain the cerebral cortex and cerebral white matter.[FMA] FMA:61817 Wikipedia:Cerebral_hemisphere Part of the telencephalon consisting of either of the two smooth, elongated halves of the cerebrum.[AAO] 2012-06-20 AAO:0010480 AAO AAO:BJB The presence of paired evaginated hemispheres and olfactory bulbs in both agnathan and gnathostome radiations suggests that such hemispheres were also present in the common ancestor.[well established][VHOG] 2012-09-17 VHOG:0001639 VHOG DOI:10.1146/annurev.ne.04.030181.001505 Northcutt RG, Evolution of the telencephalon in nonmammals. Ann. Rev. Neurosci. (1981) http://bgee.unil.ch/ UMLS:C0228174 ncithesaurus:Cerebral_Hemisphere UMLS:C0242202 BIRNLEX:1042 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=241 BIRNLEX:1042 cerebrum MA:0000133 VHOG:0001639 https://github.com/obophenotype/uberon/issues/1208 hemisphere VHOG:0001639 hemispheric regions BAMS:HEM hemispherium cerebri Wikipedia:Cerebral_hemisphere medial amygdalar nucleus NeuroNames:241 nucleus amygdaloideus medialis NeuroNames:241 nucleus medialis amygdalae NeuroNames:241 A nerve that arises from the caudal cervical nerves and is primarily the motor nerve of the diaphragm but also sends sensory fibers to the pericardium. A nerve that arises from the caudal cervical nerves and is primarily the motor nerve of the diaphragm but also sends sensory fibers to the pericardium. [TFD][VHOG] BAMS:phn BTO:0001063 EHDAA:4677 EMAPA:17813 FMA:6191 GAID:848 MA:0001170 MESH:D010791 NCIT:C52813 OpenCyc:Mx4rvtmdUJwpEbGdrcN5Y29ycA SCTID:280344009 UMLS:C0031774 VHOG:0000728 Wikipedia:Phrenic_nerve uberon diaphragmatic nerve nervus phrenicus phrenic UBERON:0001884 phrenic nerve http://upload.wikimedia.org/wikipedia/commons/3/3c/Gray806.png A nerve that arises from the caudal cervical nerves and is primarily the motor nerve of the diaphragm but also sends sensory fibers to the pericardium. VHOG:0000728 A nerve that arises from the caudal cervical nerves and is primarily the motor nerve of the diaphragm but also sends sensory fibers to the pericardium. [TFD][VHOG] 2012-09-17 VHOG:0000728 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/phrenic+nerve UMLS:C0031774 ncithesaurus:Phrenic_Nerve diaphragmatic nerve BTO:0001063 nervus phrenicus BTO:0001063 nervus phrenicus Wikipedia:Phrenic_nerve phrenic BTO:0001063 The most anterior region the brain including both the telencephalon and diencephalon. Most anterior of the three regions of the brain consisting of the telencephalon and diencephalon.[AAO] The most anterior region the brain including both the telencephalon and diencephalon. Kimmel et al, 1995.[TAO] relationship loss: develops_from forebrain neural tube (TAO:0007041)[TAO] In craniate embryos, neural expression of Distal-less-related genes is exclusively in the forebrain (...). Because the major neural expression domain of amphioxus AmphiDll is in the anterior three-fourths of the cerebral vesicle, we suggest that this region of the neural tube is homologous to parts of the craniate forebrain. This conclusion is strongly supported by three-dimensional, computer-assisted reconstruction of the neural tube of amphioxus based on serial transmission electron microscopy. At the neuroanatomical level, a number of detailed homologies are indicated between the anterior three-fourths of the amphioxus cerebral vesicle and the diencephalic region of the craniate forebrain. If one assumes that the amphioxus condition fairly represents the nervous system of the proximate ancestor of the craniates, one can suggest that they evolved from a creature that had the beginnings of a forebrain.[well established][VHOG] prosencephalic FB AAO:0010147 BAMS:FB BAMS:Forebrain BIRNLEX:1509 BTO:0000478 CALOHA:TS-0380 DHBA:10156 DMBA:15566 EFO:0000909 EHDAA2:0000556 EHDAA:3470 EMAPA:16895 FMA:61992 MA:0000170 MAT:0000105 MESH:D016548 MIAA:0000105 NCIT:C40185 SCTID:362291003 TAO:0000109 UMLS:C0085140 VHOG:0000383 Wikipedia:Forebrain XAO:0000011 ZFA:0000109 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=27 uberon prosencephalon UBERON:0001890 forebrain http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg definitional The most anterior region the brain including both the telencephalon and diencephalon. Wikipedia:Forebrain ZFIN:ZDB-PUB-961014-576 Most anterior of the three regions of the brain consisting of the telencephalon and diencephalon.[AAO] 2012-06-20 AAO:0010147 AAO AAO:BJB The most anterior region the brain including both the telencephalon and diencephalon. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000109 TAO ZFIN:curator relationship loss: develops_from forebrain neural tube (TAO:0007041)[TAO] 2012-08-14 TAO:0000109 TAO In craniate embryos, neural expression of Distal-less-related genes is exclusively in the forebrain (...). Because the major neural expression domain of amphioxus AmphiDll is in the anterior three-fourths of the cerebral vesicle, we suggest that this region of the neural tube is homologous to parts of the craniate forebrain. This conclusion is strongly supported by three-dimensional, computer-assisted reconstruction of the neural tube of amphioxus based on serial transmission electron microscopy. At the neuroanatomical level, a number of detailed homologies are indicated between the anterior three-fourths of the amphioxus cerebral vesicle and the diencephalic region of the craniate forebrain. If one assumes that the amphioxus condition fairly represents the nervous system of the proximate ancestor of the craniates, one can suggest that they evolved from a creature that had the beginnings of a forebrain.[well established][VHOG] 2012-09-17 VHOG:0000383 VHOG PMID:8787764 Holland ND, Panganiban G, Henyey EL, Holland LZ, Sequence and developmental expression of AmphiDll, an amphioxus Distal-less gene transcribed in the ectoderm, epidermis and nervous system: insights into evolution of craniate forebrain and neural crest. Development (1996) http://bgee.unil.ch/ FB BIRNLEX:1509 NIFSTD:NeuroNames_abbrevSource UMLS:C0085140 BIRNLEX:1509 UMLS:C0085140 ncithesaurus:Fore-Brain http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=27 BIRNLEX:1509 The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO]. developmental relationships need revised Middle part of the brain composed of the optic tectum and penducular region.[AAO] The brain region between the forebrain anteriorly and the hindbrain posteriorly, including the tectum dorsally and the midbrain tegmentum ventrally. Kimmel et al, 1995.[TAO] Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG] mesencephalic part of brainstem in ABA - we reject this in favor of ISBN:0471888893 which has an implicit overlaps relationships MB AAO:0010149 BAMS:MES BIRNLEX:1667 BM:MB BTO:0000138 CALOHA:TS-0630 DHBA:10648 DMBA:16649 EFO:0000919 EHDAA2:0001162 EHDAA:3694 EMAPA:16974 EV:0100242 FMA:61993 HBA:9001 MA:0000207 MAT:0000106 MBA:313 MESH:D008636 MIAA:0000106 NCIT:C12510 OpenCyc:Mx4rvsBUqpwpEbGdrcN5Y29ycA RETIRED_EHDAA2:0001104 SCTID:279099009 TAO:0000128 UMLS:C0025462 VHOG:0000069 Wikipedia:Midbrain XAO:0000014 ZFA:0000128 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=462 uberon mesencephalon UBERON:0001891 midbrain http://upload.wikimedia.org/wikipedia/commons/f/f9/Human_brain_inferior_view_description.JPG definitional Bgee:AN The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO]. GO:0030901 Middle part of the brain composed of the optic tectum and penducular region.[AAO] 2012-06-20 AAO:0010149 AAO AAO:BJB The brain region between the forebrain anteriorly and the hindbrain posteriorly, including the tectum dorsally and the midbrain tegmentum ventrally. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000128 TAO ZFIN:curator Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG] 2012-09-17 VHOG:0000069 VHOG DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999) http://bgee.unil.ch/ part of brainstem in ABA - we reject this in favor of ISBN:0471888893 which has an implicit overlaps relationships ABA MB BIRNLEX:1667 NIFSTD:NeuroNames_abbrevSource UMLS:C0025462 BIRNLEX:1667 UMLS:C0025462 ncithesaurus:Mesencephalon http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=462 BIRNLEX:1667 mesencephalon Wikipedia:Midbrain A segment of the developing hindbrain[ZFA]. In the vertebrate embryo, a rhombomere is a transiently divided segment of the developing neural tube, within the hindbrain region (a neuromere) in the area that will eventually become the rhombencephalon. The rhombomeres appear as a series of slightly constricted swellings in the neural tube, caudal to the cephalic flexure.[WP]. A segment of the developing hindbrain. Kimmel et al, 1995.[TAO] Rhombomeric segmentation is found in all living vertebrates and is of fundamental importance to the development of the vertebrate head.[well established][VHOG] In human embryonic development, the rhombomeres are present by day 29 DHBA divides this into A(1-3),B(4),C(5-7) and D(8) hindbrain segment segment of hindbrain DHBA:12664 EFO:0003617 EMAPA:16148 FMA:295666 MAT:0000272 MIAA:0000272 RETIRED_EHDAA2:0000669 TAO:0001064 VHOG:0000672 Wikipedia:Rhombomere XAO:0004079 ZFA:0001064 hindbrain neuromere hindbrain neuromeres rhombomere uberon future rhombencephalon rhombomeres UBERON:0001892 rhombomere hindbrain segment ZFA:0001064 segment of hindbrain ZFA:0001064 hindbrain neuromeres DHBA:HNM future rhombencephalon MIAA:0000272 rhombomeres VHOG:0000672 A segment of the developing hindbrain[ZFA]. In the vertebrate embryo, a rhombomere is a transiently divided segment of the developing neural tube, within the hindbrain region (a neuromere) in the area that will eventually become the rhombencephalon. The rhombomeres appear as a series of slightly constricted swellings in the neural tube, caudal to the cephalic flexure.[WP]. Wikipedia:Rhombomere ZFIN:curator A segment of the developing hindbrain. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0001064 TAO ZFIN:curator Rhombomeric segmentation is found in all living vertebrates and is of fundamental importance to the development of the vertebrate head.[well established][VHOG] 2012-09-17 VHOG:0000672 VHOG DOI:10.1006/dbio.2002.0831 Mazet F, Shimeld SM, The Evolution of Chordate Neural Segmentation. Developmental Biology (2002) http://bgee.unil.ch/ Part of the forebrain consisting of paired olfactory bulbs and cerebral hemispheres. Organ component of neuraxis that has as its parts the cerebral cortex, cerebral white matter, basal ganglia, septum and fornix, as well as subcortical gray and white matter structures[FMA:62000]. Part of the forebrain consisting of paired olfactory bulbs and cerebral hemispheres.[AAO] The anterior and dorsal forebrain neuromere, includes the olfactory bulb. Kimmel et al, 1995.[TAO] relationship loss: develops_from presumptive telencephalon (TAO:0000571)[TAO] From an evolutionary standpoint, the telencephalon is the most recent brain structure: the amphioxus does not have this structure as a morphological entity. Overt telencephalon is present in the hagfish and lamprey to receive numerous input fibers from various parts of the CNS, similar to gnathostomes.[well established][VHOG] cerebral telenencephalic In mammals the cortex covers almost the whole of the cerebral hemispheres. In ray-finned fishes and most pronounced in teleosts the roof plate of the embryonic telencephalon extends laterally with the effect that the paired alar plates forming the hemispheric walls roll out lateroventrally in a process called eversion. This is unlike the development in other vertebrate groups. [ZFA:0000079, ISBN:3764351209] In ray-finned fishes the inner surfaces of the lateral and ventral regions of the cerebrum bulge up into the ventricles. In the amniotes, the cerebrum becomes increasingly large and complex. In reptiles, the paleopallium is much larger than in amphibians, and its growth has pushed the basal nuclei into the central regions of the cerebrum. In the most primitive living vertebrates, the hagfishes and lampreys, the cerebrum is a relatively simple structure receiving nerve impulses from the olfactory bulb. The cerebrum of birds has evolved along different lines to that of mammals, although they are similarly enlarged, by comparison with reptiles. However, this enlargement is largely due to the basal ganglia, with the other areas remaining relatively primitive in structure. dolphins are the only species (other than humans) to have cerebra accounting for as much as 2 percent of their body weight. supratentorial region AAO:0010479 BAMS:CB BAMS:CH BAMS:IV BAMS:Tel BIRNLEX:1115 BM:Tel BTO:0000239 CALOHA:TS-1018 DHBA:10158 EFO:0000912 EHDAA2:0001982 EMAPA:16910 EV:0100165 FMA:62000 GAID:621 HBA:4007 MA:0000183 MAT:0000421 MBA:567 MESH:D013687 MIAA:0000421 PBA:128011350 SCTID:263353005 TAO:0000079 UMLS:C0039452 VHOG:0000283 Wikipedia:Telencephalon XAO:0000012 ZFA:0000079 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=31 cerebrum endbrain uberon UBERON:0001893 telencephalon Bgee:AN Part of the forebrain consisting of paired olfactory bulbs and cerebral hemispheres. AAO:0010479 XAO:0000012 Organ component of neuraxis that has as its parts the cerebral cortex, cerebral white matter, basal ganglia, septum and fornix, as well as subcortical gray and white matter structures[FMA:62000]. FMA:62000 Part of the forebrain consisting of paired olfactory bulbs and cerebral hemispheres.[AAO] 2012-06-20 AAO:0010479 AAO AAO:BJB The anterior and dorsal forebrain neuromere, includes the olfactory bulb. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000079 TAO ZFIN:curator relationship loss: develops_from presumptive telencephalon (TAO:0000571)[TAO] 2012-08-14 TAO:0000079 TAO From an evolutionary standpoint, the telencephalon is the most recent brain structure: the amphioxus does not have this structure as a morphological entity. Overt telencephalon is present in the hagfish and lamprey to receive numerous input fibers from various parts of the CNS, similar to gnathostomes.[well established][VHOG] 2012-09-17 VHOG:0000283 VHOG DOI:10.1016/j.ydbio.2005.02.008 Murakami Y, Uchida K, Rijli FM and Kuratani S, Evolution of the brain developmental plan: Insights from agnathans. Developmental Biology (2005) http://bgee.unil.ch/ In mammals the cortex covers almost the whole of the cerebral hemispheres. Wikipedia:Telencephalon#Variation_among_species In ray-finned fishes the inner surfaces of the lateral and ventral regions of the cerebrum bulge up into the ventricles. Wikipedia:Telencephalon#Variation_among_species In the amniotes, the cerebrum becomes increasingly large and complex. In reptiles, the paleopallium is much larger than in amphibians, and its growth has pushed the basal nuclei into the central regions of the cerebrum. Wikipedia:Telencephalon#Variation_among_species In the most primitive living vertebrates, the hagfishes and lampreys, the cerebrum is a relatively simple structure receiving nerve impulses from the olfactory bulb. Wikipedia:Telencephalon#Variation_among_species The cerebrum of birds has evolved along different lines to that of mammals, although they are similarly enlarged, by comparison with reptiles. However, this enlargement is largely due to the basal ganglia, with the other areas remaining relatively primitive in structure. Wikipedia:Telencephalon#Variation_among_species dolphins are the only species (other than humans) to have cerebra accounting for as much as 2 percent of their body weight. Wikipedia:Telencephalon#Variation_among_species supratentorial region Wikipedia:Tentorium_cerebelli UMLS:C0039452 BIRNLEX:1115 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=31 BIRNLEX:1115 cerebrum BTO:0000239 EMAPA:16910 FMA:62000 Wikipedia:Talk:Cerebrum/Archive_1 https://github.com/obophenotype/uberon/issues/1208 endbrain Swanson:2004 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=31 The division of the forebrain that develops from the foremost primary cerebral vesicle. The more posterior and ventral of two forebrain neuromeres, the other being the telencephalon; major derivatives are the eye cups, the brain pretectal region, the thalamus, hypothalamus, and epithalamus (including the habenula and epiphysis). Kimmel et al, 1995.[TAO] Unpaired part of the forebrain comprised of three major parts; the epithalamus, thalamus, and hypothalamus.[AAO] Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG] diencephalic in ABA, this is part of the brain stem DiE AAO:0010481 BAMS:DI BAMS:Di BAMS:DiE BAMS:IB BAMS:Zh. BIRNLEX:1503 BM:Die BTO:0000342 CALOHA:TS-0199 DHBA:10389 DMBA:16308 EFO:0000911 EHDAA2:0000385 EHDAA:1969 EHDAA:2645 EHDAA:3472 EMAPA:16896 EV:0100194 FMA:62001 GAID:618 HBA:4391 MA:0000171 MAT:0000420 MBA:1129 MESH:A08.186.211.730.385 MIAA:0000420 NCIT:C12456 OpenCyc:Mx4rwC-V0JwpEbGdrcN5Y29ycA PBA:128013010 SCTID:279328001 TAO:0000101 UMLS:C0012144 VHOG:0000318 Wikipedia:Diencephalon XAO:0000013 ZFA:0000101 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=288 between brain interbrain mature diencephalon thalamencephalon uberon betweenbrain diencephalon UBERON:0001894 diencephalon http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg definitional definitional The division of the forebrain that develops from the foremost primary cerebral vesicle. Wikipedia:Diencephalon not well differentiated from the cerebrum. (Ariens, p. 868) PMID:8932866 The more posterior and ventral of two forebrain neuromeres, the other being the telencephalon; major derivatives are the eye cups, the brain pretectal region, the thalamus, hypothalamus, and epithalamus (including the habenula and epiphysis). Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000101 TAO ZFIN:curator Unpaired part of the forebrain comprised of three major parts; the epithalamus, thalamus, and hypothalamus.[AAO] 2012-06-20 AAO:0010481 AAO AAO:BJB Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG] 2012-09-17 VHOG:0000318 VHOG DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999) http://bgee.unil.ch/ in ABA, this is part of the brain stem ABA DiE BIRNLEX:1503 NIFSTD:NeuroNames_abbrevSource UMLS:C0012144 BIRNLEX:1503 UMLS:C0012144 ncithesaurus:Diencephalon http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=288 BIRNLEX:1503 interbrain Swanson:2004 mature diencephalon FMA:62001 thalamencephalon MGI:anna betweenbrain BTO:0000342 diencephalon Wikipedia:Diencephalon Rostral segment of the hindbrain that has as its parts the pons (where present) and the cerebellum[WP,modified]. Anterior part of the hindbrain ventral to the cerebellum[BIRNLEX:965]. The anterior of two brain vesicles formed by specialization of the rhombencephalon in the developing embryo. It gives rise to cerebellum and pons. [TFD][VHOG] The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG] epencephalon BAMS:Met BIRNLEX:965 BTO:0000673 CALOHA:TS-2029 DHBA:10655 EHDAA2:0001149 EHDAA:5498 EMAPA:17071 FMA:62003 GAID:594 HBA:4833 MA:0000197 MESH:D020540 NCIT:C32741 UMLS:C0376353 UMLS:C1516904 VHOG:0000741 Wikipedia:Metencephalon http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=543 epencephalon-2 uberon UBERON:0001895 the terms metencephalon and myelencephalon are only meaningful in mammals and birds[Neuroanatomy of the Zebrafish Brain]. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata and thus these are not distinguished in ZFA[ZFA]. metencephalon http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg definitional Rostral segment of the hindbrain that has as its parts the pons (where present) and the cerebellum[WP,modified]. Wikipedia:Metencephalon https://github.com/obophenotype/uberon/issues/300 Anterior part of the hindbrain ventral to the cerebellum[BIRNLEX:965]. BIRNLEX:965 The anterior of two brain vesicles formed by specialization of the rhombencephalon in the developing embryo. It gives rise to cerebellum and pons. [TFD][VHOG] 2012-09-17 VHOG:0000741 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/metencephalon The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000741 VHOG ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500 http://bgee.unil.ch/ epencephalon ncithesaurus:Epencephalon UMLS:C0376353 BIRNLEX:965 UMLS:C1516904 ncithesaurus:Epencephalon http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=543 BIRNLEX:965 epencephalon-2 FMA:62003 Organ component of neuraxis that has as its parts the medullary reticular formation, inferior olivary complex and cochlear nuclear complex, among other structures[FMA]. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate[GO]. Posterior portion of the hindbrain which controls respiration, heartbeat, digestion, and swallowing as well as some locomotor responses.[AAO] The posterior region of the brain that is continuous with the spinal cord. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-17, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] Classical anatomical studies subdivided the vertebrate rhombencephalon into pons and medulla oblongata. (...) The medulla oblongata appears therefore as a tagma, that is, a group of segmental units (pseudorhombomeres, in this case) sharing some morphological and molecular characteristics, and in some aspects different from the segmental units present in adjoining brain regions, pons and spinal cord.[well established][VHOG] bulb medulla AAO:0010486 BAMS:MY BAMS:Md BIRNLEX:957 BM:Me BTO:0000041 CALOHA:TS-0607 DMBA:17352 EFO:0000924 EHDAA2:0001088 EHDAA:7588 EMAPA:17550 EV:0100275 FMA:62004 GAID:590 MA:0000206 MAT:0000111 MAT:0000367 MBA:354 MESH:D008526 MIAA:0000111 NCIT:C12442 OpenCyc:Mx4rvVjxSJwpEbGdrcN5Y29ycA OpenCyc:Mx4rwCqnXJwpEbGdrcN5Y29ycA SCTID:279104005 TAO:0000545 UMLS:C0025148 UMLS:C1269575 VHOG:0000181 Wikipedia:Bone_marrow_of_ovary_oblongata XAO:0003100 ZFA:0000545 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=698 bulbus uberon medulla oblonzata metepencephalon UBERON:0001896 medulla oblongata http://upload.wikimedia.org/wikipedia/commons/6/6b/Illu_pituitary_pineal_glands.jpg Organ component of neuraxis that has as its parts the medullary reticular formation, inferior olivary complex and cochlear nuclear complex, among other structures[FMA]. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate[GO]. FMA:62004 GO:0021550 Wikipedia:Bone_marrow_of_ovary_oblongata Posterior portion of the hindbrain which controls respiration, heartbeat, digestion, and swallowing as well as some locomotor responses.[AAO] 2012-06-20 AAO:0010486 AAO AAO:BJB The posterior region of the brain that is continuous with the spinal cord. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-17, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] 2012-09-17 VHOG:0000181 VHOG http://bgee.unil.ch/ Classical anatomical studies subdivided the vertebrate rhombencephalon into pons and medulla oblongata. (...) The medulla oblongata appears therefore as a tagma, that is, a group of segmental units (pseudorhombomeres, in this case) sharing some morphological and molecular characteristics, and in some aspects different from the segmental units present in adjoining brain regions, pons and spinal cord.[well established][VHOG] 2012-09-17 VHOG:0000181 VHOG DOI:10.1016/j.ydbio.2008.08.017 Marin F, Aroca P, Puelles L, Hox gene colinear expression in the avian medulla oblongata is correlated with pseudorhombomeric domains. Developmental Biology (2008) http://bgee.unil.ch/ medulla ABA:MY UMLS:C0025148 BIRNLEX:957 UMLS:C0025148 ncithesaurus:Medulla_Oblongata UMLS:C1269575 BIRNLEX:957 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=698 BIRNLEX:957 bulbus FMA:62004 FMA:TA medulla oblonzata Wikipedia:Medulla_oblongata metepencephalon FMA:62004 An endothelium that is part of a capillary [Automatically generated definition]. BTO:0004954 CALOHA:TS-0112 EMAPA:36292 FMA:62114 MA:0000711 NCIT:C49215 UMLS:C0006904 blood capillary endothelium capillary endothelium capillary vessel endothelium endothelium of blood capillary endothelium of capillary vessel uberon UBERON:0001915 endothelium of capillary An endothelium that is part of a capillary [Automatically generated definition]. OBOL:automatic UMLS:C0006904 ncithesaurus:Capillary_Endothelium blood capillary endothelium OBOL:automatic capillary vessel endothelium OBOL:automatic endothelium of blood capillary OBOL:automatic endothelium of capillary vessel OBOL:automatic An endothelium that is part of an arteriole [Automatically generated definition]. EMAPA:36286 FMA:62115 MA:0000705 NCIT:C49192 UMLS:C1179024 arteriole endothelium uberon UBERON:0001916 endothelium of arteriole An endothelium that is part of an arteriole [Automatically generated definition]. OBOL:automatic UMLS:C1179024 ncithesaurus:Arteriole_Endothelium An endothelium that is part of an artery [Automatically generated definition]. The endothelium is the thin layer of cells that lines the interior surface of blood vessels, forming an interface between circulating blood in the lumen and the rest of the vessel wall.[AAO] Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] AAO:0011013 BTO:0004757 EMAPA:35148 FMA:62116 MA:0000707 NCIT:C49194 UMLS:C1179025 VHOG:0001215 XAO:0000357 arterial endothelium artery endothelium uberon UBERON:0001917 endothelium of artery An endothelium that is part of an artery [Automatically generated definition]. OBOL:automatic The endothelium is the thin layer of cells that lines the interior surface of blood vessels, forming an interface between circulating blood in the lumen and the rest of the vessel wall.[AAO] 2012-06-20 AAO:0011013 AAO XAO:curator Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] 2012-09-17 VHOG:0001215 VHOG ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207 http://bgee.unil.ch/ UMLS:C1179025 ncithesaurus:Artery_Endothelium An endothelium that is part of a venule [Automatically generated definition]. EMAPA:36290 FMA:62117 MA:0000716 NCIT:C49319 UMLS:C1179026 venule endothelium uberon UBERON:0001918 endothelium of venule An endothelium that is part of a venule [Automatically generated definition]. OBOL:automatic UMLS:C1179026 ncithesaurus:Venule_Endothelium An endothelium that is part of a vein [Automatically generated definition]. Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] AAO:0011110 BTO:0004756 EMAPA:36288 FMA:62118 MA:0000712 NCIT:C49317 UMLS:C1179027 VHOG:0001216 XAO:0000358 vein endothelium venous endothelium uberon veinous endothelium UBERON:0001919 endothelium of vein An endothelium that is part of a vein [Automatically generated definition]. OBOL:automatic Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] 2012-09-17 VHOG:0001216 VHOG ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207 http://bgee.unil.ch/ UMLS:C1179027 ncithesaurus:Vein_Endothelium veinous endothelium VHOG:0001216 Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP]. Together, our results reveal a shared basic organization in the tegmental domains of the diencephalon and midbrain of developing lamprey, indicating early appearance of the domain in vertebrate phylogeny.[well established][VHOG] MTg tegmentum BAMS:MTg BIRNLEX:1200 BTO:0003388 DHBA:12195 EFO:0000921 EHDAA2:0004475 EMAPA:18215 FMA:62393 HBA:9002 MA:0000212 MAT:0000452 SCTID:362392007 TAO:0000160 UMLS:C0039441 VHOG:0001367 Wikipedia:Midbrain_tegmentum XAO:0004271 ZFA:0000160 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=491 tegmentum mesencephali tegmentum of midbrain uberon mesencephalic tegmentum tegmentum mesencephalicum UBERON:0001943 'tegmentum' is used generically for the ventral part of the brainstem (ISBN:0471888893). We use the label 'midbrain tegmentum' to denote the midbrain structure. In NIFSTD tegmentum is a composite structure and there is a separate class for midbrain tegmentum and pontine tegmentum midbrain tegmentum http://upload.wikimedia.org/wikipedia/commons/b/b6/Gray712.png ZFA Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP]. FMA:FMA ISBN:0471888893 Wikipedia:Midbrain_tegmentum Together, our results reveal a shared basic organization in the tegmental domains of the diencephalon and midbrain of developing lamprey, indicating early appearance of the domain in vertebrate phylogeny.[well established][VHOG] 2012-09-17 VHOG:0001367 VHOG DOI:10.1016/j.brainresbull.2005.05.001 Villar-Cheda B, Abalo XM, Anadon R, Rodicio MC, The tegmental proliferation region in the sea lamprey. Brain Research Bulletin (2005) http://bgee.unil.ch/ MTg BIRNLEX:1200 NIFSTD:NeuroNames_abbrevSource tegmentum ISBN:0471888893 UMLS:C0039441 BIRNLEX:1200 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=491 BIRNLEX:1200 tegmentum mesencephali Wikipedia:Midbrain_tegmentum mesencephalic tegmentum VHOG:0001367 tegmentum mesencephalicum NeuroNames:491 A multi-tissue structure that is part of a spinal cord. BIRNLEX:1496 NCIT:C33969 SCTID:244437008 UMLS:C1268166 uberon spinal cord part UBERON:0001948 regional part of spinal cord A multi-tissue structure that is part of a spinal cord. OBOL:automatic UMLS:C1268166 ncithesaurus:Spinal_Cord_Part An area of cerebral cortex defined on the basis of cytoarchitecture that have six layers. Starting from the cortical surface the layers are: molecular layer (I), external granular layer (II), external pyramidal layer (III), internal granular layer (IV), internal pyramidal layer (V), and multiform layer (VI). Neocortex is most prominent in the frontal lobe, the parietal lobe, the temporal lobe and the occipital lobe, less so in the cingulate gyrus, the parahippocampal gyrus and the insula. It is composed of two subdivisions: true isocortex and proisocortex (Carpenter-83)(NN) The 6-layer neocortex is well conserved in all extant mammals, but not present in birds or reptils BAMS:ISO BAMS:Iso-cortex BAMS:NCX BIRNLEX:2547 BTO:0000920 DHBA:10160 EHDAA2:0004662 EMAPA:32842 EMAPA:35589 FMA:62429 GAID:677 MA:0002754 MBA:315 MESH:A08.186.211.730.885.213.420 PBA:294021746 UMLS:C0175173 Wikipedia:Neocortex http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=757 cerebral neocortex homogenetic cortex homotypical cortex isocortex (sensu lato) neocortex (isocortex) neopallial cortex neopallium isocortex uberon iso-cortex nonolfactory cortex nucleus hypoglossalis UBERON:0001950 neocortex http://upload.wikimedia.org/wikipedia/commons/7/77/Neocortex.jpg Wikipedia An area of cerebral cortex defined on the basis of cytoarchitecture that have six layers. Starting from the cortical surface the layers are: molecular layer (I), external granular layer (II), external pyramidal layer (III), internal granular layer (IV), internal pyramidal layer (V), and multiform layer (VI). Neocortex is most prominent in the frontal lobe, the parietal lobe, the temporal lobe and the occipital lobe, less so in the cingulate gyrus, the parahippocampal gyrus and the insula. It is composed of two subdivisions: true isocortex and proisocortex (Carpenter-83)(NN) BIRNLEX:2547 OldNeuroNames:754 The 6-layer neocortex is well conserved in all extant mammals, but not present in birds or reptils PMID:23027930 UMLS:C0175173 BIRNLEX:2547 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=757 BIRNLEX:2547 homogenetic cortex ISBN:0471888893 homotypical cortex BIRNLEX:2547 isocortex (sensu lato) FMA:62429 neocortex (isocortex) DHBA:10160 isocortex BRAINSPAN:BRAINSPAN iso-cortex BAMS:iso-cortex nonolfactory cortex BTO:0000920 nucleus hypoglossalis NeuroNames:757 The liquid component of blood, in which erythrocytes are suspended. plasma portion of plasma BTO:0000131 CALOHA:TS-0800 EFO:0001905 EMAPA:35690 FMA:62970 GAID:1178 MA:0002501 MAT:0000052 MESH:D010949 MIAA:0000052 NCIT:C13356 OpenCyc:Mx4rEg4ZYrIbEduAAAAOpmP6tw UMLS:C0032105 Wikipedia:Blood_plasma blood plasm portion of blood plasma uberon UBERON:0001969 blood plasma The liquid component of blood, in which erythrocytes are suspended. http://orcid.org/0000-0002-6601-2165 plasma MA:0002501 portion of plasma FMA:62970 UMLS:C0032105 ncithesaurus:Plasma . BTO:0000501 FMA:62972 GAID:1160 MA:0002519 MESH:D005750 NCIT:C32661 UMLS:C0017133 Wikipedia:Gastric_juice galen:GastricJuice stomach secretion uberon succus gastricus UBERON:0001971 gastric juice . Wikipedia:Gastric_juice UMLS:C0017133 ncithesaurus:Gastric_Secretion succus gastricus BTO:0000501 A submucosa that is part of a esophagus [Automatically generated definition]. BTO:0002109 EMAPA:35325 FMA:62997 MA:0002724 SCTID:362128009 esophageal submucosa esophagus submucosa gullet submucosa oesophagus submucosa submucosa of esophagus submucosa of gullet submucosa of oesophagus tela submucosa (oesophagus) tela submucosa esophagi tela submucosa oesophageae tela submucosa of esophagus uberon submucous layer of esophagus tela submucosa oesophagi UBERON:0001972 submucosa of esophagus A submucosa that is part of a esophagus [Automatically generated definition]. OBOL:automatic gullet submucosa OBOL:automatic oesophagus submucosa OBOL:automatic submucosa of gullet OBOL:automatic submucosa of oesophagus OBOL:automatic tela submucosa (oesophagus) FMA:62997 FMA:TA tela submucosa esophagi BTO:0002109 tela submucosa oesophageae FMA:62997 FMA:TA submucous layer of esophagus BTO:0002109 tela submucosa oesophagi BTO:0002109 A lamina propria that is part of a esophagus [Automatically generated definition]. EMAPA:26987 FMA:63050 MA:0001568 NCIT:C49223 UMLS:C1707949 esophagus lamina propria esophagus lamina propria mucosa esophagus lamina propria mucosae gullet lamina propria gullet lamina propria mucosa gullet lamina propria mucosae lamina propria mucosa of esophagus lamina propria mucosa of gullet lamina propria mucosa of oesophagus lamina propria mucosae of esophagus lamina propria mucosae of gullet lamina propria mucosae of oesophagus lamina propria of gullet lamina propria of oesophagus oesophagus lamina propria mucosa oesophagus lamina propria mucosae uberon esophageal lamina propria oesophagus lamina propria UBERON:0001974 lamina propria of esophagus FMA A lamina propria that is part of a esophagus [Automatically generated definition]. OBOL:automatic UMLS:C1707949 ncithesaurus:Esophageal_Lamina_Propria esophagus lamina propria mucosa OBOL:automatic esophagus lamina propria mucosae OBOL:automatic gullet lamina propria OBOL:automatic gullet lamina propria mucosa OBOL:automatic gullet lamina propria mucosae OBOL:automatic lamina propria mucosa of esophagus OBOL:automatic lamina propria mucosa of gullet OBOL:automatic lamina propria mucosa of oesophagus OBOL:automatic lamina propria mucosae of gullet OBOL:automatic lamina propria mucosae of oesophagus OBOL:automatic lamina propria of gullet OBOL:automatic lamina propria of oesophagus OBOL:automatic oesophagus lamina propria mucosa OBOL:automatic oesophagus lamina propria mucosae OBOL:automatic esophageal lamina propria EMAPA:26987 A serous membrane that is part of a esophagus [Automatically generated definition]. EMAPA:35322 FMA:63057 MA:0001571 esophagus serosa esophagus serous membrane gullet serosa gullet serous membrane oesophagus serous membrane serosa of abdominal part of esophagus serosa of gullet serosa of oesophagus serous coat of oesophagus serous membrane of esophagus serous membrane of gullet serous membrane of oesophagus tunica serosa oesophageae uberon oesophagus serosa UBERON:0001975 serosa of esophagus A serous membrane that is part of a esophagus [Automatically generated definition]. OBOL:automatic esophagus serous membrane OBOL:automatic gullet serosa OBOL:automatic gullet serous membrane OBOL:automatic oesophagus serous membrane OBOL:automatic serosa of gullet OBOL:automatic serous membrane of esophagus OBOL:automatic serous membrane of gullet OBOL:automatic serous membrane of oesophagus OBOL:automatic tunica serosa oesophageae FMA:63057 FMA:TA the epithelial layer that lines the luminal space of the esophagus TODO check epithelium types: in FMA: Nonkeratinizing stratified squamous epithelium; mouse has basal and squamous subtypes; in ZFA it is columnar Simple columnar epithelium that lines the esophagus. Chen et al, 2007.[TAO] BTO:0001578 CALOHA:TS-0698 EFO:0003041 EHDAA2:0001287 EMAPA:16835 FMA:63063 MA:0001565 NCIT:C49221 TAO:0001499 UMLS:C1179544 ZFA:0001499 epithelial tissue of esophagus epithelial tissue of gullet epithelial tissue of oesophagus epithelium of gullet epithelium of oesophagus esophageal epithelium esophagus epithelial tissue esophagus epithelium gullet epithelial tissue gullet epithelium oesophagus epithelial tissue uberon oesophagus epithelium UBERON:0001976 epithelium of esophagus FMA the epithelial layer that lines the luminal space of the esophagus ISBN:0-683-40008-8 MP:0000468 Simple columnar epithelium that lines the esophagus. Chen et al, 2007.[TAO] 2012-08-14 TAO:0001499 TAO ZFIN:curator UMLS:C1179544 ncithesaurus:Esophageal_Epithelium epithelial tissue of esophagus OBOL:automatic epithelial tissue of gullet OBOL:automatic epithelial tissue of oesophagus OBOL:automatic epithelium of gullet OBOL:automatic epithelium of oesophagus OBOL:automatic esophagus epithelial tissue OBOL:automatic gullet epithelial tissue OBOL:automatic gullet epithelium OBOL:automatic oesophagus epithelial tissue OBOL:automatic One of the minute vessels that collect deoxygenated blood from the capillary plexuses returns it to the veins Multi-tissue structure part of the blood vasculature formed by the anastomosis of capillaries. Venules carry blood toward the heart.[TAO] BTO:0002626 EMAPA:35917 FMA:63130 MA:0000071 MESH:A07.231.432.952 NCIT:C12818 SCTID:341687009 TAO:0005315 UMLS:C0042520 VHOG:0001765 Wikipedia:Venule ZFA:0005315 uberon venula UBERON:0001979 venule Illu:capillary.jpg One of the minute vessels that collect deoxygenated blood from the capillary plexuses returns it to the veins MESH:A07.231.432.952 MP:0004125 Multi-tissue structure part of the blood vasculature formed by the anastomosis of capillaries. Venules carry blood toward the heart.[TAO] 2012-08-14 TAO:0005315 TAO ZFIN:curator UMLS:C0042520 ncithesaurus:Venule venula Wikipedia:Venule The smallest division of the artery located between the muscular arteries and the capillaries[GO]. Multi-tissue structure part of the blood vasculature, feeds into capillaries. Arterioles carry blood away from the heart.[TAO] Small, terminal branch of an artery which generally connects to capillaries.[AAO] AAO:0010253 BTO:0001997 EMAPA:35146 FMA:63182 MA:0000063 MESH:D001160 NCIT:C12672 SCTID:337724002 TAO:0002138 UMLS:C0003847 VHOG:0001763 Wikipedia:Arteriole ZFA:0005255 uberon arteriola UBERON:0001980 arteriole Illu:capillary.jpg MA The smallest division of the artery located between the muscular arteries and the capillaries[GO]. GO:0014830 Multi-tissue structure part of the blood vasculature, feeds into capillaries. Arterioles carry blood away from the heart.[TAO] 2012-08-14 TAO:0002138 TAO ZFIN:curator Small, terminal branch of an artery which generally connects to capillaries.[AAO] 2012-06-20 AAO:0010253 AAO AAO:BJB UMLS:C0003847 ncithesaurus:Arteriole arteriola Wikipedia:Arteriole A vessel through which blood circulates in the body. consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG] Any of the vessels through which blood circulates in the body.[AAO] The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] annelids have blood vessels, but this class is not applicable to annelids. FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX vascular element AAO:0011004 AEO:0000207 BTO:0001102 CALOHA:TS-0080 EFO:0000817 EHDAA2:0003252 EHDAA:240 EMAPA:32743 EMAPA:35993 FMA:50722 FMA:63183 GAID:169 MA:0000060 MAT:0000393 MESH:D001808 NCIT:C12679 NLXANAT:090901 OpenCyc:Mx4rvVjxlpwpEbGdrcN5Y29ycA SCTID:361097006 TAO:0002137 UMLS:C0005847 VHOG:0001250 Wikipedia:Blood_vessel XAO:0001011 ZFA:0005314 region of vascular tree organ vascular tree organ region uberon vas sanguineum UBERON:0001981 blood vessel http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg AEO EHDAA2 GO:0072360 A vessel through which blood circulates in the body. BTO:0001102 Wikipedia:Blood_vessel Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG] 2012-09-17 VHOG:0001250 VHOG http://bgee.unil.ch/ Any of the vessels through which blood circulates in the body.[AAO] 2012-06-20 AAO:0011004 AAO AAO:EJS The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] 2012-09-17 VHOG:0001250 VHOG DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006) http://bgee.unil.ch/ FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX FMA vascular element EMAPA:35993 UMLS:C0005847 ncithesaurus:Blood_Vessel region of vascular tree organ FMA:50722 vascular tree organ region FMA:50722 vas sanguineum Wikipedia:Blood_vessel Any of the smallest blood vessels connecting arterioles with venules. not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element Any of the tiny blood vessels connecting the arterioles to the venules.[AAO] The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] capillaries lack tunica media and tunica adventitia; only the endothelial wall of the tunica intima belongs AAO:0010252 BTO:0002045 CALOHA:TS-2006 EFO:0001906 EMAPA:35198 EV:0100035 FMA:63194 MA:0000065 MESH:A07.231.432.410 NCIT:C12685 NLXANAT:090902 OpenCyc:Mx4rvWEU-5wpEbGdrcN5Y29ycA TAO:0005250 UMLS:C0935624 VHOG:0001253 Wikipedia:Capillary XAO:0000116 ZFA:0005250 blood capillary capillary vessel uberon UBERON:0001982 capillary http://upload.wikimedia.org/wikipedia/commons/2/2f/A_red_blood_cell_in_a_capillary,_pancreatic_tissue_-_TEM.jpg FMA MA XAO ZFA Any of the smallest blood vessels connecting arterioles with venules. ISBN:0073040584 Wikipedia:Capillary https://github.com/obophenotype/uberon/issues/137 Any of the tiny blood vessels connecting the arterioles to the venules.[AAO] 2012-06-20 AAO:0010252 AAO AAO:BJB The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] 2012-09-17 VHOG:0001253 VHOG DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006) http://bgee.unil.ch/ UMLS:C0935624 ncithesaurus:Capillary A monolayer of specialized, flattened, mitochondria-rich cells that lines the posterior surface of the cornea and faces the anterior chamber of the eye[WP]. CALOHA:TS-0172 EMAPA:35935 FMA:63882 GAID:891 MA:0001242 MESH:D004728 NCIT:C12707 SCTID:368827009 TAO:0002186 UMLS:C0014259 Wikipedia:Corneal_endothelium ZFA:0001687 cornea endothelium endothelium of cornea uberon epithelium posterius corneae UBERON:0001985 corneal endothelium http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png A monolayer of specialized, flattened, mitochondria-rich cells that lines the posterior surface of the cornea and faces the anterior chamber of the eye[WP]. Wikipedia:Corneal_endothelium UMLS:C0014259 ncithesaurus:Corneal_Endothelium cornea endothelium OBOL:automatic endothelium of cornea OBOL:automatic epithelium posterius corneae Wikipedia:Corneal_endothelium A layer of epithelium that lines the heart, blood vessels (endothelium, vascular), lymph vessels (endothelium, lymphatic), and the serous cavities of the body[MESH]. Simple squamous epithelium which lines blood and lymphatic vessels and the heart[FMA] endothelial BTO:0000393 CALOHA:TS-0278 EFO:0002548 FMA:63916 GAID:520 MESH:D004727 NCIT:C12481 SCTID:27168002 UMLS:C0014257 galen:Endothelium uberon UBERON:0001986 The term 'endothelium' has been either restricted to the continuous cell layer of the vertebrates, as we are assuming here, or applied to all the cells able to adhere to the luminal surface of the vascular basement membrane (Casley-Smith 1980) endothelium FMA-text-def https://github.com/obophenotype/uberon/issues/225 A layer of epithelium that lines the heart, blood vessels (endothelium, vascular), lymph vessels (endothelium, lymphatic), and the serous cavities of the body[MESH]. Simple squamous epithelium which lines blood and lymphatic vessels and the heart[FMA] FMA:63916 MESH:A10.272.491 https://github.com/obophenotype/uberon/issues/225 UMLS:C0014257 ncithesaurus:Endothelium Portion of semisolid bodily waste discharged through the anus[MW,modified] Excretion in semisolid state processed by the intestine.[FMA] fecal excreta BTO:0000440 CALOHA:TS-2345 ENVO:00002003 FMA:64183 GAID:1199 MA:0002509 MAT:0000053 MESH:D005243 MIAA:0000053 NCIT:C13234 OpenCyc:Mx4rvVjJMZwpEbGdrcN5Y29ycA UMLS:C0015733 Wikipedia:Feces galen:Feces faeces fecal material fecal matter piece of shit portion of excrement portion of faeces portion of fecal material portion of fecal matter portion of feces portionem cacas stool cow dung cow pat dung fewmet frass guano portion of dung portion of guano portion of scat scat spraint uberon droppings excrement ordure spoor UBERON:0001988 feces Portion of semisolid bodily waste discharged through the anus[MW,modified] Wikipedia:Feces http://www.merriam-webster.com/dictionary/feces Excretion in semisolid state processed by the intestine.[FMA] FMA:64183 UMLS:C0015733 ncithesaurus:Feces piece of shit PMID:23285307 portionem cacas cow dung Wikipedia:Cow_dung cow pat Wikipedia:Cow_dung fewmet Wikipedia:Fewmet frass Wikipedia:Frass guano Wikipedia:Guano spraint Wikipedia:Spraint excrement BTO:0000440 An artery that carries deoxygenated blood from heart to the lungs. They are the only arteries (other than umbilical arteries in the fetus) that carry deoxygenated blood.. Major artery which supplies blood to the lungs.[AAO] One of two arteries, leaving from the heart, the left one supplying the left lung and the right one supplying the right lung. [TFD][VHOG] On the other hand, in the sister clade of the actinopterygians, the sarcopterygians, the gill circulation is supplemented with lung ventilation. As a result, the pulmonary artery and vein and a functional ductus arteriosus arose as a major evolutionary innovation from the sixth arch, giving the organism a flexible shunt to balance blood supply to and from gills and lungs according to environmental conditions.[well established][VHOG] In the human heart, the pulmonary trunk (pulmonary artery or main pulmonary artery) begins at the base of the right ventricle. It is short and wide - approximately 5 cm (2 inches) in length and 3 cm (1.2 inches) in diameter. It then branches into two pulmonary arteries (left and right), which deliver deoxygenated blood to the corresponding lung[WP] AAO:0010221 BTO:0000778 CALOHA:TS-0839 EFO:0001399 EHDAA2:0001575 EHDAA:4351 EMAPA:17008 FMA:66326 GAID:505 MA:0002031 MESH:D011651 NCIT:C12774 OpenCyc:Mx4rvVjbIpwpEbGdrcN5Y29ycA SCTID:181380003 UMLS:C0034052 VHOG:0000982 Wikipedia:Pulmonary_artery XAO:0004162 galen:PulmonaryArtery pulmonary arterial tree pulmonary arterial tree organ part uberon arteria pulmonalis pulmonary arterial subtree truncus pulmonalis UBERON:0002012 pulmonary artery Alveoli:diagram.png Wikipedia EHDAA2 XAO EHDAA2 An artery that carries deoxygenated blood from heart to the lungs. They are the only arteries (other than umbilical arteries in the fetus) that carry deoxygenated blood.. Wikipedia:Pulmonary_artery http://orcid.org/0000-0002-6601-2165 Major artery which supplies blood to the lungs.[AAO] 2012-06-20 AAO:0010221 AAO AAO:BJB One of two arteries, leaving from the heart, the left one supplying the left lung and the right one supplying the right lung. [TFD][VHOG] 2012-09-17 VHOG:0000982 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/pulmonary+artery On the other hand, in the sister clade of the actinopterygians, the sarcopterygians, the gill circulation is supplemented with lung ventilation. As a result, the pulmonary artery and vein and a functional ductus arteriosus arose as a major evolutionary innovation from the sixth arch, giving the organism a flexible shunt to balance blood supply to and from gills and lungs according to environmental conditions.[well established][VHOG] 2012-09-17 VHOG:0000982 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620 http://bgee.unil.ch/ UMLS:C0034052 ncithesaurus:Pulmonary_Artery pulmonary arterial tree FMA:66326 pulmonary arterial tree organ part FMA:66326 arteria pulmonalis Wikipedia:Pulmonary_artery pulmonary arterial subtree FMA:66326 truncus pulmonalis Wikipedia:Pulmonary_artery Pulmonary veins are blood vessels that transport blood from the lungs to the heart[GO]. Any of the veins which collect blood from the lungs and some small vesicles received from the esophagus.[AAO] One of two pairs of large vessels that return oxygenated blood from each lung to the left atrium of the heart. [TFD][VHOG] the veins that return oxygenated blood from the lungs to the left atrium of the heart On the other hand, in the sister clade of the actinopterygians, the sarcopterygians, the gill circulation is supplemented with lung ventilation. As a result, the pulmonary artery and vein and a functional ductus arteriosus arose as a major evolutionary innovation from the sixth arch, giving the organism a flexible shunt to balance blood supply to and from gills and lungs according to environmental conditions.[well established][VHOG] AAO:0010521 BTO:0001799 CALOHA:TS-0840 EHDAA2:0001579 EHDAA:2629 EMAPA:18645 FMA:66643 GAID:543 MA:0002206 MESH:D011667 NCIT:C12776 SCTID:430160002 UMLS:C0034090 VHOG:0001133 Wikipedia:Pulmonary_vein XAO:0000394 galen:PulmonaryVein pulmonary venous tree organ part uberon venae pulmonales UBERON:0002016 pulmonary vein Alveoli:diagram.png Pulmonary veins are blood vessels that transport blood from the lungs to the heart[GO]. GO:0060577 Any of the veins which collect blood from the lungs and some small vesicles received from the esophagus.[AAO] 2012-06-20 AAO:0010521 AAO AAO:BJB One of two pairs of large vessels that return oxygenated blood from each lung to the left atrium of the heart. [TFD][VHOG] 2012-09-17 VHOG:0001133 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/pulmonary+vein the veins that return oxygenated blood from the lungs to the left atrium of the heart MP:0002726,MGI:cwg On the other hand, in the sister clade of the actinopterygians, the sarcopterygians, the gill circulation is supplemented with lung ventilation. As a result, the pulmonary artery and vein and a functional ductus arteriosus arose as a major evolutionary innovation from the sixth arch, giving the organism a flexible shunt to balance blood supply to and from gills and lungs according to environmental conditions.[well established][VHOG] 2012-09-17 VHOG:0001133 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620 http://bgee.unil.ch/ UMLS:C0034090 ncithesaurus:Pulmonary_Vein venae pulmonales Wikipedia:Pulmonary_vein Soft tissue that lines the non-cartilaginous surfaces within joints with cavities (synovial joints). Phylogenetically, synovium is one of the newer attributes of the vertebrate locomotor apparatus. The first synovial joints developed in the piscine jaw of ancestors of modern lungfish by an evolutionary process that modified preexisting fibrous and cartilaginous joints, which were the predominant articulation of the early sea- and land-dwelling vertebrates.[well established][VHOG] synovial layer synovial membrane synovium AEO:0000181 BTO:0001823 EFO:0001393 EHDAA2_RETIRED:0003181 EMAPA:37476 EV:0100143 FMA:9865 GAID:264 MA:0000114 MESH:D013583 NCIT:C12473 SCTID:361828005 UMLS:C0039099 VHOG:0001282 Wikipedia:Synovial_membrane galen:SynovialMembrane membrana synovialis (capsula articularis) membrana synovialis capsulae articularis stratum synoviale stratum synoviale (capsula articularis) uberon synovial layer of articular capsule of synovial joint synovial membrane of articular capsule of synovial joint synovium of articular capsule of synovial joint UBERON:0002018 synovial membrane of synovial joint http://upload.wikimedia.org/wikipedia/commons/1/19/Joint.png http://upload.wikimedia.org/wikipedia/commons/5/5d/Synovium.png FMA EHDAA2 GAID Soft tissue that lines the non-cartilaginous surfaces within joints with cavities (synovial joints). Wikipedia:Synovial_membrane Phylogenetically, synovium is one of the newer attributes of the vertebrate locomotor apparatus. The first synovial joints developed in the piscine jaw of ancestors of modern lungfish by an evolutionary process that modified preexisting fibrous and cartilaginous joints, which were the predominant articulation of the early sea- and land-dwelling vertebrates.[well established][VHOG] 2012-09-17 VHOG:0001282 VHOG PMID:11068553 O'Connel JX, Pathology of the synovium. American Journal of Clinical Pathology (2000) http://bgee.unil.ch/ synovial layer FMA:66762 synovial membrane AEO:0000181 synovium BTO:0001823 VHOG:0001282 EMAPA:37476 MA:th UMLS:C0039099 ncithesaurus:Synovial_Membrane membrana synovialis (capsula articularis) FMA:9865 FMA:TA membrana synovialis capsulae articularis Wikipedia:Synovial_membrane stratum synoviale FMA:66762 FMA:TA stratum synoviale (capsula articularis) FMA:9865 FMA:TA synovial layer of articular capsule of synovial joint FMA:9865 synovial membrane of articular capsule of synovial joint FMA:9865 synovium of articular capsule of synovial joint FMA:9865 A cranial nerve that originates from neurons in the medulla and in the cervical spinal cord. A small motor nerve which emerges from the lateral wall of the medulla with the roots of the vagus nerve, and innervates a single pectoral suspensory muscle, the m.cucullaris. Cranial nerve that innervates the sternocleidomastoid and trapezius complex of muscles. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-1, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] Small motor nerve which innervates a single pectoral suspensory muscle, the m. cucullaris.[AAO] Cranial nerves XI and XII evolved in the common ancestor to amniotes (non-amphibian tetrapods) thus totalling twelve pairs.[well established][VHOG] In mice, the spinal branch of this motor nerve innervates the trapezius and the sternocleidomastoid muscles. The cranial branch joins the vagus nerve and innervates the same targets as the vagus nerve FMA has distinct cranial and spinal parts - WP says 'Traditional descriptions of the accessory nerve divide it into two parts: a spinal part and a cranial part.[1] However, because the cranial component rapidly joins the vagus nerve, becoming an integral part of said nerve, modern descriptions often consider the cranial component to be part of the vagus nerve and not part of the accessory nerve proper.[2] AAO:0010476 BAMS:11n BAMS:XIn BIRNLEX:812 EHDAA2:0000106 EHDAA:2855 EMAPA:17265 FMA:6720 FMA:80284 GAID:825 HBA:9340 MA:0001088 MBA:717 MESH:D000055 NCIT:C32041 OpenCyc:Mx4rwTEwI5wpEbGdrcN5Y29ycA SCTID:362469008 UMLS:C0000905 UMLS:C1305777 VHOG:0000699 Wikipedia:Spinal_accessory_nerve XAO:0004214 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=2085 Willis' nerve accessory XI accessory XI nerve accessory nerve accessory nerve [XI] cervical accessory nerve cranial nerve XI eleventh cranial nerve nervus accessorius [XI] pars spinalis nervus accessorius radix spinalis nervus accessorius spinal accessory nerve spinal accessory nerve tree spinal part of accessory nerve uberon CN-XI accessory spinal nerve UBERON:0002019 accessory XI nerve http://upload.wikimedia.org/wikipedia/commons/5/5e/Gray791.png A cranial nerve that originates from neurons in the medulla and in the cervical spinal cord. BIRNLEX:812 http://orcid.org/0000-0002-6601-2165 http://code.google.com/p/xenopus-anatomy-ontology/issues/detail?id=7 VHOG Wikipedia A small motor nerve which emerges from the lateral wall of the medulla with the roots of the vagus nerve, and innervates a single pectoral suspensory muscle, the m.cucullaris. ISBN:080184780X XAO:0004214 Cranial nerve that innervates the sternocleidomastoid and trapezius complex of muscles. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-1, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] 2012-09-17 VHOG:0000699 VHOG http://bgee.unil.ch/ Small motor nerve which innervates a single pectoral suspensory muscle, the m. cucullaris.[AAO] 2012-06-20 AAO:0010476 AAO AAO:EJS Cranial nerves XI and XII evolved in the common ancestor to amniotes (non-amphibian tetrapods) thus totalling twelve pairs.[well established][VHOG] 2012-09-17 VHOG:0000699 VHOG Wikipedia:Cranial_nerves http://bgee.unil.ch/ In mice, the spinal branch of this motor nerve innervates the trapezius and the sternocleidomastoid muscles. The cranial branch joins the vagus nerve and innervates the same targets as the vagus nerve GO FMA has distinct cranial and spinal parts - WP says 'Traditional descriptions of the accessory nerve divide it into two parts: a spinal part and a cranial part.[1] However, because the cranial component rapidly joins the vagus nerve, becoming an integral part of said nerve, modern descriptions often consider the cranial component to be part of the vagus nerve and not part of the accessory nerve proper.[2] FMA UMLS:C0000905 BIRNLEX:812 UMLS:C0000905 ncithesaurus:Accessory_Nerve UMLS:C1305777 BIRNLEX:812 accessory XI EHDAA2:0000106 cranial nerve XI BIRNLEX:812 eleventh cranial nerve BIRNLEX:812 nervus accessorius [XI] FMA:6720 FMA:TA pars spinalis nervus accessorius FMA:6720 FMA:TA radix spinalis nervus accessorius FMA:6720 FMA:TA spinal accessory nerve FMA:6720 CN-XI VHOG:0000699 accessory spinal nerve BAMS:XIn A nervous system structure composed primarily of nerve cell bodies (somas). May also include dendrites and the initial unmyelinated portion of axons. Multi-tissue comprised of neurons, dendrites, axon terminals, glial cells, and capillaries.[TAO] AEO:0001012 EHDAA2:0003136 EHDAA2_RETIRED:0004658 EMAPA:37596 FMA:67242 HBA:4006 MA:0001112 NCIT:C32695 OpenCyc:Mx4rwDdKMpwpEbGdrcN5Y29ycA TAO:0002197 UMLS:C0018220 VHOG:0001768 Wikipedia:Gray_matter ZFA:0001681 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=2869 gray matter gray matter of neuraxis grey matter grey matter of neuraxis grey substance neuronal grey matter substantia grisea uberon gray mater grisea UBERON:0002020 gray matter Spinal:nerve.svg A nervous system structure composed primarily of nerve cell bodies (somas). May also include dendrites and the initial unmyelinated portion of axons. Wikipedia:Gray_matter http://orcid.org/0000-0002-6601-2165 Multi-tissue comprised of neurons, dendrites, axon terminals, glial cells, and capillaries.[TAO] 2012-08-14 TAO:0002197 TAO ZFIN:curator EMAPA:37596 MA:th UMLS:C0018220 ncithesaurus:Gray_Matter gray matter of neuraxis FMA:67242 neuronal grey matter AEO:0001012 substantia grisea FMA:67242 FMA:TA gray mater ZFA:0001681 grisea the deepest layer of the epidermis, which is composed of dividing stem cells and anchoring cells replaces damaged cells on outside of body consisting of non-keratinized, viable cells, in contrast to the outer (upper) layer of epidermis made up of keratinized, anucleated, non-viable cells Malpighian layer rete Malphighii rete Malpighii stratum Malpighi stratum basale stratum germinosum AAO:0010598 BTO:0000438 EMAPA:32779 FMA:67540 MA:0000803 NCIT:C33466 NCIT:C33623 SCTID:419481005 TAO:0001180 UMLS:C0221925 Wikipedia:Stratum_germinativum XAO:0000041 ZFA:0001180 basal cell layer of epidermis basal epidermal layer epidermal basal stratum epidermis stratum basale stratum basalis of epidermis stratum germinativum stratum germinosum of epidermis uberon basal cell layer of skin basal layer of epidermis epidermis basal layer epidermis sensorial layer epidermis stratum germinativum UBERON:0002025 stratum basale of epidermis the deepest layer of the epidermis, which is composed of dividing stem cells and anchoring cells ISBN:0-683-40008-8 MP:0001231 Malpighian layer Wikipedia:Malpighian_layer rete Malphighii stratum Malpighi Wikipedia:Malpighian_layer UMLS:C0221925 ncithesaurus:Stratum_Basale basal cell layer of epidermis FMA:67540 basal epidermal layer ZFA:0001180 epidermal basal stratum TAO:0001180 epidermis sensorial layer XAO:0000041 The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA]. Posterior part of the brain consisting of the cerebellum and medulla oblongata.[AAO] The most posterior of the three principal regions of the brain, forming the rhombencephalon and all or most of the metencephalon. Kimmel et al, 1995.[TAO] relationship loss: develops_from hindbrain neural tube (TAO:0007043)[TAO] Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG] rhombencephalic in MA, brainstem and hindbrain and part-of siblings under brain, consistent with FMA and NIF. See also notes for cerebellum. We weaken the relation in ABA to overlaps AAO:0010150 BAMS:HB BIRNLEX:942 BTO:0000672 CALOHA:TS-0457 DHBA:10653 DMBA:16808 EFO:0000923 EHDAA2:0000746 EHDAA:3514 EHDAA:6487 EMAPA:16916 FMA:67687 MA:0000195 MAT:0000107 MBA:1065 MESH:D012249 MIAA:0000107 NCIT:C40336 SCTID:303456008 TAO:0000029 UMLS:C0035507 UMLS:C1522180 VHOG:0000070 Wikipedia:Rhombencephalon XAO:0000015 ZFA:0000029 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=540 uberon rhombencephalon UBERON:0002028 hindbrain http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg modified-source-relation ABA Bgee:AN The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA]. Wikipedia:Rhombencephalon ZFA:0000029 ZFIN:curator PMID:8932866 Posterior part of the brain consisting of the cerebellum and medulla oblongata.[AAO] 2012-06-20 AAO:0010150 AAO AAO:BJB The most posterior of the three principal regions of the brain, forming the rhombencephalon and all or most of the metencephalon. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000029 TAO ZFIN:curator relationship loss: develops_from hindbrain neural tube (TAO:0007043)[TAO] 2012-08-14 TAO:0000029 TAO Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG] 2012-09-17 VHOG:0000070 VHOG DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999) http://bgee.unil.ch/ in MA, brainstem and hindbrain and part-of siblings under brain, consistent with FMA and NIF. See also notes for cerebellum. We weaken the relation in ABA to overlaps MA UMLS:C0035507 BIRNLEX:942 UMLS:C0035507 ncithesaurus:Hind-Brain UMLS:C1522180 BIRNLEX:942 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=540 BIRNLEX:942 Muscle tissue that contains fibers that are divided by transverse bands into striations. Voluntary muscle tissue arranged in bundles of fibers.[AAO] AAO:0010762 AEO:0000140 CALOHA:TS-2047 EHDAA2:0003140 EMAPA:36390 FMA:67905 MA:0002438 NCIT:C12436 OpenCyc:Mx4rwAoze5wpEbGdrcN5Y29ycA UMLS:C1331262 WBbt:0005779 Wikipedia:Striated_muscle galen:StriatedMuscle striated muscle uberon UBERON:0002036 striated muscle tissue Muscle tissue that contains fibers that are divided by transverse bands into striations. CL:0000737 GOC:dph GOC:mtg_muscle Voluntary muscle tissue arranged in bundles of fibers.[AAO] 2012-06-20 AAO:0010762 AAO AAO:CAM UMLS:C1331262 ncithesaurus:Striated_Muscle_Tissue A systemic artery that supplies the lung with with oxygenated blood. EMAPA:18608 FMA:68109 GAID:477 MA:0001923 MESH:D001981 NCIT:C32230 OpenCyc:Mx4r4sy0UiNbEd2AAAACs6hRXg SCTID:244247009 UMLS:C0006257 Wikipedia:Bronchial_artery bronchial arterial tree uberon arteriae bronchiales rami bronchiales partis thoracicae aortae UBERON:0002040 Although there is much variation, there are usually two bronchial arteries that run to the left lung, and one to the right lung. bronchial artery http://upload.wikimedia.org/wikipedia/commons/a/a7/Gray1032.png A systemic artery that supplies the lung with with oxygenated blood. UBERON:cjm Wikipedia:Bronchial_artery UMLS:C0006257 ncithesaurus:Bronchial_Artery arteriae bronchiales Wikipedia:Bronchial_artery rami bronchiales partis thoracicae aortae Wikipedia:Bronchial_artery The pontine raphe nucleus is one of the raphe nuclei. It is located in the pontine tegmentum. [WP,unvetted]. BAMS:PnR BAMS:RA-PONS BAMS:RPn BIRNLEX:1110 DHBA:12471 DHBA:12475 FMA:68875 HBA:9159 MA:0001022 MBA:238 UMLS:C0175423 Wikipedia:Pontine_raphe_nucleus http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=589 raphe of pons raphe pontis uberon nucleus raphe pontis nucleus raphes pontis raphe (mediana pontina) raphe pontis nucleus UBERON:0002047 pontine raphe nucleus Wikipedia The pontine raphe nucleus is one of the raphe nuclei. It is located in the pontine tegmentum. [WP,unvetted]. Wikipedia:Pontine_raphe_nucleus UMLS:C0175423 BIRNLEX:1110 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=589 BIRNLEX:1110 raphe pontis FMA:68875 FMA:TA nucleus raphe pontis NeuroNames:589 nucleus raphes pontis Wikipedia:Pontine_raphe_nucleus raphe (mediana pontina) NeuroNames:589 Respiration organ that develops as an outpocketing of the esophagus. Either of two organs which allow gas exchange absorbing oxygen from inhaled air and releasing carbon dioxide with exhaled air.[AAO] Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata. (...) In actinopterygian fishes, apart from Cladistia, the ventral intestinal pocket migrates dorsally and becomes the swim-bladder, a mainly hydrostatical organ (reference 1); Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung (reference 2).[well established][VHOG] pulmonary respiration organ in all air-breathing animals, including most tetrapods, a few fish and a few snails. In mammals and the more complex life forms, the two lungs are located in the chest on either side of the heart. Their principal function is to transport oxygen from the atmosphere into the bloodstream, and to release carbon dioxide from the bloodstream into the atmosphere. This exchange of gases is accomplished in the mosaic of specialized cells that form millions of tiny, exceptionally thin-walled air sacs called alveoli. // Avian lungs do not have alveoli as mammalian lungs do, they have Faveolar lungs. They contain millions of tiny passages known as para-bronchi, connected at both ends by the dorsobronchi AAO:0000275 AAO:0010567 BTO:0000763 CALOHA:TS-0568 EFO:0000934 EHDAA2:0001042 EHDAA:1554 EHDAA:2205 EMAPA:16728 EV:0100042 FMA:7195 GAID:345 MA:0000415 MAT:0000135 MESH:D008168 MIAA:0000135 NCIT:C12468 OpenCyc:Mx4rvVjKy5wpEbGdrcN5Y29ycA SCTID:181216001 UMLS:C0024109 VHOG:0000310 Wikipedia:Lung XAO:0000119 galen:Lung pulmo uberon UBERON:0002048 Snakes and limbless lizards typically possess only the right lung as a major respiratory organ; the left lung is greatly reduced, or even absent. Amphisbaenians, however, have the opposite arrangement, with a major left lung, and a reduced or absent right lung [WP] lung https://github.com/obophenotype/uberon/issues/701 some species only have a single lung Respiration organ that develops as an outpocketing of the esophagus. http://orcid.org/0000-0002-6601-2165 BGEE:fb https://github.com/obophenotype/uberon/issues/701 BGEE:fb https://github.com/obophenotype/uberon/issues/701 Either of two organs which allow gas exchange absorbing oxygen from inhaled air and releasing carbon dioxide with exhaled air.[AAO] 2012-06-20 AAO:0010567 AAO AAO:SBH Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata. (...) In actinopterygian fishes, apart from Cladistia, the ventral intestinal pocket migrates dorsally and becomes the swim-bladder, a mainly hydrostatical organ (reference 1); Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000310 VHOG ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210, DOI:10.1371/journal.pone.0024019 Zheng W, Wang Z, Collins JE, Andrews RM, Stemple D, Gong Z, Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung. PLoS One (2011) http://bgee.unil.ch/ UMLS:C0024109 ncithesaurus:Lung pulmo An interconnected tubular multi-tissue structure contains fluid that is actively transported around the organism[ZFA]. Examples: vasculature of lung, vasculature of face. see also: vascular system. Consider merging? vascular BTO:0003718 FMA:69050 TAO:0005249 ZFA:0005249 vascular network uberon UBERON:0002049 vasculature http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg FMA An interconnected tubular multi-tissue structure contains fluid that is actively transported around the organism[ZFA]. Examples: vasculature of lung, vasculature of face. ZFA:0005249 vascular network FMA:69050 Anatomical structure that is part of an embryo. Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO] Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO] Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO] in FMA embryo is_a embryonic structure AAO:0000138 BILA:0000034 BTO:0000174 CALOHA:TS-2110 EFO:0000461 FBbt:00004208 FMA:69067 GAID:407 MESH:D004628 NCIT:C13229 RETIRED_EHDAA2:0003169 SCTID:667009 TAO:0001105 UMLS:C0013948 VSAO:0000178 XAO:0003042 ZFA:0001105 developing embryonic structure embryonic anatomical structure uberon developing structure embryonale Struktur embryonic structures UBERON:0002050 embryonic structure Anatomical structure that is part of an embryo. BTO:0000174 ZFIN:curator Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO] 2012-06-20 AAO:0000138 AAO AAO:BJB Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO] 2012-08-14 TAO:0001105 TAO ZFIN:curator Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO] 2012-08-14 VSAO:0000178 VSAO ZFIN:curator in FMA embryo is_a embryonic structure FMA UMLS:C0013948 ncithesaurus:Embryonic_Structure developing embryonic structure FBbt:00004208 embryonic anatomical structure RETIRED_EHDAA2:0003169 embryonale Struktur BTO:0000174 embryonic structures ZFA:0001105 An artery that supplies the diaphragm In humans this includes the superior and inferior phrenic arteries EMAPA:37108 FMA:69330 MA:0002019 NCIT:C33320 UMLS:C1181536 uberon UBERON:0002057 phrenic artery An artery that supplies the diaphragm https://orcid.org/0000-0002-6601-2165 EMAPA:37108 MA:th UMLS:C1181536 ncithesaurus:Phrenic_Artery The truncus arteriosus and bulbus cordis are divided by the aorticopulmonary septum. The truncus arteriosus gives rise to the ascending aorta and the pulmonary trunk. The bulbus cordis gives rise to the smooth parts (outflow tract) of the left and right ventricles. assume spelling error for ncit EHDAA2:0004143 EMAPA:35887 FMA:70301 GAID:554 MA:0000103 MESH:D014338 NCIT:C34317 OpenCyc:Mx4rquH9YKgNEdudWQACs5b6Bw SCTID:308828009 UMLS:C1519589 Wikipedia:Truncus_arteriosus_(embryology) uberon UBERON:0002061 truncus arteriosus EHDAA2 FMA MA EHDAA2 EHDAA2 The truncus arteriosus and bulbus cordis are divided by the aorticopulmonary septum. The truncus arteriosus gives rise to the ascending aorta and the pulmonary trunk. The bulbus cordis gives rise to the smooth parts (outflow tract) of the left and right ventricles. Wikipedia:Truncus_arteriosus_(embryology) assume spelling error for ncit ncit UMLS:C1519589 ncithesaurus:Trancus_Arteriosus The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves[GO]. Swellings of tissue present between the endocardial and myocardial cell layers that will give rise to the interstitial cells of the cardiac valves[ZFA]. Swellings of tissue present between the endocardial and myocardial cell layers that will give rise to the interstitial cells of the cardiac valves.[TAO] relationship loss: develops_from endocardial ring (TAO:0005072)[TAO] (Cardiac valve formation in vertebrates) In response to a myocardial signal, endocardial cells at chamber boundaries take on a mesenchymal character, delaminate and migrate into the cardiac jelly. There, they form an endocardial cushion that is later remodelled into a valve.[well established][VHOG] EHDAA2:0000434 EHDAA2:0004028 EHDAA:2586 EMAPA:16696 FMA:70302 MA:0000078 TAO:0001317 VHOG:0000932 Wikipedia:Atrioventricular_cushions XAO:0004189 ZFA:0001317 AV cushion atrioventricular cushion cardiac cushion endocardial cushion tissue uberon atrioventricular canal cushion endocardial cushions UBERON:0002062 GO graph seems to suggest this is an endothelium. WP: The endocardial cushions are thought to arise from a subset of endothelial cells that undergo epithelial to mesenchymal transformation, a process whereby these cells break cell-to-cell contacts and migrate into the cardiac jelly (towards to interior of the heart tube). Latest (2010-06-01) new def suggested for GO, added above. Note that EHDAA2 has a more detailed model which we may later adopt. JB: Patterning makes the cushions lay down connective tissue in three domains that force out the local endothelial lining and so the leaflets form endocardial cushion http://upload.wikimedia.org/wikipedia/commons/c/c7/Gray465.png ZFA The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves[GO]. Swellings of tissue present between the endocardial and myocardial cell layers that will give rise to the interstitial cells of the cardiac valves[ZFA]. GO:0003197 Wikipedia:Atrioventricular_cushions ZFIN:curator Swellings of tissue present between the endocardial and myocardial cell layers that will give rise to the interstitial cells of the cardiac valves.[TAO] 2012-08-14 TAO:0001317 TAO ZFIN:curator relationship loss: develops_from endocardial ring (TAO:0005072)[TAO] 2012-08-14 TAO:0001317 TAO (Cardiac valve formation in vertebrates) In response to a myocardial signal, endocardial cells at chamber boundaries take on a mesenchymal character, delaminate and migrate into the cardiac jelly. There, they form an endocardial cushion that is later remodelled into a valve.[well established][VHOG] 2012-09-17 VHOG:0000932 VHOG DOI:10.1038/35047564 Stainier DYR, Zebrafish genetics and vertebrate heart formation. Nature Reviews Genetics (2001) Figure 3 http://bgee.unil.ch/ atrioventricular cushion Wikipedia:Endocardial_cushion cardiac cushion PMID:15797462 endocardial cushion tissue EHDAA2:0000434 atrioventricular canal cushion FMA:70302 endocardial cushions The sinus venosus is a large cardiac chamber at the inflow tract that receives venous blood from systemic circulation. precedes the atrium on the venous side of the chordate heart. Heart region collecting blood from the paired common cardinal veins and delivering to the atrium. One of four components of the heart. The sinus venosus also acts as a pacemaker and is the first to contract. Kimmel et al, 1995.[TAO] Part of the circulatory system which receives blood from the systemic veins and contracts to pump the blood into the atrium of the heart.[AAO] In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...).[well established][VHOG] In fish, receives venous blood from the systemic circulation through paired hepatic veins, anterior jugular veins and Cuvierian ducts[PMID:20735616] In humans, it exists distinctly only in the embryonic heart, where it is found between the two venae cavae. In the adult, it is incorporated into the wall of the right atrium to form a smooth part called the sinus venarum, also known as the venarum sinus, which is separated from the rest of the atrium by a ridge of fibres called the crista terminalis. The sinus venosus also forms the SA node and the coronary sinus. In the embryo, the thin walls of the sinus venosus are connected below with the right ventricle, and medially with the left atrium, but are free in the rest of their extent. It receives blood from the vitelline vein, umbilical vein and common cardinal vein. It originally starts as a paired structure but shifts towards associating only with the right atrium as the embryonic heart develops. The left portion shrinks in size and eventually forms the coronary sinus and oblique vein of the left atrium, whereas the right part becomes incorporated into the right atrium to form the sinus venarmu In zebrafish, the sinus venosus also acts as a pacemaker and is the first to contract inflow tract AAO:0010505 EHDAA2:0001839 EHDAA:480 EMAPA:16237 FMA:70303 NCIT:C34299 NCIT:C34300 TAO:0000154 UMLS:C0225857 UMLS:C0231084 VHOG:0000177 Wikipedia:Sinus_venosus ZFA:0000154 uberon sinus venarum sinus venosus cordis venarum venarum sinus venosus UBERON:0002063 sinus venosus http://upload.wikimedia.org/wikipedia/commons/c/c7/Gray465.png VHOG Bgee:AN The sinus venosus is a large cardiac chamber at the inflow tract that receives venous blood from systemic circulation. precedes the atrium on the venous side of the chordate heart. PMID:20735616 Wikipedia:Sinus_venosus Heart region collecting blood from the paired common cardinal veins and delivering to the atrium. One of four components of the heart. The sinus venosus also acts as a pacemaker and is the first to contract. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000154 TAO ZFIN:curator Part of the circulatory system which receives blood from the systemic veins and contracts to pump the blood into the atrium of the heart.[AAO] 2012-06-20 AAO:0010505 AAO AAO:BJB In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...).[well established][VHOG] 2012-09-17 VHOG:0000177 VHOG ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.428 http://bgee.unil.ch/ In zebrafish, the sinus venosus also acts as a pacemaker and is the first to contract ZFA:0000154 inflow tract ZFA:0000154 UMLS:C0225857 ncithesaurus:Sinus_Venarum UMLS:C0231084 ncithesaurus:Sinus_Venosus sinus venarum Wikipedia:Sinus_venosus sinus venosus cordis Wikipedia:Sinus_venosus venarum Wikipedia:Sinus_venosus venarum sinus Wikipedia:Sinus_venosus venosus Wikipedia:Sinus_venosus The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP]. Consider adding a layer-of-skin grouping class for all skin layers A collagenous layer of the skin subjacent to the epidermis and covering the hypodermis. It contains various types of cells (e.g. fibroblasts, pigment cells, nerve, blood vessels and scales. Le Guellec et al, 2004.[TAO] When approaching controversies surrounding skin evolution, we need to remember that the skin consists of two layers, an epidermis and a dermis, not a single evolving structure. (...) It is little wonder that controversies about homology exist. If we think of the epidermis, the dermis, and their interactions as an evolving unit, then their specialized products (hair, feathers, and reptilian scales) are broadly homologous.[well established][VHOG] dermal AAO:0000128 BTO:0000294 CALOHA:TS-2076 EFO:0000953 EMAPA:17527 EV:0100154 FMA:70323 GAID:1321 MA:0000152 MAT:0000153 MESH:D020405 MIAA:0000153 NCIT:C12701 SCTID:361696001 TAO:0001119 UMLS:C0011646 VHOG:0000108 Wikipedia:Dermis XAO:0000217 ZFA:0001119 vertebrate dermis uberon corium cutis UBERON:0002067 dermis http://upload.wikimedia.org/wikipedia/commons/2/23/EpidermisPainted.svg FMA definitional The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP]. Wikipedia:Dermis ZFIN:curator A collagenous layer of the skin subjacent to the epidermis and covering the hypodermis. It contains various types of cells (e.g. fibroblasts, pigment cells, nerve, blood vessels and scales. Le Guellec et al, 2004.[TAO] 2012-08-14 TAO:0001119 TAO ZFIN:curator When approaching controversies surrounding skin evolution, we need to remember that the skin consists of two layers, an epidermis and a dermis, not a single evolving structure. (...) It is little wonder that controversies about homology exist. If we think of the epidermis, the dermis, and their interactions as an evolving unit, then their specialized products (hair, feathers, and reptilian scales) are broadly homologous.[well established][VHOG] 2012-09-17 VHOG:0000108 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.231-232 see also p.209 and p.228 and Figure 6-1 http://bgee.unil.ch/ UMLS:C0011646 ncithesaurus:Dermis corium BTO:0000294 corium Wikipedia:Dermis cutis BTO:0000294 Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP]. A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells. Le Guellec et al, 2004.[TAO] A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells[FMA:70544]. hypodermal subcutaneous subcutaneus BTO has 'subcutis', as part of dermis. We follow FMA in having distinct classes for hypodermis and superficial fascia, and including these as part of the non-skin intgeument. BTO:0001314 CALOHA:TS-2366 EMAPA:37505 FMA:70544 NCIT:C33645 TAO:0001136 UMLS:C0278403 Wikipedia:Hypodermis ZFA:0001136 hypoderm vertebrate hypodermis uberon sub-tegumental tissue subcutaneous tissue subcutis subtegumental tissue superficial fascia tela subcutanea UBERON:0002072 hypodermis http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg ZFA FMA-modified Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP]. Wikipedia:Hypodermis A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells. Le Guellec et al, 2004.[TAO] 2012-08-14 TAO:0001136 TAO ZFIN:curator A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells[FMA:70544]. FMA:70544 BTO has 'subcutis', as part of dermis. We follow FMA in having distinct classes for hypodermis and superficial fascia, and including these as part of the non-skin intgeument. BTO EMAPA:37505 MA:th UMLS:C0278403 ncithesaurus:Subcutis sub-tegumental tissue BTO:0004525 subcutaneous tissue Wikipedia:Hypodermis subtegumental tissue BTO:0004525 superficial fascia tela subcutanea Wikipedia:Hypodermis An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen. An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO] general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs. AAO:0010386 BTO:0001491 EHDAA:512 EMAPA:16245 FMA:7085 MA:0000019 MESH:D014781 NCIT:C28287 RETIRED_EHDAA2:0002201 SCTID:118760003 UMLS:C0042779 Wikipedia:Viscus XAO:0003034 visceral organ visceral organ system uberon splanchnic tissue viscera visceral tissue UBERON:0002075 viscus An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen. BTO:0001491 Wikipedia:Viscus https://github.com/obophenotype/mouse-anatomy-ontology/issues/14 An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO] 2012-06-20 AAO:0010386 AAO BTO:0001491 general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs. FMA UMLS:C0042779 ncithesaurus:Viscera visceral organ RETIRED_EHDAA2:0002201 visceral organ system MA:0000019 splanchnic tissue BTO:0001491 visceral tissue BTO:0001491 A cardiac atrium that is in the left side of the heart. It receives deoxygenated blood. In mammals, this comes from the superior and inferior vena cava and the coronary sinus, and pumps it into the right ventricle through the tricuspid valve. Right cardiac chamber which is continuous with the superior vena cava and inferior vena cava.[FMA] The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG] https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern AAO:0010248 BTO:0001703 EHDAA2:0000290 EMAPA:17321 FMA:7096 MA:0000075 NCIT:C12868 OpenCyc:Mx4runNcs6fqEdudWQACs5b6Bw OpenCyc:Mx8Ngh4rvgHsHZwpEbGdrcN5Y29ycB4rDJ89oqgPEdudWQACs5b6Bw SCTID:244383003 UMLS:C0225844 VHOG:0000328 Wikipedia:Right_atrium XAO:0003192 galen:RightAtrium cardiac right atrium heart right atrium right atrium right atrium of heart right cardiac atrium uberon atrium dextrum UBERON:0002078 right cardiac atrium http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg A cardiac atrium that is in the left side of the heart. It receives deoxygenated blood. In mammals, this comes from the superior and inferior vena cava and the coronary sinus, and pumps it into the right ventricle through the tricuspid valve. Wikipedia:Right_atrium http://orcid.org/0000-0002-6601-2165 Right cardiac chamber which is continuous with the superior vena cava and inferior vena cava.[FMA] FMA:7096 The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG] 2012-09-17 VHOG:0000328 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620 http://bgee.unil.ch/ UMLS:C0225844 ncithesaurus:Right_Atrium heart right atrium MA:0000075 right atrium VHOG:0000328 atrium dextrum Wikipedia:Right_atrium A cardiac atrium that is in the left side of the heart. It receives oxygenated blood from the pulmonary veins, In mammals this is pumped into the left ventricle, via the Mitral valve. Left cardiac chamber which is continuous with the pulmonary venous trunk.[FMA] The chamber of the heart that receives blood from the lungs[XAO:EJS]. The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG] https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern AAO:0010247 BTO:0001702 EHDAA2:0000275 EMAPA:17315 FMA:7097 MA:0000074 NCIT:C12869 OpenCyc:Mx4rkJN1AagEEdudWQACs5b6Bw OpenCyc:Mx8Ngh4rvgIFoJwpEbGdrcN5Y29ycB4rDJ89oqgPEdudWQACs5b6Bw SCTID:244387002 UMLS:C0225860 VHOG:0000369 Wikipedia:Left_atrium XAO:0003191 galen:LeftAtrium atrium sinistrum cardiac left atrium heart left atrium left atrium left atrium of heart left cardiac atrium uberon UBERON:0002079 left cardiac atrium http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg A cardiac atrium that is in the left side of the heart. It receives oxygenated blood from the pulmonary veins, In mammals this is pumped into the left ventricle, via the Mitral valve. Wikipedia:Left_atrium http://orcid.org/0000-0002-6601-2165 Left cardiac chamber which is continuous with the pulmonary venous trunk.[FMA] FMA:7097 The chamber of the heart that receives blood from the lungs[XAO:EJS]. XAO:EJS The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG] 2012-09-17 VHOG:0000369 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620 http://bgee.unil.ch/ UMLS:C0225860 ncithesaurus:Left_Atrium atrium sinistrum Wikipedia:Left_atrium heart left atrium MA:0000074 left atrium VHOG:0000369 A cardiac ventricle that is in the right side of the heart. The muscular chamber on the right and in front of the left ventricle. It generally receives venous blood from the right atrium and conveys it into the pulmonary artery. [(1988)_Dorian_AF, Amsterdam, Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B._Anatomy, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier's_Encyclopaedic_Dictionary_of_Medicine][VHOG] https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern In mammals continuous with the pulmonary arteries BTO:0001630 CALOHA:TS-0443 EHDAA2:0000196 EMAPA:17340 FMA:7098 MA:0000093 NCIT:C12870 OpenCyc:Mx4rRMlc0KgNEdudWQACs5b6Bw OpenCyc:Mx8Ngh4rvgHsHZwpEbGdrcN5Y29ycB4rvVjj1pwpEbGdrcN5Y29ycA SCTID:244384009 UMLS:C0225883 VHOG:0000717 Wikipedia:Right_ventricle galen:RightVentricle cardiac right ventricle right ventricle right ventricle of heart uberon right cardiac ventricle ventriculus dexter UBERON:0002080 heart right ventricle http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg PMID:17276708 cjm A cardiac ventricle that is in the right side of the heart. http://orcid.org/0000-0002-6601-2165 The muscular chamber on the right and in front of the left ventricle. It generally receives venous blood from the right atrium and conveys it into the pulmonary artery. [(1988)_Dorian_AF, Amsterdam, Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B._Anatomy, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier's_Encyclopaedic_Dictionary_of_Medicine][VHOG] 2012-09-17 VHOG:0000717 VHOG http://bgee.unil.ch/ UMLS:C0225883 ncithesaurus:Right_Ventricle right ventricle FMA:7098 right cardiac ventricle EMAPA:17340 ventriculus dexter Wikipedia:Right_ventricle Cardiac chamber in which blood enters the heart. One of four heart chambers.[TAO] One of two chambers of the heart which receive blood from the veins and forces it by muscular contration to the ventricle.[AAO] In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...).[well established][VHOG] AAO:0010246 BTO:0000903 CALOHA:TS-0437 EFO:0000277 EHDAA2:0000154 EHDAA:1265 EMAPA:16688 EV:0100019 FMA:7099 GAID:555 MA:0000073 MAT:0000496 MESH:D006325 NCIT:C12728 SCTID:261405004 TAO:0000471 UMLS:C0018792 VHOG:0000175 Wikipedia:Heart_atrium ZFA:0000471 galen:Atrium atria atrium atrium of heart cardiac atria heart atrium uberon atrial tissue UBERON:0002081 cardiac atrium Cardiac chamber in which blood enters the heart. Wikipedia:Heart_atrium http://orcid.org/0000-0002-6601-2165 One of four heart chambers.[TAO] 2012-08-14 TAO:0000471 TAO ZFIN:curator One of two chambers of the heart which receive blood from the veins and forces it by muscular contration to the ventricle.[AAO] 2012-06-20 AAO:0010246 AAO AAO:BJB In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...).[well established][VHOG] 2012-09-17 VHOG:0000175 VHOG ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.428 http://bgee.unil.ch/ UMLS:C0018792 ncithesaurus:Cardiac_Atrium atria atrium ZFA:0000471 cardiac atria atrial tissue BTO:0000903 Cardiac chamber through which blood leaves the heart. A chamber of the heart that receives blood from one or more atria and pumps it by muscular contraction into the arteries.[AAO] One of four heart chambers.[TAO] In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...)[well established][VHOG] ventricle AAO:0010249 BTO:0000862 CALOHA:TS-0444 EFO:0000317 EHDAA2:0004164 EHDAA:1912 EMAPA:17331 EV:0100020 FMA:7100 GAID:568 MA:0000091 MAT:0000497 MESH:D006352 NCIT:C12730 OpenCyc:Mx4rvVjj1pwpEbGdrcN5Y29ycA SCTID:277699000 TAO:0000009 UMLS:C0018827 VHOG:0000435 Wikipedia:Ventricle_(heart) XAO:0003193 ZFA:0000009 galen:Ventricle heart ventricle lower chamber of heart ventricle of heart uberon UBERON:0002082 cardiac ventricle Bgee:AN Cardiac chamber through which blood leaves the heart. Wikipedia:Ventricle_(heart) http://orcid.org/0000-0002-6601-2165 A chamber of the heart that receives blood from one or more atria and pumps it by muscular contraction into the arteries.[AAO] 2012-06-20 AAO:0010249 AAO AAO:BJB One of four heart chambers.[TAO] 2012-08-14 TAO:0000009 TAO ZFIN:curator In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...)[well established][VHOG] 2012-09-17 VHOG:0000435 VHOG ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.428 http://bgee.unil.ch/ UMLS:C0018827 ncithesaurus:Cardiac_Ventricle A cardiac ventricle that is in the left side of the heart. Thick-walled muscular chamber constituting the left border and apex of the heart. It receives oxygenated blood from the left atrium through the mitral orifice and send it off into the aorta. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] The vertebrate heart initially forms as a tube from a population of precursor cells termed the first heart field (FHF). Cells from the adjacent second heart field (SHF) are then progressively added to the developing heart. In avian and mammalian hearts, the FHF contributes mainly to the left ventricle, whereas the SHF gives rise to the outflow tract and large portions of the right ventricle and atria. Both fields arise from common mesodermal progenitors, although the detailed lineage relationships between FHF and SHF remain uncertain.[well established][VHOG] https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern In mammals continuous with aorta BTO:0001629 CALOHA:TS-0439 EHDAA2:0002178 EMAPA:17337 FMA:7101 MA:0000092 NCIT:C12871 OpenCyc:Mx4rtW8v46gEEdudWQACs5b6Bw OpenCyc:Mx8Ngh4rvgIFoJwpEbGdrcN5Y29ycB4rvVjj1pwpEbGdrcN5Y29ycA SCTID:244385005 UMLS:C0225897 VHOG:0000718 Wikipedia:Left_ventricle galen:LeftVentricle cardiac left ventricle left cardiac ventricle left ventricle left ventricle of heart uberon ventriculus sinister cordis UBERON:0002084 heart left ventricle http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg GO A cardiac ventricle that is in the left side of the heart. http://orcid.org/0000-0002-6601-2165 Thick-walled muscular chamber constituting the left border and apex of the heart. It receives oxygenated blood from the left atrium through the mitral orifice and send it off into the aorta. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000718 VHOG http://bgee.unil.ch/ The vertebrate heart initially forms as a tube from a population of precursor cells termed the first heart field (FHF). Cells from the adjacent second heart field (SHF) are then progressively added to the developing heart. In avian and mammalian hearts, the FHF contributes mainly to the left ventricle, whereas the SHF gives rise to the outflow tract and large portions of the right ventricle and atria. Both fields arise from common mesodermal progenitors, although the detailed lineage relationships between FHF and SHF remain uncertain.[well established][VHOG] 2012-09-17 VHOG:0000718 VHOG DOI:10.1126/science.1190181 Stolfi A, Gainous TB, Young JJ, Mori A, Levine M, Christiaen L, Early chordate origins of the vertebrate second heart field. Science (2010) http://bgee.unil.ch/ UMLS:C0225897 ncithesaurus:Left_Ventricle left ventricle FMA:7101 ventriculus sinister cordis Wikipedia:Left_ventricle A cardiac septum that divides the left and right atria of the heart. The partition separating the right and left atria of the heart. [TFD][VHOG] The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG] EHDAA2:0000838 EHDAA:1896 EMAPA:17011 FMA:7108 MA:0000084 NCIT:C32818 OpenCyc:Mx4rpd49nLYEEduAAAACs2IKfQ OpenCyc:Mx4rwGvku5wpEbGdrcN5Y29ycA SCTID:362016003 UMLS:C0225836 VHOG:0000385 Wikipedia:Interatrial_septum galen:InteratrialSeptum atrial septum atrium septum interatrial septal wall uberon UBERON:0002085 interatrial septum http://upload.wikimedia.org/wikipedia/commons/6/6c/Gray493.png A cardiac septum that divides the left and right atria of the heart. http://orcid.org/0000-0002-6601-2165 The partition separating the right and left atria of the heart. [TFD][VHOG] 2012-09-17 VHOG:0000385 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/interatrial+septum The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG] 2012-09-17 VHOG:0000385 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620 http://bgee.unil.ch/ UMLS:C0225836 ncithesaurus:Interatrial_Septum The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA]. Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO] The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO] The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO] The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG] axial skeleton AAO:0000034 EFO:0000942 EHDAA2:0000161 EHDAA:5049 EMAPA:17214 EMAPA:37721 FMA:71221 MA:0002986 MAT:0000148 MIAA:0000148 TAO:0000317 VHOG:0000317 VSAO:0000093 XAO:0003073 ZFA:0000317 post-cranial axial skeleton uberon UBERON:0002090 previous some AOs had used the term 'axial skeleton' to include the skull. This is being resolved (see tracker items above). Status: MA - fixed. postcranial axial skeleton http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA]. ZFA:0000317 https://sourceforge.net/tracker/?func=detail&aid=2983975&group_id=76834&atid=974957 https://sourceforge.net/tracker/?func=detail&atid=1205376&aid=2983977&group_id=76834 Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO] 2012-08-14 VSAO:0000093 VSAO PSPUB:0000170 The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO] 2012-06-20 AAO:0000034 AAO AAO:LAP The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO] 2012-08-14 TAO:0000317 TAO ZFIN:curator The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG] 2012-09-17 VHOG:0000317 VHOG DOI:10.1186/1742-9994-8-4 Schilling N, Evolution of the axial system in craniates: morphology and function of the perivertebral musculature. Frontiers in Zoology (2011) http://bgee.unil.ch/ axial skeleton FMA:71221 https://github.com/obophenotype/uberon/wiki/The-axial-skeleton EMAPA:37721 MA:th Subdivision of skeleton which which consists of all the skeletal elements in in the pectoral and pelvic appendage complexes[cjm]. Skeletal subdivision consisting of all the skeletal elements in the pectoral and pelvic appendage complexes.[VSAO] Skeletal system that consists of the paired fins (pectoral or pelvic fins).[TAO] The pectoral and pelvic girdles, which articulate with the axial skeleton, together with their associated limbs, the forelimbs and hind limbs, form the appendicular skeleton.[AAO] ontologies differ in whether they treat the term appendicular skeleton as being the entire set of bones in the limbs, or whether the fore and hind limbs/fins are treated as seperate appendicular skeletons. Here we follow FMA, and treat the appendicular skeleton as the sum total of skeletal elements in the organism (this is evidenced by the fact that in FMA, skeleton of left/right upper/lower limb is part_of a appendicular skeleton, and subtypes of 'subdivision of appendicular skeleton'). We have separate classes such as 'skeleton of limb', and 'skeleton of hindlimb' for the 4 parts of the appendicular skeleton. In future the ZFA/TAO classes may be moved. AAO:0000747 EFO:0000951 EMAPA:32729 FMA:71222 MA:0000290 MAT:0000278 MIAA:0000278 NCIT:C49477 SCTID:322050006 UMLS:C0222646 VHOG:0001666 VSAO:0000076 Wikipedia:Appendicular_skeleton XAO:0003166 appendicular skeleton entire appendicular skeleton paired fin skeleton uberon skeleton appendiculare UBERON:0002091 appendicular skeleton https://github.com/obophenotype/uberon/wiki/Appendages-and-the-appendicular-skeleton http://upload.wikimedia.org/wikipedia/commons/7/7c/Appendicular_skeleton_diagram.svg Subdivision of skeleton which which consists of all the skeletal elements in in the pectoral and pelvic appendage complexes[cjm]. UBERONREF:0000003 Wikipedia:Appendicular_skeleton https://orcid.org/0000-0002-6601-2165 Skeletal subdivision consisting of all the skeletal elements in the pectoral and pelvic appendage complexes.[VSAO] 2012-08-14 VSAO:0000076 VSAO PSPUB:0000170 https://orcid.org/0000-0002-6601-2165 Skeletal system that consists of the paired fins (pectoral or pelvic fins).[TAO] 2012-08-14 TAO:0000027 TAO TAO:wd The pectoral and pelvic girdles, which articulate with the axial skeleton, together with their associated limbs, the forelimbs and hind limbs, form the appendicular skeleton.[AAO] 2012-06-20 AAO:0000747 AAO AAO:LAP ontologies differ in whether they treat the term appendicular skeleton as being the entire set of bones in the limbs, or whether the fore and hind limbs/fins are treated as seperate appendicular skeletons. Here we follow FMA, and treat the appendicular skeleton as the sum total of skeletal elements in the organism (this is evidenced by the fact that in FMA, skeleton of left/right upper/lower limb is part_of a appendicular skeleton, and subtypes of 'subdivision of appendicular skeleton'). We have separate classes such as 'skeleton of limb', and 'skeleton of hindlimb' for the 4 parts of the appendicular skeleton. In future the ZFA/TAO classes may be moved. FMA UMLS:C0222646 ncithesaurus:Appendicular_Skeleton entire appendicular skeleton https://github.com/obophenotype/uberon/issues/59 paired fin skeleton skeleton appendiculare Wikipedia:Appendicular_skeleton Cardiac septum which separates the right ventricle from the left ventricle.[FMA] The partition separating the right and left ventricles of the heart. [TFD][VHOG] The two most progressive vertebrate classes, the birds and mammals, have completed the ventricular septum and at long last have completely separated the two blood streams along the length of the major heart chambers. This development has obviously been brought about independently in the two cases, since mammals and birds have evolved independently from primitive reptiles.[well established][VHOG] involves the recruitment of myocardial cells as well as of non- muscular mesenchymal cells (Kaufman and Bard, 1999) BTO:0002483 EFO:0001956 EHDAA:2603 EMAPA:17333 FMA:7133 MA:0000085 NCIT:C32874 OpenCyc:Mx4rwA7lp5wpEbGdrcN5Y29ycA SCTID:362019005 UMLS:C0225870 VHOG:0000386 Wikipedia:Interventricular_septum galen:InterventricularSeptum heart interventricular septum heart ventricular septum uberon interventricular septum of heart interventriculare cordis intraventricular septum s. interventriculare cordis septum inferius septum membranaceum ventricle septum ventricular septum UBERON:0002094 interventricular septum http://upload.wikimedia.org/wikipedia/commons/9/96/Gray498.png Cardiac septum which separates the right ventricle from the left ventricle.[FMA] FMA:7133 The partition separating the right and left ventricles of the heart. [TFD][VHOG] 2012-09-17 VHOG:0000386 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/interventricular+septum The two most progressive vertebrate classes, the birds and mammals, have completed the ventricular septum and at long last have completely separated the two blood streams along the length of the major heart chambers. This development has obviously been brought about independently in the two cases, since mammals and birds have evolved independently from primitive reptiles.[well established][VHOG] 2012-09-17 VHOG:0000386 VHOG ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.430 http://bgee.unil.ch/ involves the recruitment of myocardial cells as well as of non- muscular mesenchymal cells (Kaufman and Bard, 1999) ISBN:0124020607 UMLS:C0225870 ncithesaurus:Interventricular_Septum heart interventricular septum MA:0000085 heart ventricular septum MA:0000085 interventricular septum of heart BTO:0002483 interventriculare cordis BTO:0002483 intraventricular septum Wikipedia:Interventricular_septum s. interventriculare cordis Wikipedia:Interventricular_septum septum inferius Wikipedia:Interventricular_septum septum membranaceum Wikipedia:Interventricular_septum ventricular septum MA:0000085 Wikipedia:Interventricular_septum The organ covering the body that consists of the dermis and epidermis. consider 'integumentary system' for invertebrates MA uses the term skin to refer to what is called here: zone of skin BTO:0001253 CALOHA:TS-0934 EFO:0000962 EHDAA2:0001844 EMAPA:17525 FMA:7163 MESH:D012867 MFMO:0000099 NCIT:C12470 OpenCyc:Mx4rvVjX3ZwpEbGdrcN5Y29ycA SCTID:181469002 UMLS:C1123023 Wikipedia:Skin XAO:0000023 galen:Skin entire skin skin organ uberon entire integument integument integumental organ pelt skin UBERON:0002097 skin of body http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg Wikipathways:WP2062 The organ covering the body that consists of the dermis and epidermis. UBERON:cjm MA uses the term skin to refer to what is called here: zone of skin FMA UMLS:C1123023 ncithesaurus:Skin The thin membranous structure between the two heart atria or the thick muscular structure between the two heart ventricles. 'Terrestrial vertebrates have divided hearts in which septae separate the oxygenated and deoxygenated blood within the pulmonary and systemic circulations' in GO, septum morphogenesis is part of cardiac chamber morphogenesis; need to add axioms to infer this EMAPA:35400 FMA:7180 GAID:562 MA:0000083 MESH:D006346 NCIT:C49485 SCTID:362014000 UMLS:C0018819 cardiac septa heart septa heart septum septum of heart uberon spiral septa UBERON:0002099 cardiac septum The thin membranous structure between the two heart atria or the thick muscular structure between the two heart ventricles. MESH:A07.541.459 in GO, septum morphogenesis is part of cardiac chamber morphogenesis; need to add axioms to infer this GO UMLS:C0018819 ncithesaurus:Heart_Septum cardiac septa heart septa spiral septa XAO:0004141 Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present. Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO] Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO] AAO:0010339 BILA:0000116 BTO:0001493 CALOHA:TS-1071 EFO:0000966 EMAPA:31857 FMA:7181 MA:0000004 MAT:0000296 MIAA:0000296 NCIT:C33816 OpenCyc:Mx4rvVkJjpwpEbGdrcN5Y29ycA SCTID:262225004 TAO:0001115 UMLS:C0460005 Wikipedia:Torso XAO:0000054 XAO:0003025 ZFA:0001115 galen:Trunk thoracolumbar region torso trunk region uberon Rumpf UBERON:0002100 trunk Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present. TAO:0001115 UBERONREF:0000006 Wikipedia:Torso Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO] 2012-06-20 AAO:0010339 AAO AAO:BJB Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO] 2012-08-14 TAO:0001115 TAO ZFIN:curator UMLS:C0460005 ncithesaurus:Trunk trunk region XAO:0000054 Rumpf BTO:0001493 The sensory system subserving the sense of vision. The sensory system used for sight.[AAO] UBERON:0007036 AAO:0000632 BILA:0000140 EMAPA:36003 FMA:7191 MA:0002444 NCIT:C12888 OpenCyc:Mx4rvViCtpwpEbGdrcN5Y29ycA SCTID:281831001 TAO:0001127 UMLS:C0587900 Wikipedia:Visual_system XAO:0003198 ZFA:0001127 http://uri.neuinfo.org/nif/nifstd/FMAID_7191 photosensory system visual organ system uberon UBERON:0002104 visual system The sensory system subserving the sense of vision. NIFSTD:FMAID_7191 The sensory system used for sight.[AAO] 2012-06-20 AAO:0000632 AAO AAO:EJS UMLS:C0587900 ncithesaurus:Visual_System photosensory system BILA:0000140 Sensory system responsible for the perception of spatial orientation and auditory stimuli. The sensory system used for balance and hearing.[AAO] AAO:0000631 EMAPA:36002 EMAPA:37985 FMA:78500 TAO:0001138 XAO:0003195 ZFA:0001138 auditory organ system vestibuloauditory system uberon auditory system auditory/vestibular system vestibuloauditory system UBERON:0002105 vestibulo-auditory system http://upload.wikimedia.org/wikipedia/commons/d/d2/Anatomy_of_the_Human_Ear.svg Sensory system responsible for the perception of spatial orientation and auditory stimuli. ZFA:0001138 The sensory system used for balance and hearing.[AAO] 2012-06-20 AAO:0000631 AAO AAO:EJS EMAPA:37985 MA:th A portion of smooth muscle tissue that is part of an artery [Automatically generated definition]. BTO:0000087 CALOHA:TS-1198 EMAPA:36285 FMA:72024 MA:0000708 NCIT:C49195 UMLS:C1706851 arterial smooth muscle artery smooth muscle artery smooth muscle tissue smooth muscle of artery uberon arterial smooth muscle cell UBERON:0002111 artery smooth muscle tissue A portion of smooth muscle tissue that is part of an artery [Automatically generated definition]. OBOL:automatic UMLS:C1706851 ncithesaurus:Artery_Smooth_Muscle_Tissue arterial smooth muscle BTO:0000087 smooth muscle of artery FMA:72024 arterial smooth muscle cell BTO:0000087 A portion of smooth muscle tissue that is part of a esophagus [Automatically generated definition]. EMAPA:35323 FMA:72025 MA:0001573 esophageal smooth muscle esophagus involuntary muscle esophagus non-striated muscle esophagus smooth muscle esophagus smooth muscle tissue gullet involuntary muscle gullet non-striated muscle gullet smooth muscle gullet smooth muscle tissue involuntary muscle of esophagus involuntary muscle of gullet involuntary muscle of oesophagus non-striated muscle of esophagus non-striated muscle of gullet non-striated muscle of oesophagus oesophagus involuntary muscle oesophagus non-striated muscle oesophagus smooth muscle tissue smooth muscle of gullet smooth muscle of oesophagus smooth muscle tissue of esophagus smooth muscle tissue of gullet smooth muscle tissue of oesophagus uberon oesophagus smooth muscle UBERON:0002112 smooth muscle of esophagus A portion of smooth muscle tissue that is part of a esophagus [Automatically generated definition]. OBOL:automatic esophagus involuntary muscle OBOL:automatic esophagus non-striated muscle OBOL:automatic esophagus smooth muscle tissue OBOL:automatic gullet involuntary muscle OBOL:automatic gullet non-striated muscle OBOL:automatic gullet smooth muscle OBOL:automatic gullet smooth muscle tissue OBOL:automatic involuntary muscle of esophagus OBOL:automatic involuntary muscle of gullet OBOL:automatic involuntary muscle of oesophagus OBOL:automatic non-striated muscle of esophagus OBOL:automatic non-striated muscle of gullet OBOL:automatic non-striated muscle of oesophagus OBOL:automatic oesophagus involuntary muscle OBOL:automatic oesophagus non-striated muscle OBOL:automatic oesophagus smooth muscle tissue OBOL:automatic smooth muscle of gullet OBOL:automatic smooth muscle of oesophagus OBOL:automatic smooth muscle tissue of esophagus OBOL:automatic smooth muscle tissue of gullet OBOL:automatic smooth muscle tissue of oesophagus OBOL:automatic An ovary that is part of a right side of organism [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EMAPA:37367 FMA:7213 MA:0001705 NCIT:C33487 SCTID:280123002 UMLS:C0227873 uberon UBERON:0002118 right ovary An ovary that is part of a right side of organism [Automatically generated definition]. OBOL:automatic EMAPA:37367 MA:th UMLS:C0227873 ncithesaurus:Right_Ovary An ovary that is part of a left side of organism [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern In some elasmobranchs, the left ovary does not mature, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo EMAPA:37366 FMA:7214 MA:0001704 NCIT:C32969 SCTID:280124008 UMLS:C0227874 uberon UBERON:0002119 left ovary An ovary that is part of a left side of organism [Automatically generated definition]. OBOL:automatic In some elasmobranchs, the left ovary does not mature, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo Wikipedia:Ovary#In_other_animals EMAPA:37366 MA:th UMLS:C0227874 ncithesaurus:Left_Ovary A a collection of brainstem nuclei that functions in multiple aspects of hearing and is an important component of the ascending and descending auditory pathways of the auditory system. In mice, the superior olivary nucleus is a small cylindrical mass on the dorsal surface of the lateral part of the trapezoid body of the pons, and it is situated immediately above the inferior olivary nucleus. It receives projections from the cochlear nucleus and thus is involved in the perception of sound[GO:0021718] The SOC displays a significant interspecies variation, being largest in bats and rodents and smaller in primates. BAMS:SOC BIRNLEX:1307 DHBA:12462 EMAPA:35840 EV:0100263 FMA:72247 HBA:9177 MA:0001026 MBA:398 UMLS:C0175427 VHOG:0001381 Wikipedia:Superior_olivary_complex http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=569 nucleus olivaris superior superior olivary nuclei uberon regio olivaris superioris superior olivary nucleus superior olivary nucleus (Barr & Kiernan) superior olive UBERON:0002128 superior olivary complex http://upload.wikimedia.org/wikipedia/commons/4/46/Gray713.png NIFSTD A a collection of brainstem nuclei that functions in multiple aspects of hearing and is an important component of the ascending and descending auditory pathways of the auditory system. ISBN:0-19-502694-2 Wikipedia:Superior_olivary_complex UMLS:C0175427 BIRNLEX:1307 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=569 BIRNLEX:1307 nucleus olivaris superior FMA:72247 FMA:TA superior olivary nuclei FMA:72247 regio olivaris superioris NeuroNames:569 superior olivary nucleus FMA:72247 superior olivary nucleus (Barr & Kiernan) NeuroNames:569 superior olive FMA:72247 ISBN:0-19-502694-2 The locus ceruleus is a dense cluster of neurons within the dorsorostral pons. This nucleus is the major location of neurons that release norepinephrine throughout the brain, and is responsible for physiological responses to stress and panic[GO]. Bluish region in the superior angle of the fourth ventricle floor, corresponding to melanin-like pigmented nerve cells which lie lateral to the ponto-mesencephalic central gray (griseum centrale). It is also known as nucleus pigmentosus pontis[GAID]. TODO - check ZFA/pons. also GO says part of dorsorostral pons BAMS:CAE BAMS:LC BIRNLEX:905 BM:Pons-LC BTO:0001408 DHBA:12819 DMBA:16972 EFO:0001963 EMAPA:35502 FMA:72478 GAID:577 HBA:9148 MA:0001017 MBA:147 MESH:D008125 NCIT:C97333 SCTID:369016004 TAO:0000539 UMLS:C0023951 Wikipedia:Locus_ceruleus ZFA:0000539 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=583 blue nucleus caerulean nucleus locus caeruleus locus coeruleu locus coeruleus nucleus caeruleus nucleus of locus caeruleus nucleus pigmentosus pontis substantia ferruginea uberon loci coeruleus locus cinereus locus coeruleus (Vicq d'Azyr) nucleus loci caerulei UBERON:0002148 locus ceruleus http://upload.wikimedia.org/wikipedia/commons/7/77/Gray709.png check ZFA NIFSTD The locus ceruleus is a dense cluster of neurons within the dorsorostral pons. This nucleus is the major location of neurons that release norepinephrine throughout the brain, and is responsible for physiological responses to stress and panic[GO]. Bluish region in the superior angle of the fourth ventricle floor, corresponding to melanin-like pigmented nerve cells which lie lateral to the ponto-mesencephalic central gray (griseum centrale). It is also known as nucleus pigmentosus pontis[GAID]. GAID:577 GO:0021703 Wikipedia:Locus_ceruleus UMLS:C0023951 BIRNLEX:905 UMLS:C0023951 ncithesaurus:Locus_Coeruleus http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=583 BIRNLEX:905 blue nucleus BIRNLEX:905 locus caeruleus BIRNLEX:905 nucleus caeruleus FMA:72478 FMA:TA nucleus pigmentosus pontis BIRNLEX:905 substantia ferruginea BIRNLEX:905 loci coeruleus ZFA:0000539 locus cinereus BTO:0001408 locus coeruleus (Vicq d'Azyr) NeuroNames:583 nucleus loci caerulei NeuroNames:583 Nucleus containing parasympathetic neurons giving rise to the parasympathetic division of the facial nerve, innervating the salivary glands (Brodal, Neurological Anatomy, 3rd ed., 1981, pg 703). BAMS:SSN BAMS:SuS BIRNLEX:1131 DHBA:12435 EHDAA2:0004646 EMAPA:37756 FMA:72482 HBA:9194 MA:0001027 MBA:462 SCTID:369028007 UMLS:C0175447 Wikipedia:Superior_salivatory_nucleus http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=590 superior salivary nucleus uberon nucleus salivarius superior nucleus salivatorius cranialis nucleus salivatorius rostralis nucleus salivatorius superior UBERON:0002149 superior salivatory nucleus http://upload.wikimedia.org/wikipedia/commons/6/6b/Gray788.png definitional Nucleus containing parasympathetic neurons giving rise to the parasympathetic division of the facial nerve, innervating the salivary glands (Brodal, Neurological Anatomy, 3rd ed., 1981, pg 703). BIRNLEX:1131 EMAPA:37756 MA:th UMLS:C0175447 BIRNLEX:1131 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=590 BIRNLEX:1131 superior salivary nucleus GO:0021753 nucleus salivarius superior NeuroNames:590 nucleus salivatorius cranialis NeuroNames:590 nucleus salivatorius rostralis NeuroNames:590 nucleus salivatorius superior NeuroNames:590 The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers[GO]. Layer that lines the lumen of the heart.[TAO] Part of the heart comprised of thin serous membrane, composed of endothelial tissue, that lines the interior of the heart.[AAO] Tunica intima which has as its parts the endothelium of endocardium and the fibroelastic connective tissue that surrounds the cavity of a cardiac chamber. UBERON:0006225 AAO:0010408 BTO:0000387 CALOHA:TS-2075 EFO:0000821 EHDAA2:0004153 EMAPA:17868 EMAPA:32686 EV:0100021 FMA:7280 GAID:550 MA:0000076 MAT:0000455 MESH:D004699 NCIT:C13004 OpenCyc:Mx4rsWA75K1cEduAAADggVaqvw SCTID:362013006 TAO:0001320 UMLS:C0014124 VHOG:0000084 Wikipedia:Endocardium XAO:0000066 ZFA:0001320 galen:Endocardium endocardial lining endocardial tissue heart endocardium uberon heart endocardial tissue UBERON:0002165 fixed in GO to reflect FMA. See email to David/Varsha June 18 2010 endocardium http://upload.wikimedia.org/wikipedia/commons/6/6c/Gray493.png Bgee:AN The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers[GO]. GO:0003157 Layer that lines the lumen of the heart.[TAO] 2012-08-14 TAO:0001320 TAO ZFIN:curator Part of the heart comprised of thin serous membrane, composed of endothelial tissue, that lines the interior of the heart.[AAO] 2012-06-20 AAO:0010408 AAO AAO:BJB Tunica intima which has as its parts the endothelium of endocardium and the fibroelastic connective tissue that surrounds the cavity of a cardiac chamber. FMA:7280 UMLS:C0014124 ncithesaurus:Endocardium endocardial lining EMAPA:32686 endocardial tissue EMAPA:17868 heart endocardial tissue VHOG:0000084 Endocardium that is part of the atrium. EMAPA:32745 FMA:7284 MA:0000077 SCTID:192001005 TAO:0002169 VHOG:0000606 ZFA:0001614 Cardiac atria endocardium atrial endocardium atrium endocardium atrium of heart endocardium cardiac atrium endocardium endocardium of Cardiac atria endocardium of atrium of heart endocardium of cardiac atrium endocardium of heart atrium heart atrium endocardium uberon atrium endocardial tissue UBERON:0002166 endocardium of atrium Endocardium that is part of the atrium. ZFIN:curator Cardiac atria endocardium OBOL:automatic atrium of heart endocardium OBOL:automatic cardiac atrium endocardium OBOL:automatic endocardium of Cardiac atria OBOL:automatic endocardium of atrium of heart OBOL:automatic endocardium of cardiac atrium OBOL:automatic endocardium of heart atrium OBOL:automatic heart atrium endocardium OBOL:automatic atrium endocardial tissue VHOG:0000606 Lung which consists of the right upper lobe, middle lobe and right lower lobe.[FMA] Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG] https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EHDAA2:0001730 EHDAA:4969 EMAPA:17661 FMA:7309 MA:0000426 NCIT:C33483 OpenCyc:Mx8Ngh4rvgHsHZwpEbGdrcN5Y29ycB4rvVjKy5wpEbGdrcN5Y29ycA SCTID:361967000 UMLS:C0225706 VHOG:0000301 Wikipedia:Right_lung uberon UBERON:0002167 right lung http://upload.wikimedia.org/wikipedia/commons/3/32/Gray972.png Lung which consists of the right upper lobe, middle lobe and right lower lobe.[FMA] FMA:FMA Wikipedia:Right_lung Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG] 2012-09-17 VHOG:0000301 VHOG ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210 http://bgee.unil.ch/ UMLS:C0225706 ncithesaurus:Right_Lung Lung which consists of the left upper lobe and left lower lobe.[FMA] Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG] https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EHDAA2:0000943 EHDAA:4947 EMAPA:17653 FMA:7310 MA:0000425 NCIT:C32967 OpenCyc:Mx8Ngh4rvgIFoJwpEbGdrcN5Y29ycB4rvVjKy5wpEbGdrcN5Y29ycA SCTID:361982005 UMLS:C0225730 VHOG:0000618 Wikipedia:Left_lung uberon UBERON:0002168 left lung http://upload.wikimedia.org/wikipedia/commons/d/dd/Gray973.png Lung which consists of the left upper lobe and left lower lobe.[FMA] FMA:FMA Wikipedia:Left_lung Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG] 2012-09-17 VHOG:0000618 VHOG ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210 http://bgee.unil.ch/ UMLS:C0225730 ncithesaurus:Left_Lung A portion of adipose tissue that is part of the hypodermis, beneath the dermis. the superficial portion of the subcutaneous tissue which is specialized for fat storage[MP:0011156] UBERON:0008875 panniculus adiposus BTO:0004042 EMAPA:35829 FMA:74315 MA:0000473 fatty layer of subcutaneous tissue hypodermis fat layer panniculus adiposus (tela subcutanea) panniculus adiposus telae subcutaneae subcutaneous fat layer uberon fatty layer of superficial fascia subcutaneous fat UBERON:0002190 subcutaneous adipose tissue A portion of adipose tissue that is part of the hypodermis, beneath the dermis. http://orcid.org/0000-0002-6601-2165 the superficial portion of the subcutaneous tissue which is specialized for fat storage[MP:0011156] MP:0011156 panniculus adiposus MP:0011156 fatty layer of subcutaneous tissue FMA:74315 hypodermis fat layer MP:0011156 panniculus adiposus (tela subcutanea) FMA:74315 FMA:TA panniculus adiposus telae subcutaneae FMA:74315 FMA:TA subcutaneous fat layer MP:0011156 fatty layer of superficial fascia FMA:74315 subcutaneous fat BTO:0004042 Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs. CALOHA:TS-2018 EHDAA2:0004615 EMAPA:18765 FMA:74562 MA:0000013 hematolymphoid system lymphomyeloid complex uberon haemolymphoid system UBERON:0002193 hemolymphoid system MA Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs. http://orcid.org/0000-0002-6601-2165 The dermis, epidermis and hypodermis. in FMA intergument = skin+superficial fascia(hypodermis), skin=dermis+epidermis+hair_nail. Note that the definition provided here excludes the more general sense of the term 'integument' used in invertebrates; consider 'integumental system'. Note that the VSAO class appears to include adnexa by its definition. Anatomical system that protects the body from damage, comprising the skin and its appendages.[AAO] Surface structure that is the outer protective covering of the body.[VSAO] The outer protective barrier that separates the animal from its aquatic environment. Le Guellec et al, 2004.[TAO] integumental integumentary AAO:0000239 BTO:0000634 EMAPA:37504 FMA:74657 TAO:0000368 VSAO:0000029 Wikipedia:Integument ZFA:0000368 galen:Integument dermis plus epidermis plus hypodermis integumentum commune skin and subcutaneous tissue skin plus hypodermis the integument uberon dermal system dermoid system skin tegument vertebrate integument UBERON:0002199 integument FMA FMA The dermis, epidermis and hypodermis. Wikipedia:Integument Anatomical system that protects the body from damage, comprising the skin and its appendages.[AAO] 2012-06-20 AAO:0000239 AAO AAO:EJS Surface structure that is the outer protective covering of the body.[VSAO] 2012-08-14 VSAO:0000029 VSAO PSPUB:0000170 The outer protective barrier that separates the animal from its aquatic environment. Le Guellec et al, 2004.[TAO] 2012-08-14 TAO:0000368 TAO ZFIN:curator EMAPA:37504 MA:th integumentum commune FMA:74657 FMA:TA the integument FMA:74657 dermal system BTO:0000634 dermoid system BTO:0000634 tegument BTO:0000634 Vasculature that is part of a head [Automatically generated definition]. EFO:0003656 FMA:74710 TAO:0001267 XAO:0004152 ZFA:0001267 adult head vascular network adult head vasculature cranial vasculature head vascular network vascular network of adult head vascular network of head vasculature of adult head uberon head vasculature UBERON:0002200 vasculature of head Vasculature that is part of a head [Automatically generated definition]. OBOL:automatic adult head vascular network OBOL:automatic adult head vasculature OBOL:automatic head vascular network OBOL:automatic vascular network of adult head OBOL:automatic vascular network of head OBOL:automatic vasculature of adult head OBOL:automatic A vasculature that is part of a trunk [Automatically generated definition]. FMA:74712 TAO:0005024 ZFA:0005024 torso vascular network torso vasculature trunk vascular network trunk vasculature vascular network of torso vascular network of trunk vasculature of torso uberon UBERON:0002201 vasculature of trunk A vasculature that is part of a trunk [Automatically generated definition]. OBOL:automatic torso vascular network OBOL:automatic torso vasculature OBOL:automatic trunk vascular network OBOL:automatic vascular network of torso OBOL:automatic vascular network of trunk OBOL:automatic vasculature of torso OBOL:automatic Vasculature that is part of the eye region. not part of the eye in ZFA. Note this changed to a blood vessel in ZFA FMA:74743 SCTID:123846009 TAO:0007057 ZFA:0007057 eye vascular network ocular blood vessel ocular vasculature vascular network of eye uberon eye vasculature optic vasculature UBERON:0002203 vasculature of eye ISBN:0781772214 Vasculature that is part of the eye region. OBOL:automatic https://sourceforge.net/tracker/?func=detail&aid=3489658&group_id=76834&atid=994726 not part of the eye in ZFA. Note this changed to a blood vessel in ZFA ZFA eye vascular network OBOL:automatic ocular blood vessel ZFA:0007057 vascular network of eye OBOL:automatic Anatomical system that consists of the muscular and skeletal systems. Anatomical system that provides locomotion and physical support to the organism.[AAO] There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG] musculoskeletal AAO:0010546 CALOHA:TS-1311 EMAPA:32714 EV:0100139 FMA:7482 GAID:98 MA:0002418 MESH:D009141 NCIT:C12754 OpenCyc:Mx4rQRpVNgAKEdyHxgDggVfs8g SCTID:278858007 UMLS:C0026860 VHOG:0001275 VSAO:0000031 Wikipedia:Musculoskeletal_system XAO:0000168 musculo-skeletal system uberon UBERON:0002204 musculoskeletal system check ctenophore Anatomical system that consists of the muscular and skeletal systems. VSAO:0000031 VSAO:curator https://github.com/obophenotype/uberon/issues/77 Anatomical system that provides locomotion and physical support to the organism.[AAO] 2012-06-20 AAO:0010546 AAO AAO:EJS There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG] 2012-09-17 VHOG:0001275 VHOG DOI:10.1002/jez.b.21246 Shearman RM, Burke AC, The lateral somitic frontier in ontogeny and phylogeny. Journal of Experimental Zoology (2009) http://bgee.unil.ch/ UMLS:C0026860 ncithesaurus:Musculoskeletal_System Nonsynovial joint in which the articulating bones or cartilages are connected by cartilage. Examples: Spheno-occipital synchondrosis, first sternocostal joint, pubic symphysis.[FMA] EMAPA:36581 FMA:7496 MA:0000320 SCTID:58442004 TAO:0005155 Wikipedia:Cartilaginous_joint ZFA:0005155 articulatio cartilaginea uberon junctura cartilaginea UBERON:0002213 cartilaginous joint FMA Nonsynovial joint in which the articulating bones or cartilages are connected by cartilage. Examples: Spheno-occipital synchondrosis, first sternocostal joint, pubic symphysis.[FMA] FMA:FMA Wikipedia:Cartilaginous_joint junctura cartilaginea Wikipedia:Cartilaginous_joint Joint in which the articulating bones or cartilages are connected by an articular capsule which encloses a synovial membrane and a synovial cavity. Examples: Temporomandibular joint, knee joint.[FMA] Is a joint that is located at the point of contact of articulating bones allowing movement. The joint has a capsule containing synovial fluid surrounding the articulating bone surfaces.[TAO] AEO:0000183 CALOHA:TS-2138 EHDAA2:0003183 FMA:7501 MA:0000322 NCIT:C32461 OpenCyc:Mx4rv2bBV5wpEbGdrcN5Y29ycA SCTID:113234001 TAO:0005153 Wikipedia:Synovial_joint ZFA:0005153 galen:SynovialJoint articulatio synoviale diarthroses diarthrosis diarthrosis joint uberon diarthrodial joints UBERON:0002217 synovial joint Joint in which the articulating bones or cartilages are connected by an articular capsule which encloses a synovial membrane and a synovial cavity. Examples: Temporomandibular joint, knee joint.[FMA] FMA:7501 Wikipedia:Synovial_joint Is a joint that is located at the point of contact of articulating bones allowing movement. The joint has a capsule containing synovial fluid surrounding the articulating bone surfaces.[TAO] 2012-08-14 TAO:0005153 TAO ZFIN:Curator diarthroses ZFA:0005153 diarthrodial joints ZFA:0005153 The part of the coelemic cavity lumen that is enclosed by the walls of the thorax. In many species, the diaphragm separates thoracic and abdominal cavities EMAPA:36497 FMA:7565 GAID:93 MA:0000032 MESH:A01.911.800 NCIT:C12905 OpenCyc:Mx4rmvyleLfEEduAAAACs6hRXg OpenCyc:Mx4rvhU_TpwpEbGdrcN5Y29ycA SCTID:243949006 UMLS:C0230139 Wikipedia:Thoracic_cavity cavitas thoracis cavity of chest cavity of thorax chest cavity pectoral cavity space of thoracic compartment thoracic lumen uberon UBERON:0002224 thoracic cavity http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray846.png http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg The part of the coelemic cavity lumen that is enclosed by the walls of the thorax. UBERON:cjm Wikipedia:Thoracic_cavity UMLS:C0230139 ncithesaurus:Thoracic_Cavity cavitas thoracis Wikipedia:Thoracic_cavity space of thoracic compartment FMA:7565 Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal. (CUMBO) TODO - add superclass to unify with VNC? Part of the central nervous system which descends from the hindbrain within the vertebral column.[AAO] (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG] AAO:0010151 BAMS:SP BAMS:Spinal BIRNLEX:1709 BM:SpC BTO:0001279 CALOHA:TS-0953 DHBA:12890 DMBA:17651 EFO:0000110 EHDAA2:0001255 EHDAA:2863 EMAPA:17577 EV:0100316 FMA:7647 GAID:695 MA:0000216 MAT:0000183 MESH:D013116 MIAA:0000183 NCIT:C12464 OpenCyc:Mx4rvVjjk5wpEbGdrcN5Y29ycA SCTID:180959008 TAO:0000075 UMLS:C0037925 VHOG:0000601 Wikipedia:Spinal_cord XAO:0000020 ZFA:0000075 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=22 uberon SpC cerebro-cerebellar fissure cerebrocerebellar fissure fissura cerebro-cerebellaris fissura cerebrocerebellaris medulla spinalis spinal cord structure spinal medulla UBERON:0002240 spinal cord http://upload.wikimedia.org/wikipedia/commons/5/58/Spinal_cord_direv.svg ZFA definitional definitional Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal. (CUMBO) BIRNLEX:1709 Part of the central nervous system which descends from the hindbrain within the vertebral column.[AAO] 2012-06-20 AAO:0010151 AAO AAO:BJB (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000601 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 http://bgee.unil.ch/ UMLS:C0037925 BIRNLEX:1709 UMLS:C0037925 ncithesaurus:Spinal_Cord http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=22 BIRNLEX:1709 SpC cerebro-cerebellar fissure NeuroNames:22 cerebrocerebellar fissure NeuroNames:22 fissura cerebro-cerebellaris NeuroNames:22 fissura cerebrocerebellaris NeuroNames:22 medulla spinalis BTO:0001279 medulla spinalis Wikipedia:Spinal_cord spinal cord structure ZFA:0000075 spinal medulla BTO:0001279 Endoskeletal elements that encase the brain, nose, inner ear[cjm]. that part of the neurocranium formed by endochondral ossification and comprising the bones of the base of the skull[TFD]. we follow the standard evolutionary classification and treat this as endoskeletal. This means what MA calls 'chondrocranium' must in fact be neurocranium, as it includes parts of the dermatocranium (e.g. frontal, parietal) Anatomical cluster that is part of the cranium and composed of cartilage and cartilage replacement bones.[AAO] Anatomical cluster that is part of the cranium and composed of cartilage and cartilage replacement bones.[TAO] chondrocranial covers the brain dorsally in chondrichthyans AAO:0010169 EHDAA2:0000243 EMAPA:17681 TAO:0001424 VHOG:0000288 Wikipedia:Chondrocranium ZFA:0001424 uberon calvarium neurocranium UBERON:0002241 chondrocranium Endoskeletal elements that encase the brain, nose, inner ear[cjm]. that part of the neurocranium formed by endochondral ossification and comprising the bones of the base of the skull[TFD]. Wikipedia:Chondrocranium http://medical-dictionary.thefreedictionary.com/chondrocranium Anatomical cluster that is part of the cranium and composed of cartilage and cartilage replacement bones.[AAO] 2012-06-20 AAO:0010169 AAO AAO:BJB Anatomical cluster that is part of the cranium and composed of cartilage and cartilage replacement bones.[TAO] 2012-08-14 TAO:0001424 TAO ZFIN:curator calvarium MA:0000317 neurocranium MA:0000317 A composite substructure of the brainstem that consists of the midbrain reticular formation, the pontine reticular formation and the medullary reticular formation ( Carpenter-1983 ). this class denotes the generic structure, and not a specific one such as medullary or pontine reticular formation. It is essential for governing some of the basic functions of higher organisms, and is one of the phylogenetically oldest portions of the brain. FMA has a spinal cord reticular formation but we follow NNs (classical) to restrict this to brainstem structures. This means we also include the MA class for brainstem reticular formation here. FMA has subtypes of reticular formation but we treat this as a composite structure BAMS:RET EMAPA:35188 FMA:77719 MA:0003185 MESH:D012154 NLX:143558 SCTID:361552007 Wikipedia:Reticular_formation http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1223 brain stem reticular formation brainstem reticular formation reticular formation (classical) reticular formation of the brainstem uberon UBERON:0002275 reticular formation http://upload.wikimedia.org/wikipedia/commons/9/9b/Gray701.png A composite substructure of the brainstem that consists of the midbrain reticular formation, the pontine reticular formation and the medullary reticular formation ( Carpenter-1983 ). NeuroNames:1223 FMA has a spinal cord reticular formation but we follow NNs (classical) to restrict this to brainstem structures. This means we also include the MA class for brainstem reticular formation here. FMA has subtypes of reticular formation but we treat this as a composite structure FMA brain stem reticular formation NeuroNames:1223 brainstem reticular formation MA:0003185 brainstem reticular formation NeuroNames:1223 reticular formation (classical) NeuroNames:1223 reticular formation of the brainstem NeuroNames:1223 Stalk-like part of the brain that includes amongst its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,MP,generalized]. Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain.[TAO] Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,adopted][ZFA:0001707]. the stalk-like part of the brain that comprises the midbrain (aka mesencephalon), the pons (aka pons Varolii), and the medulla oblongata, and connects the cerebral hemispheres with the cervical spinal cord[MP] BAMS:BS BIRNLEX:1565 BTO:0000146 CALOHA:TS-0093 EFO:0001962 EMAPA:32678 EV:0100241 FMA:79876 MA:0000169 MBA:343 MESH:D001933 NCIT:C12441 SCTID:180925009 TAO:0002156 UMLS:C0006121 VHOG:0001457 Wikipedia:Brainstem ZFA:0001707 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=236 brain stem truncus encephali uberon accessory medullary lamina of pallidum lamella pallidi incompleta lamina medullaris accessoria lamina medullaris incompleta pallidi lamina pallidi incompleta truncus encephalicus UBERON:0002298 'brainstem' is a loose term that sometimes refers to the ventral parts o the brain except for any part of the telencephalon - sometimes it includes the diencephalon or subpallial telencephalon structures (ISBN:0471888893). Here we use it in a more restriced sense, to include only the medulla oblongata, pons (when present) and the midbrain tegmentum (following the ZFA definitions). brainstem http://upload.wikimedia.org/wikipedia/commons/b/b7/Gray719.png Stalk-like part of the brain that includes amongst its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,MP,generalized]. ISBN:0471888893 MP:0005277 Wikipedia:Brainstem ZFA:0001707 Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain.[TAO] 2012-08-14 TAO:0002156 TAO ISBN:3764351209 Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,adopted][ZFA:0001707]. ZFA:0001707 the stalk-like part of the brain that comprises the midbrain (aka mesencephalon), the pons (aka pons Varolii), and the medulla oblongata, and connects the cerebral hemispheres with the cervical spinal cord[MP] MP:0005277 UMLS:C0006121 BIRNLEX:1565 UMLS:C0006121 ncithesaurus:Brain_Stem http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=236 BIRNLEX:1565 brain stem ABA:BS truncus encephali Wikipedia:Brainstem accessory medullary lamina of pallidum NeuroNames:236 lamella pallidi incompleta NeuroNames:236 lamina medullaris accessoria NeuroNames:236 lamina medullaris incompleta pallidi NeuroNames:236 lamina pallidi incompleta NeuroNames:236 truncus encephalicus BTO:0000146 One of the layers of the neocortex. cortical layer ABA:CTX1-6b EMAPA:35588 FMA:83138 MA:0000186 layer of neocortex neocortex layer uberon cerebral cortex layer lamina of neocortex UBERON:0002301 layer of neocortex One of the layers of the neocortex. http://orcid.org/0000-0002-6601-2165 layer of neocortex FMA:83138 neocortex layer MA:0000186 cerebral cortex layer MA:0000186 lamina of neocortex FMA:83138 the atrial part of middle layer of the heart, comprised of involuntary muscle As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[uncertain][VHOG] EFO:0003087 EMAPA:32746 FMA:83509 MA:0000081 SCTID:191910002 TAO:0001374 VHOG:0000602 ZFA:0001374 atrial myocardium atrium myocardium uberon atrium cardiac muscle UBERON:0002302 myocardium of atrium the atrial part of middle layer of the heart, comprised of involuntary muscle ISBN:0-683-40008-8 MP:0010493 As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[uncertain][VHOG] 2012-09-17 VHOG:0000602 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481 http://bgee.unil.ch/ atrial myocardium ZFA:0001374 atrium cardiac muscle VHOG:0000602 A neural nucleus that is part of the brain. EMAPA:35185 FMA:83840 MA:0000811 NCIT:C49346 SCTID:426465002 UMLS:C1706993 ZFA:0005575 brain nucleus uberon brain nuclei UBERON:0002308 nucleus of brain A neural nucleus that is part of the brain. http://orcid.org/0000-0002-6601-2165 UMLS:C1706993 ncithesaurus:Brain_Nucleus brain nuclei ZFA:0005575 The ridge-shaped grey matter of the spinal cord that extends longitudunally through the center of each half of the spinal cord, and are largely or entirely composed of nerve cell bodies and their dendrites and some supportive tissue. BAMS:Scgrey DHBA:146035048 EMAPA:35792 FMA:256580 MA:0000002 NCIT:C32696 NLXANAT:100204 SCTID:279441003 UMLS:C0475853 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=2619 gray matter of spinal cord gray substance of spinal cord grey matter of spinal cord grey substance of spinal cord spinal cord gray matter spinal cord grey matter spinal cord grey substance substantia grisea medullae spinalis uberon UBERON:0002315 gray matter of spinal cord The ridge-shaped grey matter of the spinal cord that extends longitudunally through the center of each half of the spinal cord, and are largely or entirely composed of nerve cell bodies and their dendrites and some supportive tissue. MP:0008503 UMLS:C0475853 ncithesaurus:Gray_Matter_of_the_Spinal_Cord gray matter of spinal cord OBOL:automatic gray substance of spinal cord FMA:256580 spinal cord gray matter OBOL:automatic spinal cord grey substance OBOL:automatic substantia grisea medullae spinalis FMA:256580 FMA:TA The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities. check the FMA placement here; ncit placement of body cavity here probably not correct Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA]. The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO]. In mammals it forms the peritoneal, pleural, and pericardial cavities UBERON:0000169 body cavity AEO:0000186 BTO:0001707 EHDAA2:0000267 FBbt:00005060 FMA:85006 NCIT:C25444 RETIRED_EHDAA2:0003186 SCTID:361348008 TAO:0001438 UMLS:C0333343 ZFA:0001438 galen:BodyCavity coelomic cavity coelomic cavity lumen main body cavity space of body compartment ventral body cavity uberon celom coelom coelome hemocoel UBERON:0002323 coelemic cavity lumen definitional The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities. BTO:0001707 Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA]. 2012-09-12 ZFA:0001438 ZFA ZFIN:curator The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO]. 2012-09-12 BTO:0001707 BTO BTO body cavity BTO:0001707 UMLS:C0333343 ncithesaurus:Cavity coelomic cavity EHDAA2:0000267 coelomic cavity lumen EHDAA2:0000267 space of body compartment FMA:85006 ventral body cavity NCBITaxon:7742 celom BTO:0001707 coelome BTO:0001707 hemocoel FBbt:00005060 Any muscle organ that is part of a back [Automatically generated definition]. EMAPA:35161 FMA:85216 MA:0000496 back muscle back muscle organ muscle organ of back uberon UBERON:0002324 muscle of back prolog Any muscle organ that is part of a back [Automatically generated definition]. OBOL:automatic back muscle organ OBOL:automatic muscle organ of back OBOL:automatic A flexible rod-shaped body found in embryos of all chordates. It is composed of cells derived from the mesoderm and defines the primitive axis of the embryo. In some chordates, it persists throughout life as the main axial support of the body, while in most vertebrates it becomes the nucleus pulposus of the intervertebral disc. The notochord is found ventral to the neural tube. Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO] Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO] Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO] relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO] (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG] notochordal In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord. AAO:0000327 BTO:0001768 CALOHA:TS-0690 EHDAA2:0001277 EHDAA:1241 EHDAA:6021 EMAPA:16191 EV:0100002 FMA:85521 GAID:1311 MAT:0000281 MESH:A16.254.610 NCIT:C12463 SCTID:308820002 TAO:0000135 UMLS:C0028439 VHOG:0000199 VSAO:0000032 Wikipedia:Notochord XAO:0000055 ZFA:0000135 http://evolution.berkeley.edu/evolibrary/images/history/notochords.jpg embryonic notocord notocord uberon notochorda UBERON:0002328 The notochord appears early in embryogeny and plays an important role in promoting or organizing the embryonic development of nearby structures. In most adult chordates the notochord disappears or becomes highly modified. In some non-vertebrate chordates and fishes the notochord persists as a laterally flexible but incompressible skeletal rod that prevents telescopic collapse of the body during swimming[TOLWEB] notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png VSAO http://tolweb.org/Chordata/2499 ZFA EHDAA2 A flexible rod-shaped body found in embryos of all chordates. It is composed of cells derived from the mesoderm and defines the primitive axis of the embryo. In some chordates, it persists throughout life as the main axial support of the body, while in most vertebrates it becomes the nucleus pulposus of the intervertebral disc. The notochord is found ventral to the neural tube. ISBN:0815318960 Wikipedia:Notochord http://tolweb.org/Chordata/2499 https://github.com/obophenotype/uberon/issues/25 https://github.com/obophenotype/uberon/issues/271 Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO] 2012-08-14 VSAO:0000032 VSAO PSPUB:0000170 Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000135 TAO ZFIN:curator Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO] 2012-06-20 AAO:0000327 AAO AAO:LAP relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO] 2012-06-20 AAO:0000327 AAO (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG] 2012-09-17 VHOG:0000199 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 http://bgee.unil.ch/ UMLS:C0028439 ncithesaurus:Notochord notocord ZFA:0000135 notochorda Wikipedia:Notochord Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk Post-cranial axial segments which form sclerotome and dermomyotome.[AAO] Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO] relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO] relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO] relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO] (...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG] somitic mesodermal cluster AAO:0010569 AEO:0001015 BTO:0001558 EHDAA2:0003436 EHDAA:366 EHDAA:699 EMAPA:31169 FMA:85522 GAID:1306 MAT:0000068 MESH:A16.254.425.660.750 MIAA:0000068 NCIT:C34302 TAO:0000155 UMLS:C0376449 VHOG:0000191 Wikipedia:Somite XAO:0000058 ZFA:0000155 uberon epimere epimere mesoderm epithelial somite somites somitic mesoderm somitus UBERON:0002329 When the somite becomes segmented from the segmental plate, it is composed of an epithelial sac enclosing mesenchymal somitocoel cells. Thereafter the somite differentiates into two parts, the ventro-medial mesenchymal sclerotome and the dorso-lateral epithelial dermomyotome. This change in the epithelial somite depends on surrounding tissue [PMID:15906248] somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png EHDAA2 GOTAX:0000352 ZFA Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. DOI:10.1111/j.1439-0426.2012.01987.x Wikipedia:Somite PMID:17237766 Post-cranial axial segments which form sclerotome and dermomyotome.[AAO] 2012-06-20 AAO:0010569 AAO AAO:EJS Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000155 TAO ZFIN:curator relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO] 2012-08-14 TAO:0000155 TAO relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO] 2012-08-14 TAO:0000155 TAO relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO] 2012-06-20 AAO:0010569 AAO (...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000191 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.40, DOI:10.1093/icb/43.1.137 Balavoine G, Adoutte A, The segmented urbilateria: a testable scenario. Integrative and Comparative Biology (2003) http://bgee.unil.ch/ mesodermal cluster GO:0001756 UMLS:C0376449 ncithesaurus:Somite epimere ISBN:0073040584 epithelial somite https://github.com/obophenotype/uberon/wiki/The-neural-crest somites somitus Wikipedia:Somite Anatomical system that consists of the glands and parts of glands that produce exocrine secretions and help to integrate and control bodily metabolic activity. Exocrine glands are glands that secrete their products (hormones) into ducts (duct glands). They are the counterparts to endocrine glands, which secrete their products (hormones) directly into the bloodstream (ductless glands) or release hormones (paracrines) that affect only target cells nearby the release site. [Wikipedia]. CALOHA:TS-2057 EHDAA2:0002225 EMAPA:35329 FMA:85539 MA:0002411 NCIT:C12957 UMLS:C1516995 Wikipedia:Exocrine_gland WikipediaCategory:Exocrine_system exocrine glandular system uberon UBERON:0002330 exocrine system Anatomical system that consists of the glands and parts of glands that produce exocrine secretions and help to integrate and control bodily metabolic activity. Exocrine glands are glands that secrete their products (hormones) into ducts (duct glands). They are the counterparts to endocrine glands, which secrete their products (hormones) directly into the bloodstream (ductless glands) or release hormones (paracrines) that affect only target cells nearby the release site. [Wikipedia]. Wikipedia:Exocrine_gland UMLS:C1516995 ncithesaurus:Exocrine_System exocrine glandular system EHDAA2:0002225 An arterial trunk which is continuous with the heart and branches into the pulmonary arteries. An arterial trunk with origin from the right ventricle of the heart, and dividing into the right and left pulmonary arteries, which enter the corresponding lungs and branch with the bronchi. [TFD][VHOG] As in birds, the conus arteriosus split during embryonic development in mammals to produce the pulmonary trunk and single aortic trunk of the adult.[well established][VHOG] EHDAA2:0001576 EHDAA:9831 EMAPA:17015 FMA:8612 MA:0002033 NCIT:C116918 OpenCyc:Mx4rv-6d0ZwpEbGdrcN5Y29ycA VHOG:0001134 galen:PulmonaryTrunk pulmonary artery (trunk) trunk of pulmonary arterial tree uberon main pulmonary artery UBERON:0002333 pulmonary trunk Alveoli:diagram.png MA An arterial trunk which is continuous with the heart and branches into the pulmonary arteries. http://orcid.org/0000-0002-6601-2165 An arterial trunk with origin from the right ventricle of the heart, and dividing into the right and left pulmonary arteries, which enter the corresponding lungs and branch with the bronchi. [TFD][VHOG] 2012-09-17 VHOG:0001134 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/pulmonary+trunk As in birds, the conus arteriosus split during embryonic development in mammals to produce the pulmonary trunk and single aortic trunk of the adult.[well established][VHOG] 2012-09-17 VHOG:0001134 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481 http://bgee.unil.ch/ main pulmonary artery Wikipedia:Pulmonary_artery A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams). A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO] Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO] A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831] We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG] AAO:0010578 BTO:0001764 CALOHA:TS-0676 EHDAA2:0004419 EMAPA:32737 FMA:86666 GAID:1310 MAT:0000066 MESH:A16.254.600 MIAA:0000066 NCIT:C34222 SCTID:361462002 TAO:0000045 UMLS:C0027789 VHOG:0000057 Wikipedia:Neural_crest XAO:0000048 ZFA:0000045 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1366 NC uberon crista neuralis neural crest material UBERON:0002342 Gene notes: Many factors and genes, such as Pax3 (Tremblay et al., 1995), slug (Nieto et al., 1994), AP-2 (Zhang et al., 1996; Schorle et al., 1996), and Wnt-1/3a (Ikeya et al., 1997) are expressed in the dorsal most region of the neural tube, and have been shown to be involved in the generation of neural crest cells. neural crest Neural:Crest.png http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png XAO https://github.com/obophenotype/uberon/wiki/The-neural-crest Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells ISBN:0073040584 BTO PMID:11523831 pre migratory https://github.com/obophenotype/uberon/wiki/The-neural-crest PMID:11523831 A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. MP:0009846 ISBN:0073040584 PMID:17377535 A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000045 TAO ZFIN:curator Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO] 2012-06-20 AAO:0010578 AAO AAO:EJS A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831] PMID:11523831 We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG] 2012-09-17 VHOG:0000057 VHOG DOI:10.1111/j.1469-7580.2012.01495.x Hall BK, Gillis JA, Incremental evolution of the neural crest, neural crest cells and neural crest-derived skeletal tissues. J Anat (2012) http://bgee.unil.ch/ UMLS:C0027789 ncithesaurus:Neural_Crest NC XAO:0000048 crista neuralis Wikipedia:Neural_crest neural crest material VHOG:0000057 Set of all muscles in abdomen. distinction between abdomen muscle and abdomen musculature FMA:71294 FMA:86917 TAO:0001327 ZFA:0001327 abdominal musculature muscle group of abdomen muscles of abdomen musculature of abdomen musculature of abdominal wall set of muscles of abdomen uberon UBERON:0002343 abdomen musculature Set of all muscles in abdomen. OBOL:automatic muscle group of abdomen FMA:71294 muscles of abdomen FMA:71294 musculature of abdominal wall FMA:86917 set of muscles of abdomen FMA:71294 Embryonic ectoderm that gives rise to nervous tissue. (...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG] neurectodermal we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here AAO:0011074 BILA:0000039 CALOHA:TS-1212 EHDAA2:0001248 EHDAA:1498 EHDAA:255 EMAPA:16073 EV:0100004 FBbt:00001061 FMA:87657 MAT:0000176 MIAA:0000176 NCIT:C34228 TAO:0001120 UMLS:C1518271 VHOG:0000150 Wikipedia:Neuroectoderm XAO:0000042 ZFA:0001120 neural ectoderm neuroectoderm uberon epithelium tubi neuralis; neuroectoderma neuaral ectoderm presumptive central nervous system ventral neurogenic region UBERON:0002346 neurectoderm ZFA Embryonic ectoderm that gives rise to nervous tissue. Wikipedia:Neuroectoderm (...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG] 2012-09-17 VHOG:0000150 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) http://bgee.unil.ch/ UMLS:C1518271 ncithesaurus:Neuroectoderm epithelium tubi neuralis; neuroectoderma Wikipedia:Neuroectoderm ventral neurogenic region VHOG:0000150 A thoracic vertebra endochondral element that is composed primarily of a bone tissue. Thoracic vertebrae in all species are defined as those vertebrae which also carry a pair of ribs, and lie caudal to the cervical vertebrae. In humans, they are distinguished by the presence of facets on the sides of the bodies for articulation with the heads of the ribs, and facets on the transverse processes of all, except the eleventh and twelfth, for articulation with the tubercles of the ribs EMAPA:18011 FMA:9139 GAID:244 MA:0000314 MESH:D013904 NCIT:C12798 OpenCyc:Mx4rvdZIBpwpEbGdrcN5Y29ycA SCTID:181821009 UMLS:C0039987 Wikipedia:Thoracic_vertebrae dorsal vertebra thorax vertebra vertebra of thorax vertebra thoracica uberon UBERON:0002347 thoracic vertebra http://upload.wikimedia.org/wikipedia/commons/d/d2/Gray90.png A thoracic vertebra endochondral element that is composed primarily of a bone tissue. OBOL:automatic UMLS:C0039987 ncithesaurus:Thoracic_Vertebra thorax vertebra OBOL:automatic vertebra of thorax OBOL:automatic a region of the serous membrane that forms the innermost layer of the pericardium and the outer surface of the heart. TODO - check links with UBERON:0002425 visceral serous pericardium. develops from proepicardium. WP:Epicardium -- When considered as a part of the pericardium, it is the inner layer, or visceral pericardium, continuous with the serous layer. External layer of the heart.[TAO] The inner layer of the pericardium that is in contact with the surface of the heart.[AAO] The visceral pericardium apparently produces the pericardial fluid, which lubricates motion between the inner and outer layers of the pericardium. During ventricular contraction, the wave of depolarization moves from endocardial to epicardial surface. [Wikipedia:Epicardium] AAO:0010409 EHDAA2:0002202 FMA:9461 NCIT:C13164 TAO:0005057 UMLS:C0225968 VHOG:0000119 Wikipedia:Epicardium XAO:0000316 ZFA:0005057 galen:Epicardium heart epicardium visceral serous pericardium of heart visceral serous pericardium proper uberon pericardium visceral mesothelium UBERON:0002348 epicardium multiple FMA-inferred FMA a region of the serous membrane that forms the innermost layer of the pericardium and the outer surface of the heart. http://orcid.org/0000-0002-6601-2165 External layer of the heart.[TAO] 2012-08-14 TAO:0005057 TAO ZFIN:curator The inner layer of the pericardium that is in contact with the surface of the heart.[AAO] 2012-06-20 AAO:0010409 AAO AAO:BJB UMLS:C0225968 ncithesaurus:Epicardium visceral serous pericardium of heart FMA:9461 visceral serous pericardium proper FMA:9461 pericardium visceral mesothelium EMAPA:16589 the middle layer of the heart, comprised mainly of striated cardiac muscle fibers TODO - check 'Myocardum proper' in FMA. We superclass the more generic class for now. FMA has is_a muscle layer - should we add this? ZFA and BTO both have is_a 'cardiac muscle' (tissue?). But in U we also follow FMA and have cardiac muscle tissue of myocardium (there is also Fibrocollagenous connective tissue of myocardium), which would be identical (see issue-10). Note that GO also treats left/right ventricular cardiac muscle tissue synonymous with ventricular myocardium Robust muscular tunic of the heart which forms the basic part of its walls. Its external surface is covered by the pericardium and its internal one by the endocardium. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] The middle layer of the heart, consisting of cardiac muscle.[AAO] myocardial AAO:0010410 BSA:0000089 BTO:0000901 CALOHA:TS-0440 EFO:0000819 EHDAA2:0004150 EMAPA:32688 EV:0100022 FMA:9462 GAID:173 MA:0000164 MAT:0000453 MESH:D009206 NCIT:C12371 OpenCyc:Mx4ro36AFrCvEduAAAAOpmP6tw RETIRED_EHDAA2:0001220 SCTID:362012001 TAO:0001319 UMLS:C0027061 VHOG:0000083 Wikipedia:Myocardium XAO:0000065 ZFA:0001319 galen:Myocardium heart myocardium muscle of heart uberon cardiac muscle heart muscle UBERON:0002349 myocardium http://upload.wikimedia.org/wikipedia/commons/6/6e/Glanzstreifen.jpg the middle layer of the heart, comprised mainly of striated cardiac muscle fibers ISBN:0-683-40008-8 MP:0005329 Robust muscular tunic of the heart which forms the basic part of its walls. Its external surface is covered by the pericardium and its internal one by the endocardium. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000083 VHOG http://bgee.unil.ch/ The middle layer of the heart, consisting of cardiac muscle.[AAO] 2012-06-20 AAO:0010410 AAO AAO:BJB UMLS:C0027061 ncithesaurus:Myocardium muscle of heart FMA:9462 cardiac muscle ZFA:0001319 heart muscle FMA:9462 heart muscle ZFA:0001319 The cardiac conduction system consists of specialized cardiomyocytes that regulate the frequency of heart beat[GO] EHDAA2 divides the system from the tissue The fish heart displays clear polarity of contraction in a posterior-to-anterior direction. The contraction waves originate in the sinus venosus and terminate in the conus arteriosus. The nodal phenotype persists in the inflow region of the heart, varying from the venosinus to the sinoatrial junctional areas in different species . Similar to the mammalian situation, pacemaker tissue with a lower intrinsic rhythmicity is also found at the atrioventricular junction.[uncertain][VHOG] EFO:0003909 EHDAA2:0004185 EMAPA:35428 EV:0100025 FMA:9476 MA:0000094 MESH:D006329 SCTID:281489000 TAO:0005063 VHOG:0001271 ZFA:0005063 cardiac conducting system cardiac conduction system cardiac impulse conducting system cardionector complexus stimulans cordis heart conduction system impulse conducting system systema conducente cordis uberon central conduction system UBERON:0002350 conducting system of heart FMA FMA FMA FMA FMA FMA The cardiac conduction system consists of specialized cardiomyocytes that regulate the frequency of heart beat[GO] GO:0003161 The fish heart displays clear polarity of contraction in a posterior-to-anterior direction. The contraction waves originate in the sinus venosus and terminate in the conus arteriosus. The nodal phenotype persists in the inflow region of the heart, varying from the venosinus to the sinoatrial junctional areas in different species . Similar to the mammalian situation, pacemaker tissue with a lower intrinsic rhythmicity is also found at the atrioventricular junction.[uncertain][VHOG] 2012-09-17 VHOG:0001271 VHOG DOI:10.1152/physrev.00006.2003 Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003) http://bgee.unil.ch/ cardiac conducting system VHOG:0001271 cardiac impulse conducting system GO:0003161 complexus stimulans cordis FMA:9476 FMA:TA heart conduction system GO:0003161 impulse conducting system MA:0000094 systema conducente cordis FMA:9476 FMA:TA The part of the cardiac conduction system that controls the timing of heart muscle contraction. It relays electrical signals to the AV node[GO]. Subdivision of conducting system of heart at the junction of the right atrium and the superior vena cava, around the sinoatrial nodal branch of right coronary artery and is continuous with the internodal tract[FMA]. BTO:0004358 EHDAA2:0004184 EMAPA:35772 FMA:9477 GAID:561 MA:0000097 MESH:D012849 NCIT:C33555 OpenCyc:Mx4rOhejDGMcEd2AAABQjYGu0g SCTID:277687007 TAO:0005069 UMLS:C0037189 Wikipedia:Sinoatrial_node ZFA:0005069 Koch's node SA nodal muscle tissue SA node cardiac pacemaker node of Keith-Flack nodus sinuatrialis sinoatrial node sinu-atrial node sinuatrial nodal muscle tissue sinuatrial node sinus node sinus node of Keith and Flack uberon nodus sinuatrialis UBERON:0002351 WP:Heart states: "The SA node is found in all amniotes but not in more primitive vertebrates. In these animals, the muscles of the heart are relatively continuous and the sinus venosus coordinates the beat which passes in a wave through the remaining chambers. Indeed, since the sinus venosus is incorporated into the right atrium in amniotes, it is likely homologous with the SA node. In teleosts, with their vestigial sinus venosus, the main centre of coordination is, instead, in the atrium.". Note however that ZFA has SA node. sinoatrial node http://upload.wikimedia.org/wikipedia/commons/d/d2/Sinoatrial_node_low_mag.jpg http://upload.wikimedia.org/wikipedia/commons/d/de/Sinoatrial_node_2_low_mag.jpg cjm ZFA The part of the cardiac conduction system that controls the timing of heart muscle contraction. It relays electrical signals to the AV node[GO]. Subdivision of conducting system of heart at the junction of the right atrium and the superior vena cava, around the sinoatrial nodal branch of right coronary artery and is continuous with the internodal tract[FMA]. GO:0003163 Wikipedia:Sinoatrial_node UMLS:C0037189 ncithesaurus:Sinoatrial_Node Koch's node FMA:9477 SA nodal muscle tissue FMA:9477 SA node FMA:9477 cardiac pacemaker FMA:9477 node of Keith-Flack FMA:9477 nodus sinuatrialis FMA:9477 FMA:TA sinoatrial node FMA:9477 sinu-atrial node FMA:9477 sinuatrial nodal muscle tissue FMA:9477 sinuatrial node FMA:9477 sinus node FMA:9477 sinus node of Keith and Flack FMA:9477 nodus sinuatrialis Wikipedia:Sinoatrial_node An area of conducting tissue between the atria and the ventricles of the heart that conducts the normal electrical impulse from the atria to the ventricles. Three major adaptations, or 'novel cardiac components', that were not present in the ancestor chordate heart tube can be distinguished in the lower vertebrate heart: the atrium, ventricle, and possibly the muscular sinus venosus. Furthermore, within the ventricular component a compact outer myocardial component and an interiorly localized extensive trabecular component can be distinguished. The specific activation of the ventricle adds to its complexity as follows. The depolarizing impulse travels rapidly from the atrioventricular node toward the apex and then toward the conal region, achieving activation from apex to base.[uncertain][VHOG] BTO:0005689 EFO:0000276 EHDAA2:0004183 EMAPA:35153 FMA:9478 GAID:558 MA:0000095 MAT:0000498 MESH:D001283 NCIT:C32161 OpenCyc:Mx4rMfD91mMcEd2AAABQjYGu0g SCTID:277688002 TAO:0005070 UMLS:C0004247 VHOG:0001474 Wikipedia:Atrioventricular_node ZFA:0005070 AV nodal muscle tissue AV node Aschoff-Tawara node atrioventricular nodal muscle tissue node of Tawara nodus atrioventricularis uberon A-V node atrio-ventricular node atriovetricular node downstream pacemaker nodus atrioventricularis UBERON:0002352 atrioventricular node http://upload.wikimedia.org/wikipedia/commons/5/50/ConductionsystemoftheheartwithouttheHeart.png http://upload.wikimedia.org/wikipedia/commons/9/92/Gray501.png cjm An area of conducting tissue between the atria and the ventricles of the heart that conducts the normal electrical impulse from the atria to the ventricles. UBERON:cjm Wikipedia:Atrioventricular_node Three major adaptations, or 'novel cardiac components', that were not present in the ancestor chordate heart tube can be distinguished in the lower vertebrate heart: the atrium, ventricle, and possibly the muscular sinus venosus. Furthermore, within the ventricular component a compact outer myocardial component and an interiorly localized extensive trabecular component can be distinguished. The specific activation of the ventricle adds to its complexity as follows. The depolarizing impulse travels rapidly from the atrioventricular node toward the apex and then toward the conal region, achieving activation from apex to base.[uncertain][VHOG] 2012-09-17 VHOG:0001474 VHOG DOI:10.1152/physrev.00006.2003 Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003) http://bgee.unil.ch/ UMLS:C0004247 ncithesaurus:Atrioventricular_Node AV nodal muscle tissue FMA:9478 AV node FMA:9478 MA:0000095 Aschoff-Tawara node FMA:9478 atrioventricular nodal muscle tissue FMA:9478 node of Tawara FMA:9478 nodus atrioventricularis FMA:TA A-V node EMAPA:35153 atrio-ventricular node EMAPA:35153 atriovetricular node TAO:0005070 downstream pacemaker ZFA:0005070 nodus atrioventricularis Wikipedia:Atrioventricular_node The lower segment of the trunk, inferioposterior to the abdomen proper, in the transition area between the trunk and the lower limbs. pelvic MA and FMA differ in what they consider to be parts of the pelvis. MA includes ureter, urethra, urinary bladder, reproductive organs BTO:0001006 CALOHA:TS-2227 EFO:0002805 EMAPA:35931 EV:0100012 FMA:9578 GAID:87 MA:0000030 MESH:A01.673 NCIT:C12767 OpenCyc:Mx4rvVjiTJwpEbGdrcN5Y29ycA SCTID:229765004 UMLS:C0030797 Wikipedia:Pelvis galen:Pelvis lesser pelvis pelvic region pelvis pelvis region true pelvis uberon UBERON:0002355 pelvic region of trunk The lower segment of the trunk, inferioposterior to the abdomen proper, in the transition area between the trunk and the lower limbs. Wikipedia:Pelvis http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/720 MA and FMA differ in what they consider to be parts of the pelvis. MA includes ureter, urethra, urinary bladder, reproductive organs MA UMLS:C0030797 ncithesaurus:Pelvis lesser pelvis FMA:9578 pelvis FMA:9578 MA:0000030 true pelvis FMA:9578 Serous membrane which is divided into parietal and visceral serous pericardium. EMAPA:19030 FMA:9582 MA:0002739 SCTID:243954002 Wikipedia:Serous_pericardium serous portion of pericardium uberon pericardium serosum UBERON:0002357 serous pericardium FMA FMA Serous membrane which is divided into parietal and visceral serous pericardium. Wikipedia:Serous_pericardium http://orcid.org/0000-0002-6601-2165 serous portion of pericardium FMA:9582 pericardium serosum Wikipedia:Serous_pericardium A serous membrane that lines the peritoneal cavity[VHOG,modified]. TODO - in ZFA is_a epithelium An epithelium that lines the peritoneal cavity.[TAO] Serous membrane that forms the lining of the abdominal cavity or the coelom. It covers most of the intra-abdominal organs, supports the abdominal organs, and serves as a conduit for their blood and lymph vessels and nerves. It is composed of a layer of mesothelium.[AAO] peritoneal todo: check MA/EMAPA. AAO:0010814 BTO:0001472 CALOHA:TS-2072 EV:0100087 FMA:9584 GAID:18 MA:0000449 MESH:A01.047.025.600 NCIT:C12770 OpenCyc:Mx4rvjJ72ZwpEbGdrcN5Y29ycA TAO:0005120 UMLS:C0031153 VHOG:0001257 Wikipedia:Peritoneum XAO:0000139 ZFA:0005120 galen:Peritoneum uberon peritonaeum UBERON:0002358 peritoneum http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray1040.png MP A serous membrane that lines the peritoneal cavity[VHOG,modified]. VHOG:0001257 An epithelium that lines the peritoneal cavity.[TAO] 2012-08-14 TAO:0005120 TAO ZFIN:curator Serous membrane that forms the lining of the abdominal cavity or the coelom. It covers most of the intra-abdominal organs, supports the abdominal organs, and serves as a conduit for their blood and lymph vessels and nerves. It is composed of a layer of mesothelium.[AAO] 2012-06-20 AAO:0010814 AAO AAO:JMG todo: check MA/EMAPA. MA UMLS:C0031153 ncithesaurus:Peritoneum peritonaeum VHOG:0001257 Membrane organ which is attached to the pericardial sac proper and the central tendon of diaphragm and is continuous with the pretracheal fascia.[FMA] most superficial part of pericardium; continuous with the outer adventitial layer of the neighboring great blood vessels. [Wikipedia:Pericardium] EMAPA:19029 FMA:9586 MA:0002738 SCTID:243953008 Wikipedia:Fibrous_pericardium fibrous portion of pericardium uberon pericardium fibrosum UBERON:0002359 fibrous pericardium FMA FMA WP Membrane organ which is attached to the pericardial sac proper and the central tendon of diaphragm and is continuous with the pretracheal fascia.[FMA] FMA:9586 pericardium fibrosum Wikipedia:Fibrous_pericardium A gland that secretes products (excluding hormones and other chemical messengers) into ducts (duct glands) which lead directly into the external environment[WP]. Typical exocrine glands include sweat glands, salivary glands, mammary glands, stomach, liver, pancreas Currently this is logically defined by the system it belongs to, but a better system may be base this on presence/absence of ducts. However, the dual nature of the liver should be taken into consideration here. Consider adding subclasses AEO:0000097 BTO:0000765 CALOHA:TS-2012 EHDAA2:0003097 EMAPA:35327 FMA:9596 GAID:34 MA:0002564 MESH:D005088 NCIT:C12712 SCTID:115976003 UMLS:C0015282 Wikipedia:Exocrine_gland ducted gland glandula exocrina uberon UBERON:0002365 exocrine gland A gland that secretes products (excluding hormones and other chemical messengers) into ducts (duct glands) which lead directly into the external environment[WP]. Typical exocrine glands include sweat glands, salivary glands, mammary glands, stomach, liver, pancreas Wikipedia:Exocrine_gland UMLS:C0015282 ncithesaurus:Exocrine_Gland ducted gland AEO:0000097 glandula exocrina Wikipedia:Exocrine_gland Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified]. AEO:0000098 BTO:0001488 CALOHA:TS-1300 EHDAA2:0003098 EMAPA:35999 FMA:9602 GAID:335 MA:0002563 MESH:D004702 NCIT:C12704 OpenCyc:Mx4rvbkiRZwpEbGdrcN5Y29ycA SCTID:40818001 UMLS:C0014133 Wikipedia:Endocrine_gland ductless gland glandula endocrina uberon ductless gland glandulae endocrinae UBERON:0002368 endocrine gland http://upload.wikimedia.org/wikipedia/commons/d/da/Illu_endocrine_system.png Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified]. Wikipedia:Endocrine_gland UMLS:C0014133 ncithesaurus:Endocrine_Gland ductless gland AEO:0000098 ductless gland Wikipedia:Ductless_gland glandulae endocrinae Wikipedia:Endocrine_gland the soft tissue that fills the cavities of bones TODO - create superclass for bone marrow / head kidney. both are portions of tissue in the hematopoetic system. also consider adding as subclass of zone of bone organ for consistency with FMA. See also: Leydig and epigonal organs consider placement of NCIT:C53466 medullary bone The bone marrow is the hematopoietic organ in all vertebrates but fishes, in which hematopoiesis occurs in the kidney.[well established][VHOG] In adults, marrow in large bones produces new blood cells[Wikipedia:Bone_marrow] AAO:0011007 BTO:0000141 BTO:0000829 CALOHA:TS-0087 EFO:0000868 EMAPA:32760 EV:0100046 FMA:9608 GAID:1287 MA:0000134 MAT:0000084 MESH:D001853 MIAA:0000084 NCIT:C12431 OpenCyc:Mx4rvVm-FpwpEbGdrcN5Y29ycA SCTID:421320006 UMLS:C0005953 VHOG:0001218 Wikipedia:Bone_marrow XAO:0000123 galen:BoneMarrow medulla ossea medulla ossium uberon medulla of bone medullary bone UBERON:0002371 bone marrow http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg FMA MA the soft tissue that fills the cavities of bones MGI:cwg MP:0002397 The bone marrow is the hematopoietic organ in all vertebrates but fishes, in which hematopoiesis occurs in the kidney.[well established][VHOG] 2012-09-17 VHOG:0001218 VHOG DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood Cells and Blood Cell Development in the Animal Kingdom. Annual Review of Cell and Developmental Biology (2006) http://bgee.unil.ch/ UMLS:C0005953 ncithesaurus:Bone_Marrow medulla ossea BTO:0000141 FMA:9608 medulla ossium BTO:0000141 Wikipedia:Bone_marrow medulla of bone BTO:0000141 Any skeletal muscle that is part of the head region. UBERON:0003899 AAO:0000107 BTO:0000021 EFO:0003524 EHDAA2:0000322 EMAPA:18172 FMA:9616 MA:0000578 SCTID:244718003 ZFA:0001652 cephalic muscle cephalic musculature head muscle head muscle organ muscle of head muscle organ of adult head muscle organ of head musculus caput adult head muscle organ uberon cranial muscle head muscles UBERON:0002376 defined generically so could in theory encompass FBbt:00003260 'skeletal muscle of head', or the muscle of a starfish Aristotle's lantern, but we restrict this to craniates. Skeletal muscles of the head originate from the non-segmented head mesoderm (Noden, 1983; Wachtler et al., 1984) cranial muscle https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships EHDAA2-abduced Any skeletal muscle that is part of the head region. http://orcid.org/0000-0002-6601-2165 cephalic muscle ZFA:0001652 head muscle MA:0000578 head muscle organ OBOL:automatic muscle of head FMA:9616 muscle organ of adult head OBOL:automatic muscle organ of head OBOL:automatic adult head muscle organ OBOL:automatic cranial muscle ZFA:0001652 Any muscle that is part of the cervical (neck) region. EMAPA:36050 FMA:9617 GAID:149 MA:0000587 MESH:D009334 NCIT:C33163 UMLS:C0027532 muscle organ of neck muscle organ of neck (volume) neck (volume) muscle organ neck muscle neck muscle organ uberon UBERON:0002377 muscle of neck prolog Any muscle that is part of the cervical (neck) region. http://orcid.org/0000-0002-6601-2165 UMLS:C0027532 ncithesaurus:Neck_Muscle muscle organ of neck OBOL:automatic muscle organ of neck (volume) OBOL:automatic neck (volume) muscle organ OBOL:automatic neck muscle organ OBOL:automatic Muscle (organ) which is a part of the abdomen. Examples: external oblique, rectus abdominis. BTO:0001261 EMAPA:35103 FMA:9620 GAID:89 MA:0000520 MESH:D000009 NCIT:C32040 OpenCyc:Mx4rvlygNJwpEbGdrcN5Y29ycA SCTID:361352008 UMLS:C0000739 Wikipedia:Abdominal_muscle abdomen muscle abdomen muscle organ abdominal muscle abdominal wall muscle muscle organ of abdomen uberon abdominal wall musculature UBERON:0002378 muscle of abdomen prolog Muscle (organ) which is a part of the abdomen. Examples: external oblique, rectus abdominis. Wikipedia:Abdominal_muscle UMLS:C0000739 ncithesaurus:Abdominal_Muscle abdomen muscle organ OBOL:automatic muscle organ of abdomen OBOL:automatic abdominal wall musculature EMAPA:35103 Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance. One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO] Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO] Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO] MA also has set of connective tissues AAO:0000098 BTO:0000421 CALOHA:TS-2009 EFO:0000952 EMAPA:35251 FMA:9640 GAID:100 MA:0000011 MAT:0000301 MESH:D003238 MIAA:0000301 NCIT:C12374 OpenCyc:Mx4rv-aBgZwpEbGdrcN5Y29ycA SCTID:361919005 TAO:0001641 UMLS:C0009780 VSAO:0000017 XAO:0001017 ZFA:0001632 galen:ConnectiveTissue portion of connective tissue textus connectivus uberon Bindegewebe UBERON:0002384 connective tissue Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance. GO_REF:0000034 PSPUB:0000170 VSAO:0000017 http://dx.plos.org/10.1371/journal.pone.0051070 https://github.com/obophenotype/uberon/issues/23 One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO] 2012-06-20 AAO:0000098 AAO AAO:LAP Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO] 2012-08-14 TAO:0001641 TAO TAO:wd Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO] 2012-08-14 VSAO:0000017 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 PSPUB:0000170 MA also has set of connective tissues MA UMLS:C0009780 ncithesaurus:Connective_Tissue portion of connective tissue FMA:9640 Bindegewebe BTO:0000421 Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO]. One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO] AAO:0000306 AEO:0000122 CALOHA:TS-0642 EHDAA2:0003122 EMAPA:32715 FMA:9641 MA:0002437 MESH:D009132 NCIT:C12435 SCTID:91727004 UMLS:C2328219 Wikipedia:Muscle_tissue galen:MuscleTissue muscular tissue portion of muscle tissue textus muscularis uberon UBERON:0002385 Vertebrate muscle is categorized into three major muscle types defined by their structural and functional properties: skeletal, cardiac and smooth. In Dmel the counterparts are somatic, heart/cardiac and visceral. Here we take a cell type based approach. muscle tissue Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO]. GO:0060537 Wikipedia:Muscle_tissue https://sourceforge.net/tracker/index.php?func=detail&aid=2801266&group_id=36855&atid=440764 One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO] 2012-06-20 AAO:0000306 AAO AAO:LAP UMLS:C2328219 ncithesaurus:Muscle_Tissue muscular tissue portion of muscle tissue FMA:9641 Anatomical system that is involved in the production of hematopoietic cells. Anatomical system that consists of the blood and blood forming tissues.[AAO] Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG] hematopoietic In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes AAO:0011002 BTO:0000570 CALOHA:TS-0449 EFO:0000798 EMAPA:35402 EV:0100045 FMA:9667 GAID:1008 MA:0002434 MAT:0000022 MESH:D006413 MIAA:0000022 NCIT:C12909 SCTID:362587009 TAO:0005023 UMLS:C0018957 VHOG:0001624 Wikipedia:Haematopoiesis XAO:0000122 ZFA:0005023 haematological system haemopoietic system organa haemopoietica uberon Blutbildungssystem haematopoietic system hematological system hematolymphoid system hemopoietic system UBERON:0002390 hematopoietic system FMA definitional Anatomical system that is involved in the production of hematopoietic cells. Wikipedia:Haematopoiesis Anatomical system that consists of the blood and blood forming tissues.[AAO] 2012-06-20 AAO:0011002 AAO AAO:EJS Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG] 2012-09-17 VHOG:0001624 VHOG DOI:10.1016/j.coph.2010.05.004 Ellett F, Lieschke GJ, Zebrafish as a model for vertebrate hematopoiesis. Current Opinion in Pharmacology (2010) http://bgee.unil.ch/ In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes WP UMLS:C0018957 ncithesaurus:Hematopoietic_System Blutbildungssystem BTO:0000570 The outer serous membrane of the pulmonary pleural. EMAPA:16776 FMA:9733 MA:0002488 NCIT:C33273 OpenCyc:Mx4rvv2Uq5wpEbGdrcN5Y29ycA SCTID:361998003 UMLS:C0225777 VHOG:0001495 Wikipedia:Parietal_pleura uberon pleura parietalis UBERON:0002400 the part of the pleura external to the visceral pleura. It lines the inner surface of the chest wall, covers the diaphragm, and is reflected over the structures occupying the middle of the thorax parietal pleura The outer serous membrane of the pulmonary pleural. UBERON:cjm Wikipedia:Pulmonary_pleurae UMLS:C0225777 ncithesaurus:Parietal_Pleura pleura parietalis Wikipedia:Parietal_pleura The inner serous membrane of the pulmonary pleural. The visceral pleura lines the lungs. Each lung is invested by an exceedingly delicate serous membrane, the pleura, which is arranged in the form of a closed invaginated sac. A portion of the serous membrane covers the surface of the lung and dips into the fissures between its lobes; it is called the pulmonary pleura (or visceral pleura). The visceral pleura is attached directly to the lungs[Wikipedia:Visceral_pleura]. FMA treats this as part of the lungs EHDAA2:0002205 EMAPA:16777 FMA:9734 MA:0002489 NCIT:C33881 OpenCyc:Mx4rwNFqppwpEbGdrcN5Y29ycA SCTID:361997008 UMLS:C0225776 VHOG:0001496 pleura pulmonalis pleura visceralis pleura visceralis (pulmonalis) pulmonary visceral pleura uberon lung mesothelium lung pleura pulmonary pleura UBERON:0002401 visceral pleura FMA The inner serous membrane of the pulmonary pleural. The visceral pleura lines the lungs. UBERON:cjm Wikipedia:Pulmonary_pleurae Each lung is invested by an exceedingly delicate serous membrane, the pleura, which is arranged in the form of a closed invaginated sac. A portion of the serous membrane covers the surface of the lung and dips into the fissures between its lobes; it is called the pulmonary pleura (or visceral pleura). The visceral pleura is attached directly to the lungs[Wikipedia:Visceral_pleura]. Wikipedia:Visceral_pleura FMA treats this as part of the lungs FMA UMLS:C0225776 ncithesaurus:Visceral_Pleura pleura pulmonalis FMA:9734 FMA:TA pleura visceralis Wikipedia:Visceral_pleura lung mesothelium EHDAA2:0002205 pulmonary pleura FMA:9734 The fluid-filled cavity that lies between the visceral and parietal pleurae. In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart [of other tetrapods] is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG] The contraction of the diaphragm creates a negative pressure within the pleural cavity which forces the lungs to expand resulting in passive exhalation and active inhalation. This breathing process can be made forceful through the contraction of the external intercostal muscles which forces the rib cage to expand and add to the negative pressure in the pleural cavity causing the lungs to fill with air. The fluid in the cavity provides lubrication and cushioning the EHDAA2 class of the same is not equivalent. See https://github.com/obophenotype/uberon/issues/86 BTO:0004422 EHDAA2:0001475 EMAPA:16773 EMAPA:16774 FMA:9740 GAID:95 MA:0000055 MESH:A01.911.800.650 NCIT:C12840 OpenCyc:Mx4rwCKAppwpEbGdrcN5Y29ycA SCTID:361999006 UMLS:C0178802 VHOG:0000581 Wikipedia:Pleural_cavity cavitas pleuralis uberon cavitum pleuralae cavitum pleurale UBERON:0002402 pleural cavity http://upload.wikimedia.org/wikipedia/commons/a/ab/Gray965.png Wikipedia The fluid-filled cavity that lies between the visceral and parietal pleurae. Wikipedia:Pleural_cavity https://github.com/obophenotype/uberon/issues/86 In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart [of other tetrapods] is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG] 2012-09-17 VHOG:0000581 VHOG ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206 http://bgee.unil.ch/ the EHDAA2 class of the same is not equivalent. See https://github.com/obophenotype/uberon/issues/86 EHDAA2 UMLS:C0178802 ncithesaurus:Pleural_Cavity cavitas pleuralis Wikipedia:Pleural_cavity cavitum pleuralae Wikipedia:Pleural_cavity cavitum pleurale Wikipedia:Pleural_cavity Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies. The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG] AAO:0011003 BILA:0000104 BTO:0005810 FMA:9825 GAID:328 MA:0002711 MESH:D007107 NCIT:C12735 OpenCyc:Mx4rvWNkm5wpEbGdrcN5Y29ycA SCTID:362590003 TAO:0001159 UMLS:C0020962 VHOG:0001247 Wikipedia:Immune_system XAO:0003152 ZFA:0001159 uberon UBERON:0002405 immune system Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies. Wikipedia:Immune_system The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG] 2012-09-17 VHOG:0001247 VHOG PMID:21046016 Dzik JM, The ancestry and cumulative evolution of immune reactions. Acta biochimica Polonica (2010) http://bgee.unil.ch/ UMLS:C0020962 ncithesaurus:Immune_System a double-walled sac containing the heart and the roots of the great vessels. FMA:9868 RETIRED_EHDAA2:0001443 SCTID:361326002 TAO:0000054 uberon pericardium UBERON:0002406 pericardial sac http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png FMA a double-walled sac containing the heart and the roots of the great vessels. Wikipedia:Pericardium https://github.com/obophenotype/uberon/issues/86 The combination of pericardial sac (a double-walled sac containing the heart and the roots of the great vessels) plus fibrous pericardium. Peritoneum that surrounds the heart.[AAO] pericardial In GO the concept of pericardium is developmental implicitly epithelial, but here it represents a multi-tissue structure encompassing the sac (epithelium plus connective) and cavity this class denotes a combination of fibrous PC + PC sac (itself a combination of cavity, epithelium and connective tissue). Many sources use the term 'pericardium' to denote either just the serous membrane (ZFA) or the epithelium (GO) we follow FMA in dividing pericardium into pericardial sac and fibrous pericardium AAO:0010817 BSA:0000090 BTO:0000717 CALOHA:TS-0761 EFO:0000820 EHDAA:5376 EMAPA:16133 EV:0100023 FMA:9869 GAID:569 MA:0000099 MAT:0000454 MESH:D010496 NCIT:C13005 OpenCyc:Mx4rvoCLgJwpEbGdrcN5Y29ycA RETIRED_EHDAA2:0001443 SCTID:181295003 TAO:0000054 UMLS:C0031050 VHOG:0001280 Wikipedia:Pericardium XAO:0004182 ZFA:0000054 galen:Pericardium uberon UBERON:0002407 pericardium http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png MA The combination of pericardial sac (a double-walled sac containing the heart and the roots of the great vessels) plus fibrous pericardium. Wikipedia:Pericardium http://orcid.org/0000-0002-6601-2165 Peritoneum that surrounds the heart.[AAO] 2012-06-20 AAO:0010817 AAO AAO:JMG In GO the concept of pericardium is developmental implicitly epithelial, but here it represents a multi-tissue structure encompassing the sac (epithelium plus connective) and cavity FMA this class denotes a combination of fibrous PC + PC sac (itself a combination of cavity, epithelium and connective tissue). Many sources use the term 'pericardium' to denote either just the serous membrane (ZFA) or the epithelium (GO) ZFA we follow FMA in dividing pericardium into pericardial sac and fibrous pericardium FMA UMLS:C0031050 ncithesaurus:Pericardium Parietal serous membrane which is part of the pericardium and forms the outer layer of the pericardial sac. EHDAA:3422 EHDAA:5378 EMAPA:19031 FMA:9870 MA:0000483 NCIT:C94500 SCTID:243956000 UMLS:C0225969 VHOG:0000537 Wikipedia:Parietal_pericardium lamina parietalis (pericardii serosum) lamina parietalis pericardii parietal layer of serous pericardium parietal pericardium uberon pericardial sac UBERON:0002408 parietal serous pericardium http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png Parietal serous membrane which is part of the pericardium and forms the outer layer of the pericardial sac. http://orcid.org/0000-0002-6601-2165 UMLS:C0225969 ncithesaurus:Parietal_Pericardium lamina parietalis pericardii FMA:9870 FMA:TA parietal pericardium VHOG:0000537 pericardial sac DOI:10.5962/bhl.title.1013 Transudate contained in the pericardial cavity.[FMA] BTO:0001016 FMA:9887 MA:0002530 Wikipedia:Pericardial_fluid uberon UBERON:0002409 pericardial fluid FMA Transudate contained in the pericardial cavity.[FMA] FMA:9887 Wikipedia:Pericardial_fluid The autonomic nervous system is composed of neurons that are not under conscious control, and is comprised of two antagonistic components, the sympathetic and parasympathetic nervous systems. The autonomic nervous system regulates key functions including the activity of the cardiac (heart) muscle, smooth muscles (e.g. of the gut), and glands[GO]. Nervous system including a portion of the central and peripheral systems and presiding over the control and coordination of the vegetative functions of the organism. It innervates smooth and cardiac muscles and glandular tissues and is responsible for many actions which are more or less automatic (e.g. secretion, vasoconstriction etc.). It consists of the sympathetic and parasympathetic nervous systems. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] Part of the peripheral nervous system which regulates involuntary functions of the body and consists of the sympathetic and parasympathetic system.[AAO] From comparative analyses of craniate brains, a morphotype of the brain in the earliest craniate stock can be constructed. In marked contrast to cephalochordates, the ancestral craniate morphotype had a plethora of unique features, which included a telencephalon with pallial and subpallial parts, paired olfactory bulbs with substantial projections to most or all of the telencephalic pallium, paired lateral eyes and ears, a lateral line system for both electroreception and mechanoreception, spinal cord dorsal root ganglia, and an autonomic nervous system.[well established][VHOG] FMA splits this into peripheral and nervous parts; GO has ANS directly under NS; PNS is a sib AAO:0000033 BIRNLEX:1123 BTO:0002507 CALOHA:TS-2001 EHDA:10095 EHDAA2:0000158 EHDAA:3767 EMAPA:16984 FMA:65553 GAID:706 MA:0000219 MESH:D001341 NCIT:C12673 SCTID:362481007 TAO:0001574 UMLS:C0004388 UMLS:C1305381 VHOG:0000396 Wikipedia:Autonomic_nervous_system ZFA:0001574 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=2054 autonomic division of peripheral nervous system autonomic part of peripheral nervous system divisio autonomica systematis nervosi peripherici pars autonomica systematis nervosi peripherici peripheral autonomic nervous system visceral nervous system uberon ANS divisio autonomica systematis nervosi peripherici UBERON:0002410 autonomic nervous system http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png cjm EMAPA MA NIFSTD ZFA-modified-from-isa The autonomic nervous system is composed of neurons that are not under conscious control, and is comprised of two antagonistic components, the sympathetic and parasympathetic nervous systems. The autonomic nervous system regulates key functions including the activity of the cardiac (heart) muscle, smooth muscles (e.g. of the gut), and glands[GO]. GO:0048483 Nervous system including a portion of the central and peripheral systems and presiding over the control and coordination of the vegetative functions of the organism. It innervates smooth and cardiac muscles and glandular tissues and is responsible for many actions which are more or less automatic (e.g. secretion, vasoconstriction etc.). It consists of the sympathetic and parasympathetic nervous systems. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000396 VHOG http://bgee.unil.ch/ Part of the peripheral nervous system which regulates involuntary functions of the body and consists of the sympathetic and parasympathetic system.[AAO] 2012-06-20 AAO:0000033 AAO AAO:BJB From comparative analyses of craniate brains, a morphotype of the brain in the earliest craniate stock can be constructed. In marked contrast to cephalochordates, the ancestral craniate morphotype had a plethora of unique features, which included a telencephalon with pallial and subpallial parts, paired olfactory bulbs with substantial projections to most or all of the telencephalic pallium, paired lateral eyes and ears, a lateral line system for both electroreception and mechanoreception, spinal cord dorsal root ganglia, and an autonomic nervous system.[well established][VHOG] 2012-09-17 VHOG:0000396 VHOG DOI:10.1002/1097-0185(20000615)261:3<111::AID-AR6>3.0.CO;2-F Butler AB, Chordate evolution and the origin of craniates: An old brain in a new head. AnaT Rec (New Anat) (2000) http://bgee.unil.ch/ FMA splits this into peripheral and nervous parts; GO has ANS directly under NS; PNS is a sib FMA UMLS:C0004388 BIRNLEX:1123 UMLS:C0004388 ncithesaurus:Autonomic_Nervous_System UMLS:C1305381 BIRNLEX:1123 autonomic division of peripheral nervous system FMA:65553 autonomic part of peripheral nervous system FMA:65553 divisio autonomica systematis nervosi peripherici FMA:TA pars autonomica systematis nervosi peripherici FMA:TA peripheral autonomic nervous system FMA:65553 ANS divisio autonomica systematis nervosi peripherici Wikipedia:Autonomic_nervous_system The ossified form of a vertebral element, a skeletal element that forms around the notochord and is part of the vertebral column. Consider changing name to make distinction from inferred superclass 'vertebral element' clear we follow FMA in making this an irregular bone - however vertebra have 'epiphyses' which are currently classified as belonging to long bones Endochondral bone that forms around the notochord and is part of the vertebral column.[TAO] Main component of the vertebral column. It consists of two essential parts, a dorsal neural arch and a ventral centrum.[AAO] AAO:0000691 CALOHA:TS-2352 EFO:0001371 EMAPA:32740 FMA:9914 MA:0000309 NCIT:C12933 OpenCyc:Mx4rvt2Dh5wpEbGdrcN5Y29ycA SCTID:181817002 TAO:0001189 UMLS:C0549207 Wikipedia:Vertebra XAO:0004019 ZFA:0001189 galen:Vertebra vertebra bone vertebrae uberon UBERON:0002412 vertebra FMA The ossified form of a vertebral element, a skeletal element that forms around the notochord and is part of the vertebral column. GO_REF:0000034 VSAO:0000184 http://dx.plos.org/10.1371/journal.pone.0051070 http://orcid.org/0000-0002-6601-2165 Wikipedia Endochondral bone that forms around the notochord and is part of the vertebral column.[TAO] 2012-08-14 TAO:0001189 TAO ZFIN:curator Main component of the vertebral column. It consists of two essential parts, a dorsal neural arch and a ventral centrum.[AAO] 2012-06-20 AAO:0000691 AAO AAO:Pugener_and_Maglia_2008 UMLS:C0549207 ncithesaurus:Vertebra vertebrae PHENOSCAPE:ad A vertebra that is located in the cervical region of the vertebral column. In some species, some parts of the skull may be composed of vertebra-like elements, e.g. the occipital bone in humans is composed of four vertebra-like segments. In many vertebrate species, cervical vertebrae are variable in number; however, almost all mammals have seven (including those with very short necks relative to body size, such as elephants or whales, and those with very long necks, such as giraffes). The few exceptions include the manatee and the sloths, of which the two-toed sloth has six cervical vertebrae and the three-toed sloth has up to nine cervical vertebrae. In many species, though not in mammals, the cervical vertebrae bear ribs. In many other groups, such as lizards and saurischian dinosaurs, the cervical ribs are large; in birds they are small and completely fused to the vertebrae. The transverse processes of mammals are homologous to the cervical ribs of other amniotes. Thoracic vertebrae in all species are defined as those vertebrae which also carry a pair of ribs, and lie caudal to the cervical vertebrae. In humans, cervical vertebrae are the smallest of the true vertebrae, and can be readily distinguished from those of the thoracic or lumbar regions by the presence of a foramen (hole) in each transverse process, through which passes the vertebral artery. EMAPA:17674 FMA:9915 GAID:235 MA:0000311 MESH:D002574 NCIT:C12693 SCTID:181820005 Wikipedia:Cervical_vertebrae XAO:0003076 galen:CervicalVertebra cervical vertebrae uberon vertebrae cervicales UBERON:0002413 cervical vertebra http://upload.wikimedia.org/wikipedia/commons/f/f8/Illu_vertebral_column.jpg true A vertebra that is located in the cervical region of the vertebral column. http://orcid.org/0000-0002-6601-2165 cervical vertebrae vertebrae cervicales Wikipedia:Cervical_vertebrae An external caudal extension of the body. In chordates, the tail is post-anal, in other animals the anus ends in the tail Note we also have a subclass post-anal tail, for the chordate specific structure. currently defined very generally, inclusive of caudal fin AEO:0000109 BILA:0000117 BTO:0001348 EFO:0000963 EHDAA:9198 GAID:1245 MAT:0000094 MESH:D013623 MIAA:0000094 OpenCyc:Mx4rvVjiC5wpEbGdrcN5Y29ycA WBbt:0005741 Wikipedia:Tail caudal subdivision uberon UBERON:0002415 tail An external caudal extension of the body. In chordates, the tail is post-anal, in other animals the anus ends in the tail AEO:0000109 Wikipedia:Tail caudal subdivision https://orcid.org/0000-0002-6601-2165 Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle. (...) the integument of many tetrapods is reinforced by a morphologically and structurally diverse assemblage of skeletal elements. These elements are widely understood to be derivatives of the once all-encompassing dermal skeleton of stem-gnathostomes (...).[well established][VHOG] UBERON:0007029 AEO:0000154 BILA:0000118 CALOHA:TS-1299 CARO:0002001 EFO:0000807 EHDAA2:0000836 EHDAA2_RETIRED:0003154 EHDAA:6520 EMAPA:17524 EV:0100151 FBbt:00004969 FMA:72979 HAO:0000421 MA:0000014 MAT:0000033 MESH:D034582 MIAA:0000033 NCIT:C12907 SCTID:361692004 TADS:0000108 UMLS:C0037267 VHOG:0000403 Wikipedia:Integumentary_system XAO:0000176 galen:Surface integumentary system uberon body surface dermal system external covering of organism integumentum commune organism surface surface UBERON:0002416 integumental system Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle. CARO:0002001 http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/29 (...) the integument of many tetrapods is reinforced by a morphologically and structurally diverse assemblage of skeletal elements. These elements are widely understood to be derivatives of the once all-encompassing dermal skeleton of stem-gnathostomes (...).[well established][VHOG] 2012-09-17 VHOG:0000403 VHOG DOI:10.1111/j.1469-7580.2008.01043.x Vickaryous MK, Sire JY, The integumentary skeleton of tetrapods: origin, evolution, and development. J Anat (2009) http://bgee.unil.ch/ UMLS:C0037267 ncithesaurus:Integumentary_System integumentary system FMA:72979 dermal system MIAA:0000033 integumentum commune Wikipedia:Integumentary_system organism surface EHDAA2:0003154 surface BILA:0000118 The abdominal segment of the torso. EMAPA:35104 FMA:259211 MA:0000021 SCTID:362875007 Wikipedia:Lumbar uberon abdomen/pelvis/perineum lower body lower trunk lumbar region UBERON:0002417 abdominal segment of trunk FMA The abdominal segment of the torso. Wikipedia:Lumbar abdomen/pelvis/perineum MA:0000021 lower body MA:0000021 lower trunk FMA:259211 lumbar region https://orcid.org/0000-0002-6601-2165 Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts. A type of dense connective tissue. It is composed of cells called chondrocytes which are dispersed in a firm gel-like ground substance, called the matrix. Cartilage is avascular (contains no blood vessels) and nutrients are diffused through the matrix. Cartilage is found in the joints, the rib cage, the ear, the nose, in the throat and between intervertebral disks. It makes up virtually the entire skeleton in chondrichthyes.[AAO] Portion of tissue which is connective tissue composed of collagen and/or elastin fibers and chondrocytes. Cartilage is avascular and provides both skeletal functions and a framework upon which bone is deposited.[TAO] Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts.[VSAO] relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] Phylogenetic analysis suggests that cartilage arose independently in cnidarians, hemichordates, vertebrates, arthropods, annelids, brachiopods, and molluscs - or a common ancestor of brachiopods and molluscs (...). Analyses of cartilage as a tissue and of the development of invertebrate cartilages are consistent with homology between invertebrate and vertebrate cartilage. From the discussion above, it will be clear that understanding genetic changes underlying cartilage evolution is key to determining whether the multiple origins of cartilage represent parallel evolution.[well established][VHOG] AAO:0000060 AEO:0000087 BTO:0000206 EFO:0000949 EHDAA2:0003087 EMAPA:32730 EV:0100141 FMA:37377 GAID:99 MA:0000104 MAT:0000189 MESH:D002356 MIAA:0000189 NCIT:C12373 NCIT:C32268 OpenCyc:Mx4rvVjeOZwpEbGdrcN5Y29ycA SCTID:309312004 TAO:0001501 UMLS:C0007301 VHOG:0001207 VSAO:0000040 Wikipedia:Cartilage XAO:0000170 ZFA:0005622 galen:Cartilage cartilage tissue cartilaginous tissue chondrogenic tissue uberon cartilage cartilages portion of cartilage tissue UBERON:0002418 Previous: "A portion of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate[GO]. Regular connective tissue, which consists of chondrocytes and related cells, the intercellular matrix of which is chondrified. Examples: hyaline cartilage, fibrocartilage, elastic cartilage[FMA]. an avascular supporting and articular skeletal tissue. It also functions as the primary endoskeletal support in vertebrate embryos. Cartilage is deposited by and is composed of chondroblasts and chondrocytes separated by an extracellular matrix, which may or may not mineralize depending on cartilage type, age, or taxon[Hall and Witten]." See also FMA:71500 Set of cartilages, FMA:55107 Cartilage organ, FMA:12264 Articular cartilage. // elements made from cartilage, cartilage-like, or chondroid tissues evolved in invertebrates[H&W] cartilage tissue http://upload.wikimedia.org/wikipedia/commons/e/ee/Hypertrophic_Zone_of_Epiphyseal_Plate.jpg https://github.com/obophenotype/uberon/issues/117 Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts. GO_REF:0000034 PSPUB:0000170 VSAO:0000040 http://dx.plos.org/10.1371/journal.pone.0051070 https://github.com/obophenotype/uberon/issues/37 https://sourceforge.net/p/obo/vertebrate-skeletal-anatomy-vsao-term-requests/5 A type of dense connective tissue. It is composed of cells called chondrocytes which are dispersed in a firm gel-like ground substance, called the matrix. Cartilage is avascular (contains no blood vessels) and nutrients are diffused through the matrix. Cartilage is found in the joints, the rib cage, the ear, the nose, in the throat and between intervertebral disks. It makes up virtually the entire skeleton in chondrichthyes.[AAO] 2012-06-20 AAO:0000060 AAO AAO:LAP Portion of tissue which is connective tissue composed of collagen and/or elastin fibers and chondrocytes. Cartilage is avascular and provides both skeletal functions and a framework upon which bone is deposited.[TAO] 2012-08-14 TAO:0001501 TAO ZFIN:curator Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts.[VSAO] 2012-08-14 VSAO:0000040 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 PSPUB:0000170 relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] 2012-06-20 AAO:0000060 AAO Phylogenetic analysis suggests that cartilage arose independently in cnidarians, hemichordates, vertebrates, arthropods, annelids, brachiopods, and molluscs - or a common ancestor of brachiopods and molluscs (...). Analyses of cartilage as a tissue and of the development of invertebrate cartilages are consistent with homology between invertebrate and vertebrate cartilage. From the discussion above, it will be clear that understanding genetic changes underlying cartilage evolution is key to determining whether the multiple origins of cartilage represent parallel evolution.[well established][VHOG] 2012-09-17 VHOG:0001207 VHOG DOI:10.1111/j.1525-142X.2011.00520.x Hall BK, Parallelism, deep homology, and evo-devo. Evolution and Development (2012) http://bgee.unil.ch/ UMLS:C0007301 ncithesaurus:Cartilage cartilage tissue FMA:37377 chondrogenic tissue VSAO:0000040 cartilages VHOG:0001207 portion of cartilage tissue FMA:37377 A gland that is part of a skin of body [Automatically generated definition]. check FMA, use plural for now as general class not there EMAPA:35774 FMA:71878 MA:0000146 SCTID:110485007 glandulae cutis uberon set of skin glands skin glands skin glands set UBERON:0002419 skin gland A gland that is part of a skin of body [Automatically generated definition]. OBOL:automatic glandulae cutis FMA:71878 FMA:TA set of skin glands FMA:71878 skin glands skin glands set An epithelium that is part of the mouth and lines the oral cavity, typically stratified squamous, and may be para-, ortho- or non- keratinized. Primary barrier between oral environment and deeper tissues consider including separate class for developmental structure (adult human is stratified; in EHDAA2 is unilaminar) The epithelium that lines the oral cavity. The oral epithelium epithelial cells with many short microvilli as well as mucous cells, rodlet cells and taste buds[ZFIN:ZDB-PUB-060921-12, ZFIN:ZDB-PUB-091204-24]. the avian oral epithelium has the developmental capacity to initiate tooth developmental programs with underlying grafts of non-avian oral ectomesenchyme AAO:0010357 BTO:0001775 CALOHA:TS-0715 EHDAA2:0001325 EHDAA:2187 EMAPA:16839 EMAPA:26942 FMA:265152 MA:0000344 NCIT:C49595 TAO:0000816 UMLS:C1709332 VHOG:0000187 XAO:0003201 ZFA:0000816 epithelium of mucosa of mouth epithelium of oral mucosa uberon UBERON:0002424 oral epithelium AAO-modified An epithelium that is part of the mouth and lines the oral cavity, typically stratified squamous, and may be para-, ortho- or non- keratinized. Primary barrier between oral environment and deeper tissues https://orcid.org/0000-0002-6601-2165 The epithelium that lines the oral cavity. The oral epithelium epithelial cells with many short microvilli as well as mucous cells, rodlet cells and taste buds[ZFIN:ZDB-PUB-060921-12, ZFIN:ZDB-PUB-091204-24]. ZFA:0000816 the avian oral epithelium has the developmental capacity to initiate tooth developmental programs with underlying grafts of non-avian oral ectomesenchyme PMID:16488870 UMLS:C1709332 ncithesaurus:Oral_Cavity_Epithelium epithelium of mucosa of mouth FMA:265152 epithelium of oral mucosa FMA:265152 Visceral serous membrane which is continuous with the parietal serous pericardium and is attached to the myocardium[FMA]. EMAPA:16589 EMAPA:19032 FMA:84882 MA:0000484 SCTID:243955001 VHOG:0000538 Wikipedia:Visceral_pericardium lamina visceralis pericardii serosi serous visceral pericardium visceral lamina of serous pericardium visceral layer of serous pericardium visceral pericardium uberon epicardium pericardium visceral mesothelium UBERON:0002425 visceral serous pericardium cjm FMA Visceral serous membrane which is continuous with the parietal serous pericardium and is attached to the myocardium[FMA]. Wikipedia:Visceral_pericardium lamina visceralis pericardii serosi Wikipedia:Epicardium visceral pericardium VHOG:0000538 epicardium MA:0000484 pericardium visceral mesothelium EMAPA:16589 A blood vessel that is part of a choroid [Automatically generated definition]. EMAPA:17828 FMA:76550 MA:0001237 blood vessel of choroid blood vessel of choroid coat blood vessel of choroidea blood vessel of posterior uvea choroid blood vessel choroid blood vessels choroid blood vessels set choroid coat blood vessel choroidea blood vessel posterior uvea blood vessel vasa sanguinea choroideae uberon set of choroid blood vessels UBERON:0002443 cannot find singular in FMA, using Set class choroidal blood vessel A blood vessel that is part of a choroid [Automatically generated definition]. OBOL:automatic blood vessel of choroid OBOL:automatic blood vessel of choroid coat OBOL:automatic blood vessel of choroidea OBOL:automatic blood vessel of posterior uvea OBOL:automatic choroid blood vessel OBOL:automatic choroid coat blood vessel OBOL:automatic choroidea blood vessel OBOL:automatic posterior uvea blood vessel OBOL:automatic vasa sanguinea choroideae FMA:76550 FMA:TA set of choroid blood vessels FMA:76550 Arteries that supply the spinal cord. EHDAA2:0001890 EHDAA:4355 EMAPA:18241 MA:0002043 NCIT:C33587 SCTID:244228006 TAO:0000682 UMLS:C0447043 Wikipedia:Spinal_artery ZFA:0000682 spinal arteries uberon UBERON:0002458 spinal artery Arteries that supply the spinal cord. Wikipedia:Spinal_artery https://orcid.org/0000-0002-6601-2165 UMLS:C0447043 ncithesaurus:Spinal_Artery spinal arteries ZFA:0000682 Clear to pale yellow watery secretions from the glands lining the small intestine walls. Secretion is stimulated by the mechanical pressure of partly digested food in the intestine. BTO:0000644 FMA:62974 GAID:1162 MA:0002515 MESH:D007419 NCIT:C32875 UMLS:C0021849 Wikipedia:Succus_entericus intestinal secretion succus entericus uberon intestinal juice UBERON:0002466 intestine secretion Clear to pale yellow watery secretions from the glands lining the small intestine walls. Secretion is stimulated by the mechanical pressure of partly digested food in the intestine. Wikipedia:Succus_entericus UMLS:C0021849 ncithesaurus:Intestinal_Secretion intestinal secretion FMA:62974 succus entericus Wikipedia:Succus_entericus intestinal juice BTO:0000644 A mucosa that is part of a esophagus [Automatically generated definition]. UBERON:0003345 BTO:0002859 EMAPA:26981 FMA:62996 MA:0002680 NCIT:C32538 SCTID:362127004 UMLS:C0227176 esophageal mucosa esophageal mucous membrane esophagus mucosa esophagus mucous membrane lamina muscularis mucosae oesophageae mucosa of esophagus mucosa of oesophagus mucous membrane of esophagus mucous membrane of oesophagus oesophageal mucosa oesophagus mucosa oesophagus mucous membrane tunica mucosa esophagi tunica mucosa oesophageae tunica mucosa oesophagi uberon muscularis mucosae of oesophagus tunica mucosa oesophagi UBERON:0002469 esophagus mucosa A mucosa that is part of a esophagus [Automatically generated definition]. OBOL:automatic UMLS:C0227176 ncithesaurus:Esophageal_Mucosa esophagus mucosa FMA:62996 esophagus mucous membrane OBOL:automatic lamina muscularis mucosae oesophageae FMA:62996 FMA:TA mucosa of esophagus OBOL:automatic mucosa of oesophagus OBOL:automatic mucous membrane of oesophagus FMA:62996 oesophageal mucosa FMA:62996 oesophagus mucous membrane OBOL:automatic tunica mucosa oesophageae FMA:62996 FMA:TA muscularis mucosae of oesophagus FMA:62996 tunica mucosa oesophagi BTO:0002859 Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts. see https://github.com/obophenotype/uberon/issues/27 Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.[VSAO] CALOHA:TS-2011 EMAPA:35179 FMA:224804 MA:0002780 MESH:D001842 NCIT:C13076 UMLS:C0391978 VSAO:0000047 Wikipedia:Bone_tissue XAO:0004040 ZFA:0005621 galen:BoneTissue calcium tissue osseous tissue osteogenic tissue mineralized bone tissue uberon bone portion of bone tissue UBERON:0002481 bone tissue VSAO https://github.com/obophenotype/uberon/issues/117 Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts. GO_REF:0000034 PSPUB:0000170 VSAO:0000047 http://dx.plos.org/10.1371/journal.pone.0051070 Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.[VSAO] 2012-08-14 VSAO:0000047 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 PSPUB:0000170 UMLS:C0391978 ncithesaurus:Bone_Tissue osteogenic tissue VSAO:curator mineralized bone tissue XAO:0004040 bone MESH:A02.835.232 portion of bone tissue FMA:224804 An epithelium that is part of a iris [Automatically generated definition]. EMAPA:35447 FMA:58517 MA:0002826 epithelial tissue of iris epithelium of iris epithelium pigmentosum (iris) epithelium pigmentosum iridis iris epithelial tissue iris epithelium pigmented epithelium of iris uberon iris pigmented epithelium UBERON:0002506 iris epithelium FMA MA MP An epithelium that is part of a iris [Automatically generated definition]. OBOL:automatic epithelial tissue of iris OBOL:automatic epithelium of iris OBOL:automatic epithelium pigmentosum (iris) FMA:58517 epithelium pigmentosum iridis FMA:58517 FMA:TA iris epithelial tissue OBOL:automatic iris epithelium FMA:58517 pigmented epithelium of iris FMA:58517 iris pigmented epithelium MA:0002826 Replacement bone that forms within cartilage. placement in this class to be inferred Replacement bone that forms within cartilage.[VSAO] some structures, e.g. in ZFA are both intramembrane and endochondral AAO:0010776 AEO:0000083 BTO:0002157 EHDAA2:0003083 FMA:24321 TAO:0001591 VSAO:0000145 XAO:0004018 ZFA:0001591 ossified chondrogenic bone uberon cartilaginous bone endochondral bones UBERON:0002513 endochondral bone https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern http://upload.wikimedia.org/wikipedia/commons/e/ee/Hypertrophic_Zone_of_Epiphyseal_Plate.jpg VSAO Replacement bone that forms within cartilage. GO:0001958 GO_REF:0000034 VSAO:0000145 http://dx.plos.org/10.1371/journal.pone.0051070 https://github.com/obophenotype/uberon/issues/54 Replacement bone that forms within cartilage.[VSAO] 2012-08-14 VSAO:0000145 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 PSPUB:0000170 some structures, e.g. in ZFA are both intramembrane and endochondral ZFA ossified chondrogenic bone VSAO:0000145 cartilaginous bone BTO:0002157 endochondral bones ZFA:0001591 Bone tissue forms directly within mesenchyme, and does not replace other tissues[TAO]. Intramembranous ossification is the formation of bone in which osteoblasts secrete a collagen-proteoglycan matrix that binds calcium salts and becomes calcified[GO]. Intramembranous ossification is the way flat bones and the shell of a turtle are formed[GO]. Unlike endochondral ossification, cartilage is not present during intramembranous ossification[WP]. Bone that forms directly within mesenchyme, and does not replace other tissues.[TAO] [In TAO], This term was made obsolete because it is considered a synonym of membrane bone (VSAO:0000023).[TAO] EMAPA:36615 TAO:0001644 Wikipedia:Intramembranous_ossification ZFA:0001635 uberon intramembranous bones membrane bone UBERON:0002514 intramembranous bone VSAO Bone tissue forms directly within mesenchyme, and does not replace other tissues[TAO]. Intramembranous ossification is the formation of bone in which osteoblasts secrete a collagen-proteoglycan matrix that binds calcium salts and becomes calcified[GO]. Intramembranous ossification is the way flat bones and the shell of a turtle are formed[GO]. Unlike endochondral ossification, cartilage is not present during intramembranous ossification[WP]. GO:0001957 Wikipedia:Intramembranous_ossification https://github.com/obophenotype/uberon/issues/267 Bone that forms directly within mesenchyme, and does not replace other tissues.[TAO] 2012-08-14 TAO:0001644 TAO TAO:wd [In TAO], This term was made obsolete because it is considered a synonym of membrane bone (VSAO:0000023).[TAO] 2012-09-06 TAO:0001644 TAO Curator intramembranous bones ZFA:0001635 membrane bone AEO:0000085 Connective tissue composed of elastic fibers. FMA:20113 GAID:926 MA:0002853 MESH:D004547 NCIT:C32495 SCTID:27197004 Wikipedia:Elastic_fiber elastic connective tissue textus connectivus elasticus elastic fiber uberon UBERON:0002521 elastic tissue http://upload.wikimedia.org/wikipedia/commons/c/cb/Gray377.png Connective tissue composed of elastic fibers. http://orcid.org/0000-0002-6601-2165 textus connectivus elasticus The middle layer of an artery or vein. [WP,unvetted]. BTO:0002011 EMAPA:36298 FMA:55590 GAID:170 MA:0002855 MESH:D017540 NCIT:C33821 SCTID:61695000 UMLS:C0162867 Wikipedia:Tunica_media uberon tunica media vasorum UBERON:0002522 May be composed of smooth muscle and elastic tissue tunica media Illu:artery.jpg MA cjm cjm The middle layer of an artery or vein. [WP,unvetted]. Wikipedia:Tunica_media UMLS:C0162867 ncithesaurus:Tunica_Media tunica media vasorum BTO:0002011 tunica media vasorum Wikipedia:Tunica_media The innermost layer of a blood vessel which is a lining of endothelial cells facing the lumen[Kardong]. the FMA class represents a more generic layer which is the superclass of the layer found in both blood vessels and lymph vessels (and also endocardium) - we should probably follow this structure the FMA class represents a structure which may have both epithelium and fibroelastic connective tissue as parts The tunica intima (or just intima) is the innermost layer of an artery or vein. It is made up of one layer of endothelial cells and is supported by an internal elastic lamina. The endothelial cells are in direct contact with the blood flow. The inner coat (tunica intima) can be separated from the middle by a little maceration, or it may be stripped off in small pieces; but, on account of its friability, it cannot be separated as a complete membrane. It is a fine, transparent, colorless structure which is highly elastic, and, after death, is commonly corrugated into longitudinal wrinkles. The inner coat consists of: A layer of pavement endothelium, the cells of which are polygonal, oval, or fusiform, and have very distinct round or oval nuclei. This endothelium is brought into view most distinctly by staining with silver nitrate. A subendothelial layer, consisting of delicate connective tissue with branched cells lying in the interspaces of the tissue; in arteries of less than 2 mm. in diameter the subendothelial layer consists of a single stratum of stellate cells, and the connective tissue is only largely developed in vessels of a considerable size. An elastic or fenestrated layer, which consists of a membrane containing a net-work of elastic fibers, having principally a longitudinal direction, and in which, under the microscope, small elongated apertures or perforations may be seen, giving it a fenestrated appearance. It was therefore called by Henle the fenestrated membrane. This membrane forms the chief thickness of the inner coat, and can be separated into several layers, some of which present the appearance of a network of longitudinal elastic fibers, and others a more membranous character, marked by pale lines having a longitudinal direction. In minute arteries the fenestrated membrane is a very thin layer; but in the larger arteries, and especially in the aorta, it has a very considerable thickness. [WP,unvetted].[Wikipedia] BTO:0002012 EMAPA:36297 FMA:55589 GAID:523 MA:0002861 MESH:D017539 NCIT:C33820 SCTID:8361002 SCTID:87483006 UMLS:C0162864 Wikipedia:Tunica_intima uberon Bichat's tunic intima tunica intima vasorum UBERON:0002523 tunica intima Illu:artery.jpg FMA check for exceptions, e.g. capillaries ISBN:0073040584 The innermost layer of a blood vessel which is a lining of endothelial cells facing the lumen[Kardong]. ISBN:0073040584 NCIT:C33820 Wikipedia:Tunica_intima The tunica intima (or just intima) is the innermost layer of an artery or vein. It is made up of one layer of endothelial cells and is supported by an internal elastic lamina. The endothelial cells are in direct contact with the blood flow. The inner coat (tunica intima) can be separated from the middle by a little maceration, or it may be stripped off in small pieces; but, on account of its friability, it cannot be separated as a complete membrane. It is a fine, transparent, colorless structure which is highly elastic, and, after death, is commonly corrugated into longitudinal wrinkles. The inner coat consists of: A layer of pavement endothelium, the cells of which are polygonal, oval, or fusiform, and have very distinct round or oval nuclei. This endothelium is brought into view most distinctly by staining with silver nitrate. A subendothelial layer, consisting of delicate connective tissue with branched cells lying in the interspaces of the tissue; in arteries of less than 2 mm. in diameter the subendothelial layer consists of a single stratum of stellate cells, and the connective tissue is only largely developed in vessels of a considerable size. An elastic or fenestrated layer, which consists of a membrane containing a net-work of elastic fibers, having principally a longitudinal direction, and in which, under the microscope, small elongated apertures or perforations may be seen, giving it a fenestrated appearance. It was therefore called by Henle the fenestrated membrane. This membrane forms the chief thickness of the inner coat, and can be separated into several layers, some of which present the appearance of a network of longitudinal elastic fibers, and others a more membranous character, marked by pale lines having a longitudinal direction. In minute arteries the fenestrated membrane is a very thin layer; but in the larger arteries, and especially in the aorta, it has a very considerable thickness. [WP,unvetted].[Wikipedia] Wikipedia Wikipedia:Tunica_intima UMLS:C0162864 ncithesaurus:Tunica_Intima Bichat's tunic BTO:0002012 intima BTO:0002012 tunica intima vasorum BTO:0002012 an organ that functions as a secretory or excretory organ glandular UBERON:MIAA_0000021 AAO:0000212 AEO:0000096 BTO:0000522 EFO:0000797 EHDAA2:0003096 EHDAA:2161 EHDAA:4475 EHDAA:6522 EMAPA:18425 FBbt:00100317 FMA:7146 FMA:86294 HAO:0000375 MA:0003038 MAT:0000021 MIAA:0000021 NCIT:C13319 OpenCyc:Mx4rwP3vyJwpEbGdrcN5Y29ycA SCTID:134358001 UMLS:C1285092 Wikipedia:Gland WikipediaCategory:Glands galen:Gland glandular organ uberon Druese glandula UBERON:0002530 gland http://upload.wikimedia.org/wikipedia/commons/a/a1/Gray1026.png an organ that functions as a secretory or excretory organ MGI:csmith MP:0002163 UMLS:C1285092 ncithesaurus:Gland glandular organ http://orcid.org/0000-0002-6601-2165 Druese BTO:0000522 glandula BTO:0000522 glandula Wikipedia:Gland In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA] MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG] BTO:0004593 FMA:296704 MAT:0000067 MIAA:0000067 VHOG:0000243 Wikipedia:Epiblast epiblast uberon blastocyst ectoblast epiblastus primitive ectoderm UBERON:0002532 epiblast (generic) http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA] Wikipedia:Epiblast ZFIN:curator In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG] 2012-09-17 VHOG:0000243 VHOG DOI:10.1146/annurev.cellbio.042308.113344 Zorn AM, Wells JM, Vertebrate endoderm development and organ formation. Annual Review of Cell Developmental Biology (2009) http://bgee.unil.ch/ epiblast VHOG:0000243 ectoblast MP:0003886 epiblastus Wikipedia:Epiblast primitive ectoderm VHOG:0000243 The rapidly proliferating mass of cells at the caudal extremity of the embryo; remnant of the primitive node. See notes from https://github.com/obophenotype/uberon/wiki/The-neural-crest Rapidly proliferating mass of cells at the caudal extremity of the embryo. Its formation is reflected in a caudal carving of the posterior portion of the archenteric canal at NF stage 22. With its further outgrowth, the postanal gut primordium becomes stretched. Its lumen is in broad communication with the hindgut at NF stage 25.[AAO] (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (5) a larva or embryo with a postanal tail.[well established][VHOG] AAO:0011104 BTO:0001445 EFO:0002748 EHDAA2:0001976 EHDAA:1595 EMAPA:16580 MAT:0000070 MIAA:0000070 TAO:0000077 VHOG:0000201 XAO:0000107 ZFA:0000077 tail bud tailbud uberon end bud tail bud mesenchyme UBERON:0002533 post-anal tail bud The rapidly proliferating mass of cells at the caudal extremity of the embryo; remnant of the primitive node. BTO:0001445 Rapidly proliferating mass of cells at the caudal extremity of the embryo. Its formation is reflected in a caudal carving of the posterior portion of the archenteric canal at NF stage 22. With its further outgrowth, the postanal gut primordium becomes stretched. Its lumen is in broad communication with the hindgut at NF stage 25.[AAO] 2012-06-20 AAO:0011104 AAO ISBN:0815318960 OMD:tail+bud (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (5) a larva or embryo with a postanal tail.[well established][VHOG] 2012-09-17 VHOG:0000201 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 http://bgee.unil.ch/ tail bud ZFA:0000077 end bud BTO:0001445 tail bud mesenchyme ZFA:0000077 One of a series of paired bulges that develop along the lateral walls of the foregut. The pharyngeal arches have developmental contributions from endoderm, mesoderm, and neural crest cells and are separated by anterior lateral endoderm out-pockets known as pharyngeal pouches. One of a series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO] A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down.[well established][VHOG] Numbered cranial to caudal. different in mammals. branchial arch = ZFA:0001613 pharyngeal arch 3-7. generally gill arch 1 = pharyngeal arch 3. terminology varies as to whether branchial arch follows gill or pharyngeal numbering AAO:0010359 BTO:0001785 EFO:0000959 EHDAA:571 EMAPA:16117 FMA:293015 GAID:1292 MAT:0000242 MESH:A16.254.160 MIAA:0000242 NCIT:C34249 SCTID:308766004 TAO:0001306 UMLS:C0080322 VHOG:0000155 Wikipedia:Pharyngeal_arch XAO:0000096 ZFA:0001306 pharyngeal arches branchial arch uberon arcus pharyngei visceral arch UBERON:0002539 pharyngeal arch http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray41.png EHDAA2 PMID:16313389 http://tolweb.org/Chordata/2499 PMID:16313389 One of a series of paired bulges that develop along the lateral walls of the foregut. The pharyngeal arches have developmental contributions from endoderm, mesoderm, and neural crest cells and are separated by anterior lateral endoderm out-pockets known as pharyngeal pouches. PMID:16313389 ZFA:yb http://orcid.org/0000-0002-6601-2165 One of a series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO] 2012-06-20 AAO:0010359 AAO NLM:branchial+arch A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down.[well established][VHOG] 2012-09-17 VHOG:0000155 VHOG DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005) http://bgee.unil.ch/ UMLS:C0080322 ncithesaurus:Pharyngeal_Arch pharyngeal arches branchial arch BTO:0001785 MP:0002884 arcus pharyngei Wikipedia:Pharyngeal_arch Ectodermal placode that develops in the head into a part of the sensory nervous system. With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic. Do not merge with neurogenic placode Comparisons of developmental gene expression suggest that the anterior ectoderm in amphioxus may be homologous to the vertebrate olfactory placode, the only vertebrate placode with primary, not secondary, neurons The term placode or placodes also applies to developing organs such as teeth, mammary glands, hair follicles, feathers and scales. We include a separate parent class for this. to avoid confusion, we include neurogenic placode as a subclass ectodermal placode placode AAO:0010466 EFO:0001650 FMA:293966 MAT:0000369 MIAA:0000369 XAO:0000305 ectodermal cranial placode uberon cranial placodes UBERON:0002546 cranial placode cjm PMID:11523831 PMID:22512454 Ectodermal placode that develops in the head into a part of the sensory nervous system. With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic. http://www.ncbi.nlm.nih.gov/books/NBK53175/ https://github.com/obophenotype/uberon/issues/135 https://github.com/seger/aao/issues/4 https://orcid.org/0000-0002-6601-2165 https://sourceforge.net/p/obo/xenopus-anatomy-xao-term-requests/11/ Comparisons of developmental gene expression suggest that the anterior ectoderm in amphioxus may be homologous to the vertebrate olfactory placode, the only vertebrate placode with primary, not secondary, neurons PMID:11523831 ectodermal placode FMA:293966 PMID:22512454 placode Wikipedia:Placode ectodermal cranial placode UBERON:cjm cranial placodes XAO:0000305 Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina. cavity BIRNLEX:1011 EMAPA:37442 FMA:67552 MA:0002447 NCIT:C34007 galen:Cavity uberon UBERON:0002553 anatomical cavity Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina. FMA:67552 EMAPA:37442 MA:th BIRNLEX:1019 FMA:12237 SCTID:362606005 cavity of organ uberon UBERON:0002558 organ cavity cavity of organ FMA:12237 The cavity that is enclosed by the central nervous system. In vertebrates this is the cavity that includes as parts ventricular cavities and the central canal of the spinal cord that develops from the lumen of the neura tube BIRNLEX:1029 FMA:75007 cavity of neuraxis cavity of ventricular system of neuraxis neuraxis cavity neuraxis lumen uberon UBERON:0002561 lumen of central nervous system The cavity that is enclosed by the central nervous system. In vertebrates this is the cavity that includes as parts ventricular cavities and the central canal of the spinal cord that develops from the lumen of the neura tube https://orcid.org/0000-0002-6601-2165 DOI:10.1186/s12983-014-0089-2 cavity of neuraxis FMA:75007 cavity of ventricular system of neuraxis FMA:75007 neuraxis cavity FMA:75007 Anatomical divisons of the brain according to one or more criteria, e.g. cytoarchitectural, gross anatomy. Parts may be contiguous in 3D or not, e.g., basal ganglia. BIRNLEX:1167 FMA:55676 NCIT:C13031 SCTID:384763002 UMLS:C0445620 anatomical structure of brain biological structure of brain brain anatomical structure brain biological structure brain part neuraxis segment neuroanatomical region segment of brain uberon UBERON:0002616 regional part of brain Anatomical divisons of the brain according to one or more criteria, e.g. cytoarchitectural, gross anatomy. Parts may be contiguous in 3D or not, e.g., basal ganglia. BIRNLEX:1167 UMLS:C0445620 ncithesaurus:Brain_Part anatomical structure of brain OBOL:automatic biological structure of brain OBOL:automatic brain anatomical structure OBOL:automatic brain biological structure OBOL:automatic neuraxis segment FMA:55676 segment of brain BIRNLEX:1167 A spinal cord segment that adjacent_to a cervical region. BIRNLEX:1499 FMA:71166 MA:0003081 NCIT:C12892 SCTID:180960003 UMLS:C0581619 UMLS:C1278837 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1654 cervical segment of spinal cord cervical segments of spinal cord [1-8] cervical spinal cord pars cervicalis medullae spinalis segmenta cervicalia medullae spinalis [1-8 uberon UBERON:0002726 cervical spinal cord A spinal cord segment that adjacent_to a cervical region. OBOL:automatic UMLS:C0581619 BIRNLEX:1499 UMLS:C0581619 ncithesaurus:Cervical_Spinal_Cord UMLS:C1278837 BIRNLEX:1499 cervical segment of spinal cord FMA:71166 cervical segments of spinal cord [1-8] FMA:71166 cervical spinal cord FMA:71166 pars cervicalis medullae spinalis FMA:71166 FMA:TA segmenta cervicalia medullae spinalis [1-8 FMA:71166 FMA:TA A cerebral hemisphere that is in the left side of a brain. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern BIRNLEX:1795 FMA:61819 NCIT:C32955 SCTID:362323007 UMLS:C0228176 left hemisphere uberon UBERON:0002812 left cerebral hemisphere A cerebral hemisphere that is in the left side of a brain. OBOL:automatic UMLS:C0228176 ncithesaurus:Left_Cerebral_Hemisphere left hemisphere BIRNLEX:1795 A cerebral hemisphere that is in the right side of a brain. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern BIRNLEX:1797 FMA:67292 NCIT:C33472 OpenCyc:Mx8Ngh4rvgHsHZwpEbGdrcN5Y29ycB4rvigx5ZwpEbGdrcN5Y29ycA SCTID:362322002 UMLS:C0228175 right hemisphere uberon UBERON:0002813 right cerebral hemisphere A cerebral hemisphere that is in the right side of a brain. OBOL:automatic UMLS:C0228175 ncithesaurus:Right_Cerebral_Hemisphere right hemisphere BIRNLEX:1797 A nucleus of brain that is part of a trigeminal nuclear complex. massive inconsistencies between GO, MA, wikipedia. Part of pons in MA, but this leads to inconsistencies with ABA. BM:V BTO:0001074 CALOHA:TS-2077 EMAPA:35883 EV:0100271 FMA:71247 GAID:604 MA:0001028 MESH:D014278 NCIT:C12807 SCTID:280164007 UMLS:C0040999 VHOG:0001353 http://uri.neuinfo.org/nif/nifstd/nifext_11 nucleus of trigeminal nuclear complex trigeminal V nucleus trigeminal nuclear complex nucleus trigeminal nucleus uberon nucleus mesencephalicus nervi trigemini nucleus mesencephalicus trigeminalis nucleus tractus mesencephali nervi trigeminalis UBERON:0002925 trigeminal nucleus A nucleus of brain that is part of a trigeminal nuclear complex. OBOL:automatic massive inconsistencies between GO, MA, wikipedia. Part of pons in MA, but this leads to inconsistencies with ABA. GO https://github.com/obophenotype/mouse-anatomy-ontology/issues/58 UMLS:C0040999 ncithesaurus:Trigeminal_Nucleus nucleus of trigeminal nuclear complex FMA:71247 trigeminal V nucleus MA:0001028 trigeminal nuclear complex nucleus FMA:71247 trigeminal nucleus FMA:71248 nucleus mesencephalicus nervi trigemini BTO:0001074 nucleus mesencephalicus trigeminalis BTO:0001074 nucleus tractus mesencephali nervi trigeminalis BTO:0001074 A sensory epithelium that is part of a gustatory system. FMA:62412 http://uri.neuinfo.org/nif/nifstd/nifext_12 uberon UBERON:0002926 gustatory epithelium NIFSTD A sensory epithelium that is part of a gustatory system. OBOL:automatic Dorsal portion of the pons, containing cranial nervee nuclei, ascending and descending tracts and reticular nuclei. It is continuous with the reticular formation of the medulla (Carpenter, A Core Text of Neuroanatomy, 3rd ed, 1985, pg 133). involved in the initiation of REM sleep [Wikipedia:Pontine_tegmentum] BAMS:PTg BIRNLEX:923 DHBA:12416 FMA:71108 HBA:9135 SCTID:362401009 UMLS:C0228426 Wikipedia:Pontine_tegmentum http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=557 dorsal pons dorsal portion of pons tegmental portion of pons tegmentum of pons tegmentum pontis uberon pars dorsalis pontis pars posterior pontis tegmentum pontis UBERON:0003023 pontine tegmentum Brainstem:Abducens.png Dorsal portion of the pons, containing cranial nervee nuclei, ascending and descending tracts and reticular nuclei. It is continuous with the reticular formation of the medulla (Carpenter, A Core Text of Neuroanatomy, 3rd ed, 1985, pg 133). BIRNLEX:923 UMLS:C0228426 BIRNLEX:923 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=557 BIRNLEX:923 dorsal portion of pons FMA:71108 tegmental portion of pons FMA:71108 tegmentum of pons FMA:71108 tegmentum pontis FMA:71108 FMA:TA pars dorsalis pontis NeuroNames:557 pars posterior pontis NeuroNames:557 tegmentum pontis Wikipedia:Pontine_tegmentum A wall, dividing a cavity or structure into smaller ones[WP]. septal AAO:0011127 FMA:86461 OpenCyc:Mx4rrqot_on_EdaAAAACs0uFOQ Wikipedia:Septum septa uberon UBERON:0003037 general anatomical term in FMA septum A wall, dividing a cavity or structure into smaller ones[WP]. Wikipedia:Septum septa The thoracic nerves are the spinal nerves emerging from the thoracic vertebrae. [WP,unvetted]. BIRNLEX:966 FMA:71167 MA:0003082 NCIT:C12894 SCTID:278750009 UMLS:C0581620 Wikipedia:Thoracic_spinal_cord http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1718 pars thoracica medullae spinalis segmenta thoracica medullae spinalis [1-12] thoracic region of spinal cord thoracic segment of spinal cord thoracic segments of spinal cord [1-12] thoracic spinal cord uberon UBERON:0003038 thoracic spinal cord http://upload.wikimedia.org/wikipedia/commons/6/68/Gray820.png The thoracic nerves are the spinal nerves emerging from the thoracic vertebrae. [WP,unvetted]. Wikipedia:Thoracic_spinal_cord UMLS:C0581620 BIRNLEX:966 UMLS:C0581620 ncithesaurus:Thoracic_Spinal_Cord pars thoracica medullae spinalis FMA:71167 FMA:TA segmenta thoracica medullae spinalis [1-12] FMA:71167 FMA:TA thoracic region of spinal cord FMA:71167 thoracic segment of spinal cord FMA:71167 thoracic segments of spinal cord [1-12] FMA:71167 thoracic spinal cord FMA:71167 The part of the brain that is the morphological boundary between the midbrain and hindbrain and that is the location of an organizing center which patterns the midbrain and hindbrain primordia of the neural plate. consider adding class for organizer. Consider adding separate class for isthmus as a structure Lampreys also have an MHB [midbrain hindbrain boundary], expressing a similar repertoire of regulatory gene cognates as in gnathostomes.[well established][VHOG] AAO:0011064 DMBA:16810 EHDAA2:0004395 EHDAA:5789 EMAPA:32857 NCIT:C93172 TAO:0000042 VHOG:0000649 XAO:0000016 ZFA:0000042 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=2076 MHB mid-hindbrain boundary mid-hindbrain junction midbrain hindbrain boundary uberon isthmic organizer territory isthmo-cerebellar region isthmus isthmus/MHB UBERON:0003052 midbrain-hindbrain boundary ZFA https://sourceforge.net/p/obo/zebrafish-anatomy-zfa-term-requests/106/ ZFA ZFA The part of the brain that is the morphological boundary between the midbrain and hindbrain and that is the location of an organizing center which patterns the midbrain and hindbrain primordia of the neural plate. GO:0021555 Lampreys also have an MHB [midbrain hindbrain boundary], expressing a similar repertoire of regulatory gene cognates as in gnathostomes.[well established][VHOG] 2012-09-17 VHOG:0000649 VHOG DOI:10.1016/j.ydbio.2005.02.008 Murakami Y, Uchida K, Rijli FM and Kuratani S, Evolution of the brain developmental plan: Insights from agnathans. Developmental Biology (2005) http://bgee.unil.ch/ isthmic organizer territory XAO:0000016 isthmo-cerebellar region VHOG:0000649 isthmus/MHB Geisha:syn NCBITaxon:8782 A temporary epithelium that derives from the outer layer of the ectdoerm and is shed once the inner layer differentiates to form a true epidermis. The outermost epidermal layer covering the fish at embryonic stages; derived from the EVL and thought to eventually be replaced by the superficial stratum of the epidermis. Sometimes used synonymously with EVL. Le Guellec et al, 2004.[TAO] relationship type change: OBO_REL:part_of ectoderm (TAO:0000016) CHANGED TO: develops_from ectoderm (UBERON:0000924)[TAO] In mice, the first non-basal layer formed at ~E9.5; it is a temporary structure composed of simple squamous epithelium that serves as the first barrier to the embryo's physical environment, exists throughout the entire keratinocyte stratification process, and sheds off at ~E17, when it is replaced by corneocytes[MP] In some mammals, Eyelid Fusion is thought to be driven by a population of cells which are derived from the periderm, the outermost layer of the developing epidermis Originally the epidermis is one layer thick, in most vertebrates it soon becomes a two-layered structure. The outer layer gives rise to the periderm. The periderm goes through distinct developmental phases and is ultimately sloughed into the amniotic fluid when differentiation of the underlying epidermal layers is complete. The function of the periderm is not known, but is thought to be related to transport/exchange between the fetus and the amniotic fluid (http://courses.washington.edu/hubio567/devbio/periderm.html) EHDAA2:0001846 EHDAA:6538 FMA:295662 NCIT:C34247 TAO:0001185 UMLS:C1518973 VHOG:0001680 XAO:0000029 ZFA:0001185 skin periderm uberon EVL epidermis epithelial layer epidermis outer layer epitrichium periderm UBERON:0003055 periderm EHDAA2 EHDAA2 ZFA A temporary epithelium that derives from the outer layer of the ectdoerm and is shed once the inner layer differentiates to form a true epidermis. ISBN:9780878932504 The outermost epidermal layer covering the fish at embryonic stages; derived from the EVL and thought to eventually be replaced by the superficial stratum of the epidermis. Sometimes used synonymously with EVL. Le Guellec et al, 2004.[TAO] 2012-08-14 TAO:0001185 TAO ZFIN:curator relationship type change: OBO_REL:part_of ectoderm (TAO:0000016) CHANGED TO: develops_from ectoderm (UBERON:0000924)[TAO] 2012-08-14 TAO:0001185 TAO UMLS:C1518973 ncithesaurus:Periderm skin periderm EHDAA2:0001846 EVL ZFA:0001185 epitrichium MP:0013530 The portion of neural plate anterior to the mid-hindbrain junction. (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] AAO:0011084 TAO:0007016 VHOG:0001200 XAO:0000045 ZFA:0007016 uberon anterior neural plate UBERON:0003056 pre-chordal neural plate The portion of neural plate anterior to the mid-hindbrain junction. XB:curator (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] 2012-09-17 VHOG:0001200 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 http://bgee.unil.ch/ The portion of neural plate posterior to the mid-hindbrain junction. (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] TAO:0007017 VHOG:0001201 XAO:0000046 ZFA:0007017 uberon posterior neural plate UBERON:0003057 chordal neural plate The portion of neural plate posterior to the mid-hindbrain junction. XB:curator (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] 2012-09-17 VHOG:0001201 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 http://bgee.unil.ch/ Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO] It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG] AAO:0011086 EFO:0001982 EMAPA:16189 EMAPA:16752 TAO:0000279 VHOG:0000559 XAO:0000057 ZFA:0000279 segmental plate unsegmented paraxial mesoderm uberon PSM presumptive somite mesoderm somitogenic mesoderm somitomeric mesoderm unsegmented mesenchyme UBERON:0003059 presomitic mesoderm Bgee:AN Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. ZFIN:curator Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000279 TAO ZFIN:curator It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG] 2012-09-17 VHOG:0000559 VHOG DOI:10.1006/dbio.2001.0460 Schubert M, Holland LZ, Dale Stokes M and Holland ND, Three Amphoxius Wnt Genes (AmphiWnt3, AmphiWnt5, and AmphiWnt6) Associated with the Tail Bud: the Evolution of Somitogenesis in Chordates. Developmental Biology (2001) http://bgee.unil.ch/ unsegmented paraxial mesoderm https://orcid.org/0000-0002-6601-2165 somitomeric mesoderm GO:0002075 unsegmented mesenchyme VHOG:0000559 Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted]. Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO] Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO] relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO] Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG] EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac ventral lateral plate mesoderm AAO:0011006 EFO:0003489 EHDAA:207 NCIT:C34113 TAO:0000094 TE:E5.11.2.0.0.0.4 UMLS:C1511224 VHOG:0000085 Wikipedia:Blood_island_of_umbilical_vesicle XAO:0000067 ZFA:0000094 blood islands uberon VBI caudal hematopoietic tissue posterior ICM posterior blood island ventral blood island UBERON:0003061 blood island ISBN:0073040584 ISBN:0073040584 Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted]. Wikipedia:Blood_island_of_umbilical_vesicle Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000094 TAO ZFIN:curator Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO] 2012-06-20 AAO:0011006 AAO AAO:EJS relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO] 2012-08-14 TAO:0000094 TAO Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000085 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.450, DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual Review of Cell and Developmental Biology (2006) http://bgee.unil.ch/ EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac EHDAA2 UMLS:C1511224 ncithesaurus:Blood_Island blood islands A horseshoe-shaped thickening of the endoderm at the cranial (rostral) end of the primitive streak formed by the involution of Spemann's organizer cells which, together with the notochord, induces the formation of the neural plate from the overlying ectodermal cells and contributes mesodermal type cells to the surrounding tissue TODO - check; developmental relationship to anterior hypoblast in ZFA? Axial hypoblast located anterior to the chorda mesoderm; the polster is its most anterior region. Kimmel et al, 1995.[TAO] Axial mesoderm that lies anterior to the notochord and that underlies the forebrain. [Amphioxus_goosecoid_and_the_evolution_of_the_head_organizer_and_prechordal_plate._Evolution_and_Development_(2008)_2(6):303-310, Neidert_AH, Panopoulou_G_and_Langeland_JA][VHOG] There are two opposing models that can potentially explain the differences in gsc (goosecoid) expression between amphioxus and vertebrates. In one model, the vertebrate gsc expression pattern more closely resembles the common ancestral state and the amphioxus gsc expression pattern is a derivation associated with its unique morphology. (...) In an alternate model, the amphioxus gsc expression pattern most closely represents the common ancestral state and the vertebrate pattern is derived. This model suggests that the evolution of vertebrates was accompanied by the segregation of gsc expression, from a more general domain underlying the entire brain anlage to a distinct forebrain organizer domain and subsequent prechordal plate. We feel this second model is more parsimonious than the first model in that what would be novel anterior gsc expression in vertebrates directly correlates with a novel vertebrate anterior structure, the prechordal plate.[well established][VHOG] UBERON:0004881 head mesenchyme head mesoderm AAO:0011085 EHDAA2:0001493 EHDAA:181 FMA:295532 TAO:0000060 VHOG:0000086 Wikipedia:Prechordal_plate XAO:0000079 ZFA:0000060 uberon UBERON:0003063 prechordal plate ZFA PMID:16313393 A horseshoe-shaped thickening of the endoderm at the cranial (rostral) end of the primitive streak formed by the involution of Spemann's organizer cells which, together with the notochord, induces the formation of the neural plate from the overlying ectodermal cells and contributes mesodermal type cells to the surrounding tissue ISBN:0838580343 MP:0004387 Axial hypoblast located anterior to the chorda mesoderm; the polster is its most anterior region. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000060 TAO ZFIN:curator Axial mesoderm that lies anterior to the notochord and that underlies the forebrain. [Amphioxus_goosecoid_and_the_evolution_of_the_head_organizer_and_prechordal_plate._Evolution_and_Development_(2008)_2(6):303-310, Neidert_AH, Panopoulou_G_and_Langeland_JA][VHOG] 2012-09-17 VHOG:0000086 VHOG http://bgee.unil.ch/ There are two opposing models that can potentially explain the differences in gsc (goosecoid) expression between amphioxus and vertebrates. In one model, the vertebrate gsc expression pattern more closely resembles the common ancestral state and the amphioxus gsc expression pattern is a derivation associated with its unique morphology. (...) In an alternate model, the amphioxus gsc expression pattern most closely represents the common ancestral state and the vertebrate pattern is derived. This model suggests that the evolution of vertebrates was accompanied by the segregation of gsc expression, from a more general domain underlying the entire brain anlage to a distinct forebrain organizer domain and subsequent prechordal plate. We feel this second model is more parsimonious than the first model in that what would be novel anterior gsc expression in vertebrates directly correlates with a novel vertebrate anterior structure, the prechordal plate.[well established][VHOG] 2012-09-17 VHOG:0000086 VHOG DOI:10.1046/j.1525-142x.2000.00073.x Neidert AH, Panopoulou G and Langeland JA, Amphioxus goosecoid and the evolution of the head organizer and prechordal plate. Evolution and Development (2008) http://bgee.unil.ch/ head mesenchyme XAO:0000079 head mesoderm XAO:0000079 The intermediate mesoderm is located between the lateral mesoderm and the paraxial mesoderm. It develops into the kidney and gonads. Mesoderm between somite and lateral plate. Traditionally thought to give rise to the urogenital system.[AAO] (...)the mesoderm of a developing vertebrate transitionally differentiates into the following sub-types: Chordamesoderm (also known as axial mesoderm) which later on gives rise to notochord in all chordates, Paraxial mesoderm, Intermediate mesoderm, Lateral plate mesoderm (reference 1); The mesoderm is present in Bilateria, therefore they are sometimes called triploblasts. Ectoderm and endoderm are usually organized as epithelial layers, while mesoderm can be epithelial or a compact, three-dimensional tissue.[well established][VHOG] all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). AAO:0010575 EMAPA:16056 EMAPA:16178 FMA:293147 NCIT:C34193 SCTID:361476001 TAO:0001206 UMLS:C1284010 VHOG:0000087 Wikipedia:Intermediate_mesoderm XAO:0000085 ZFA:0001206 uberon IM intermediate mesenchyme intermediate plate intermediate plate mesoderm mesenchyma intermedium UBERON:0003064 intermediate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png AAO EMAPA XAO The intermediate mesoderm is located between the lateral mesoderm and the paraxial mesoderm. It develops into the kidney and gonads. GOC:curators Wikipedia:Intermediate_mesoderm Mesoderm between somite and lateral plate. Traditionally thought to give rise to the urogenital system.[AAO] 2012-06-20 AAO:0010575 AAO AAO:EJS (...)the mesoderm of a developing vertebrate transitionally differentiates into the following sub-types: Chordamesoderm (also known as axial mesoderm) which later on gives rise to notochord in all chordates, Paraxial mesoderm, Intermediate mesoderm, Lateral plate mesoderm (reference 1); The mesoderm is present in Bilateria, therefore they are sometimes called triploblasts. Ectoderm and endoderm are usually organized as epithelial layers, while mesoderm can be epithelial or a compact, three-dimensional tissue.[well established][VHOG] 2012-09-17 VHOG:0000087 VHOG Wikipedia:Mesoderm, ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.43 http://bgee.unil.ch/ all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). ZFA UMLS:C1284010 ncithesaurus:Intermediate_Mesoderm intermediate mesenchyme https://github.com/obophenotype/uberon/wiki/The-neural-crest intermediate plate EMAPA:16178 intermediate plate mesoderm https://orcid.org/0000-0002-6601-2165 mesenchyma intermedium Wikipedia:Intermediate_mesoderm Lateral neurogenic placodes positioned dorsal of the epibranchial placodes. In summary, the collective term 'placodes' refers to some rather different structures, probably with different evolutionary origins. Some sensory placodes (at least the otic and olfactory) may have homologues in basal chordates. Even if this is so, it is apparent that they were elaborated considerably during early vertebrate evolution. Epibranchial and dorsolateral placodes appear to be new; we infer that their origin depended on the evolution of specific inductive signals.[well established][VHOG] TAO:0001310 VHOG:0000103 XAO:0000187 ZFA:0001310 dorsolateral placodes uberon UBERON:0003067 The only remaining dorsolateral placode in land vertebrates is the otic/octaval placode dorsolateral placode NCBIBook:NBK53175 Lateral neurogenic placodes positioned dorsal of the epibranchial placodes. ZFIN:curator In summary, the collective term 'placodes' refers to some rather different structures, probably with different evolutionary origins. Some sensory placodes (at least the otic and olfactory) may have homologues in basal chordates. Even if this is so, it is apparent that they were elaborated considerably during early vertebrate evolution. Epibranchial and dorsolateral placodes appear to be new; we infer that their origin depended on the evolution of specific inductive signals.[well established][VHOG] 2012-09-17 VHOG:0000103 VHOG DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) http://bgee.unil.ch/ dorsolateral placodes ZFA:0001310 The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord. The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] AAO:0011017 EFO:0003647 TAO:0001204 VHOG:0000107 Wikipedia:Chordamesoderm XAO:0000205 ZFA:0001204 uberon chordamesoderm UBERON:0003068 axial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord. GO:0048318 Wikipedia:Chordamesoderm The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] 2012-09-17 VHOG:0000107 VHOG http://bgee.unil.ch/ chordamesoderm Wikipedia:Chordamesoderm A neurogenic placode that arises at the level of the midbrain-hindbrain boundary and develops into a trigeminal ganglion. The ectodermal precursor of the trigeminal ganglion. The profundal and the trigeminal ganglia are separate distally but fused at their proximal end as they condense around NF stage 24.[XAO] The ectodermal rudiment of the trigeminal ganglion, distinguishable during much of the segmentation period. Kimmel et al, 1995.[TAO] The dorsolateral placodes (trigeminal and vestibular) develop from ectoderm lateral to the brain (...). In summary, the collective term 'placodes' refers to some rather different structures, probably with different evolutionary origins. Some sensory placodes (at least the otic and olfactory) may have homologues in basal chordates. Even if this is so, it is apparent that they were elaborated considerably during early vertebrate evolution. Epibranchial and dorsolateral placodes appear to be new; we infer that their origin depended on the evolution of specific inductive signals.[well established][VHOG] Consider naming this 'trigeminal placode complex'. Also, Fig9-5 of ISBN:0471888893 calls this the profundus placode; XAO says 'profundal and the trigeminal ganglia are separate distally but fused at their proximal end...' EFO:0003433 EHDAA2:0004209 TAO:0000162 VHOG:0000109 XAO:0000225 ZFA:0000162 trigeminal V placode trigeminal placode uberon profundus V placode profundus placode trigeminal placodes UBERON:0003070 trigeminal placode complex ISBN:0471888893 A neurogenic placode that arises at the level of the midbrain-hindbrain boundary and develops into a trigeminal ganglion. PMID:22512454 http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/693 The ectodermal precursor of the trigeminal ganglion. The profundal and the trigeminal ganglia are separate distally but fused at their proximal end as they condense around NF stage 24.[XAO] XAO The ectodermal rudiment of the trigeminal ganglion, distinguishable during much of the segmentation period. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000162 TAO ZFIN:curator The dorsolateral placodes (trigeminal and vestibular) develop from ectoderm lateral to the brain (...). In summary, the collective term 'placodes' refers to some rather different structures, probably with different evolutionary origins. Some sensory placodes (at least the otic and olfactory) may have homologues in basal chordates. Even if this is so, it is apparent that they were elaborated considerably during early vertebrate evolution. Epibranchial and dorsolateral placodes appear to be new; we infer that their origin depended on the evolution of specific inductive signals.[well established][VHOG] 2012-09-17 VHOG:0000109 VHOG DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) http://bgee.unil.ch/ trigeminal placode EHDAA2:0004209 VHOG:0000109 XAO:0000225 ZFA:0000162 profundus V placode ISBN:0471888893 profundus placode ISBN:0471888893 trigeminal placodes ZFA:0000162 Portion of tissue that is part of the anterior neural keel and will form the optic vesicle[ZFA]. A paired ectodermal placode that becomes invaginated to form the embryonic lens vesicles. TODO - check that GO's optic placode is the same as ZFA's eye primordium; we may want to have separate term for ocular primordium precursor. XAO has both optic field and eye primordium. UBERON:0005060 AAO:0011038 EFO:0003541 EHDAA2:0004431 TAO:0000570 XAO:0000227 XAO:0004090 ZFA:0000570 eye placode occular primordium ocular primordium optic placode optic placode of camera-type eye optic primordium uberon eye anlage eye field optic field optic placodes UBERON:0003071 eye primordium EHDAA2 PMID:16496288 XAO Portion of tissue that is part of the anterior neural keel and will form the optic vesicle[ZFA]. A paired ectodermal placode that becomes invaginated to form the embryonic lens vesicles. GO:0046619 ZFA:0000570 TODO - check that GO's optic placode is the same as ZFA's eye primordium; we may want to have separate term for ocular primordium precursor. XAO has both optic field and eye primordium. GO eye placode OBOL:automatic optic placode GO:0046619 optic placode of camera-type eye GO:0046619 https://orcid.org/0000-0002-6601-2165 eye anlage XAO:0000227 optic placodes Multi-tissue structure that is comprised of neural and non-neural epithelial layers which will form the retina and retinal pigmented epithelium of the mature eye[ZFA]. double walled structured formed by expansion and invagination of the distal end of the optic vesicle that develops into the pigmented and sensory layers of the retina while the mouth of the optic cup eventually forms the pupil of the eye[MP]. (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup.[well established][VHOG] BTO:0005351 EHDAA2:0001303 EHDAA:2912 EMAPA:16674 NCIT:C34233 SCTID:308789007 TAO:0001202 UMLS:C0231109 VHOG:0000167 ZFA:0001202 uberon eye cup eyecup ocular cup ophtalmic cup UBERON:0003072 optic cup ZFA ZFA Multi-tissue structure that is comprised of neural and non-neural epithelial layers which will form the retina and retinal pigmented epithelium of the mature eye[ZFA]. double walled structured formed by expansion and invagination of the distal end of the optic vesicle that develops into the pigmented and sensory layers of the retina while the mouth of the optic cup eventually forms the pupil of the eye[MP]. MP:0004269 Wikipedia:Optic_cup_(embryology) ZFA:0001202 (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup.[well established][VHOG] 2012-09-17 VHOG:0000167 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 http://bgee.unil.ch/ UMLS:C0231109 ncithesaurus:Optic_Cup eyecup BTO:0005351 ocular cup VHOG:0000167 ophtalmic cup BTO:0005351 A thickened portion of ectoderm which serves as the precursor to the lens. SOX2 and Pou2f1 are involved in its development[WP]. Ectodermal primordium of the lens of the eye. Kimmel et al, 1995.[TAO] (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG] Classical transplantation experiments using amphibian embryos suggested that the optic vesicle is the source of lens-inducing signals sufficient to generate lens tissues in competent ectoderm (reviewed in Grainger et al., 1996). More recent findings suggest a multistep model for lens induction. There is now good evidence that lens specification occurs at the neurula stage, before the optic vesicle contact the surface ectoderm, and that neural crest cell migration in the frontonasal region is required to restrict the position of the lens placode (Bailey et al., 2006) AAO:0011055 EFO:0003494 EHDAA2:0000982 EHDAA:2908 EMAPA:16672 FMA:296767 NCIT:C34202 TAO:0000122 UMLS:C1517770 VHOG:0000166 Wikipedia:Lens_placode XAO:0000240 ZFA:0000122 uberon lens placodes placoda lentis UBERON:0003073 lens placode http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png NCBIBook:NBK53175 ZFA A thickened portion of ectoderm which serves as the precursor to the lens. SOX2 and Pou2f1 are involved in its development[WP]. Wikipedia:Lens_placode ZFIN:curator Ectodermal primordium of the lens of the eye. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000122 TAO ZFIN:curator (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG] 2012-09-17 VHOG:0000166 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 http://bgee.unil.ch/ Classical transplantation experiments using amphibian embryos suggested that the optic vesicle is the source of lens-inducing signals sufficient to generate lens tissues in competent ectoderm (reviewed in Grainger et al., 1996). More recent findings suggest a multistep model for lens induction. There is now good evidence that lens specification occurs at the neurula stage, before the optic vesicle contact the surface ectoderm, and that neural crest cell migration in the frontonasal region is required to restrict the position of the lens placode (Bailey et al., 2006) NCBIBook:NBK53175 UMLS:C1517770 ncithesaurus:Lens_Placodes lens placodes ZFA:0000122 placoda lentis Wikipedia:Lens_placode A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA] The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO] (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] AAO:0011072 BTO:0001765 DHBA:10153 DMBA:15565 EHDAA:346 EHDAA:902 EMAPA:35593 FMA:293879 NCIT:C34225 RETIRED_EHDAA2:0001252 TAO:0000132 UMLS:C0920623 VHOG:0000068 Wikipedia:Neural_plate XAO:0000249 ZFA:0000132 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1362 uberon lamina neuralis presumptive central nervous system UBERON:0003075 neural plate Neural:Crest.png GOTAX:0000352 Wikipedia Bgee:AN A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA] ISBN:0815318960 OMD:neural+plate Wikipedia:Neural_plate ZFIN:curator The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000132 TAO ZFIN:curator (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] 2012-09-17 VHOG:0000068 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 http://bgee.unil.ch/ UMLS:C0920623 ncithesaurus:Neural_Plate lamina neuralis Wikipedia:Neural_plate (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] AAO:0011082 TAO:0007037 VHOG:0001383 XAO:0000250 ZFA:0007037 uberon UBERON:0003076 posterior neural tube lexical (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] 2012-09-17 VHOG:0001383 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 http://bgee.unil.ch/ The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO] Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO] Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG] note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here) AAO:0010568 EFO:0003515 EMAPA:16183 EMAPA:16751 FMA:293145 NCIT:C34244 SCTID:361475002 TAO:0000255 UMLS:C1284009 VHOG:0000114 Wikipedia:Paraxial_mesoderm XAO:0000259 ZFA:0000255 paraxial mesenchyme somitic mesoderm uberon mesoderma paraxiale UBERON:0003077 paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png EHDAA2 Bgee:AN The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO] GO:0048339 https://github.com/obophenotype/uberon/issues/30 Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO] 2012-06-20 AAO:0010568 AAO AAO:EJS Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG] 2012-09-17 VHOG:0000114 VHOG DOI:10.1002/dvdy.21177 Kusakabe R and Kuratani S. Evolutionary perspectives from development of mesodermal components in the lamprey. Developmental dynamics (2007) http://bgee.unil.ch/ note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here) ZFA UMLS:C1284009 ncithesaurus:Paraxial_Mesoderm paraxial mesenchyme ZFA:0000255 https://github.com/obophenotype/uberon/issues/30 https://github.com/obophenotype/uberon/wiki/The-neural-crest somitic mesoderm ISBN:9780878932504 mesoderma paraxiale Wikipedia:Paraxial_mesoderm Focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches and that produce the neuroblasts that migrate and condense to form the distal cranial ganglia. Focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches and that produce the neuroblasts that migrate and condense to form the distal cranial ganglia. [Graham_A, The_development_and_evolution_of_the_pharyngeal_arches._J_Anat_(2001)_199:_133-141][VHOG] These (the epibranchial placodes) are focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches in all vertebrates, and they produce the neuroblasts which migrate and condense to form the distal cranial ganglia: the geniculate, petrosal and nodose ganglia. (...) The one substantial difference between the vertebrate pharyngeal arches and those of the protochordates is the presence of the epibranchial placodes but the evolution of these structures was undoubtedly driven by the endoderm.[well established][VHOG] Epibranchial placodes-derived neurons innervate internal organs to transmit information such as heart rate, blood pressure, and visceral distension from the periphery to the central nervous system (Baker and Bronner-Fraser, 2001). From rostral to caudal the epibranchial placodes comprise the geniculate, petrosal, and nodose placodes, each associated in sequence with the first, second and third branchial clefts. Each placode contributes sensory neurons to cranial nerves VII (facial nerve), IX (glossopharyngeal nerve), and X (vagal nerve), respectively in XAO this develops_from dorsolateral placode, but in NBK53175, this is a separate group AAO:0011036 EFO:0003455 FMA:293968 TAO:0001294 VHOG:0000117 XAO:0000284 ZFA:0001294 epibranchial placodes uberon ventrolateral placode UBERON:0003078 epibranchial placode NCBIBook:NBK53175 ZFA ZFA EHDAA2-abduced Focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches and that produce the neuroblasts that migrate and condense to form the distal cranial ganglia. VHOG:0000117 Focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches and that produce the neuroblasts that migrate and condense to form the distal cranial ganglia. [Graham_A, The_development_and_evolution_of_the_pharyngeal_arches._J_Anat_(2001)_199:_133-141][VHOG] 2012-09-17 VHOG:0000117 VHOG http://bgee.unil.ch/ These (the epibranchial placodes) are focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches in all vertebrates, and they produce the neuroblasts which migrate and condense to form the distal cranial ganglia: the geniculate, petrosal and nodose ganglia. (...) The one substantial difference between the vertebrate pharyngeal arches and those of the protochordates is the presence of the epibranchial placodes but the evolution of these structures was undoubtedly driven by the endoderm.[well established][VHOG] 2012-09-17 VHOG:0000117 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A, The development and evolution of the pharyngeal arches. J Anat (2001) http://bgee.unil.ch/ Epibranchial placodes-derived neurons innervate internal organs to transmit information such as heart rate, blood pressure, and visceral distension from the periphery to the central nervous system (Baker and Bronner-Fraser, 2001). From rostral to caudal the epibranchial placodes comprise the geniculate, petrosal, and nodose placodes, each associated in sequence with the first, second and third branchial clefts. Each placode contributes sensory neurons to cranial nerves VII (facial nerve), IX (glossopharyngeal nerve), and X (vagal nerve), respectively NCBIBook:NBK53175 in XAO this develops_from dorsolateral placode, but in NBK53175, this is a separate group XAO epibranchial placodes ZFA:0001294 ventrolateral placode ISBN:0471888893 TODO - add grouping class for the anterior end of the neural tube at all stages (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] AAO:0011012 TAO:0007038 VHOG:0001384 XAO:0000307 ZFA:0007038 uberon UBERON:0003080 anterior neural tube lexical (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] 2012-09-17 VHOG:0001384 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 http://bgee.unil.ch/ Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP]. Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO] The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG] subclass of mesoderm in ZFA. UBERON:0006258 AAO:0010574 EHDAA2:0000919 EHDAA:379 EMAPA:16179 FMA:293149 NCIT:C34199 SCTID:361477005 TAO:0000121 UMLS:C1517749 VHOG:0000118 Wikipedia:Lateral_plate_mesoderm XAO:0000311 ZFA:0000121 LPM lateral mesoderm uberon lateral plate lateral plate mesenchyme mesoderma laminae lateralis UBERON:0003081 lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png EHDAA2 EHDAA2 VHOG Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP]. MP:0010117 Wikipedia:Lateral_plate_mesoderm Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO] 2012-06-20 AAO:0010574 AAO AAO:EJS The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] 2012-09-17 VHOG:0000118 VHOG http://bgee.unil.ch/ A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG] 2012-09-17 VHOG:0000118 VHOG DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) http://bgee.unil.ch/ subclass of mesoderm in ZFA. ZFA UMLS:C1517749 ncithesaurus:Lateral_Mesoderm LPM ZFA:0000121 lateral mesoderm GO:0048368 lateral plate mesenchyme EHDAA2:0000919 mesoderma laminae lateralis Wikipedia:Lateral_plate_mesoderm A transitional population of migrating mesenchymal cells that derive from somites and that will become muscle cells. The term 'myotome' is also used to describe the muscles served by a single nerve root / spinal segment - consider adding new class, myomere. Portion of the somites giving rise to body wall muscle masses. Kimmel et al, 1995.[TAO] In all vertebrates, the skeletal muscle of the body axis is chiefly derived from an early embryonic compartment, known as the myotome.[well established][VHOG] AAO:0011067 AEO:0001018 BTO:0000742 EHDAA2_RETIRED:0003431 EHDAA:1721 EHDAA:1727 EHDAA:1733 EHDAA:1739 EMAPA:32841 FMA:295658 NCIT:C34214 SCTID:344535001 TAO:0001056 UMLS:C1513802 VHOG:0001244 Wikipedia:Myotome XAO:0000315 ZFA:0001056 myomeres uberon muscle plate myomere myotome region myotomes myotomus UBERON:0003082 myotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png AEO EHDAA2-abduced A transitional population of migrating mesenchymal cells that derive from somites and that will become muscle cells. AEO:0001018 Portion of the somites giving rise to body wall muscle masses. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0001056 TAO ZFIN:curator In all vertebrates, the skeletal muscle of the body axis is chiefly derived from an early embryonic compartment, known as the myotome.[well established][VHOG] 2012-09-17 VHOG:0001244 VHOG DOI:10.1038/sj.embor.embor920 Hollway GE, Currie PD, Myotome meanderings. Cellular morphogenesis and the making of muscle. EMBO Rep.(2003) http://bgee.unil.ch/ UMLS:C1513802 ncithesaurus:Myotome_Region myomeres TAO:0001056 myotomus Wikipedia:Myotome Trunk portion of the neural crest. The trunk neural crest lies between the vagal and sacral neural crest and gives rise to two groups of cells. One group migrates dorsolateral and populates the skin, forming pigment cells and the other migrates ventrolateral through the anterior sclerotome to become the epinephrine-producing cells of the adrenal gland and the neurons of the sympathetic nervous system. Some cells remain in the sclerotome to form the dorsal root ganglia [Wikipedia]. Post-cranial portion of the neural crest. Exact anatomical derivations not experimentally resolved in amphibians.[AAO] We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] AAO:0010582 EFO:0003605 EHDAA2:0001901 TAO:0001024 VHOG:0000062 Wikipedia:Trunk_neural_crest XAO:0000319 ZFA:0001024 TNC uberon trunk crest UBERON:0003083 trunk neural crest ZFA Trunk portion of the neural crest. The trunk neural crest lies between the vagal and sacral neural crest and gives rise to two groups of cells. One group migrates dorsolateral and populates the skin, forming pigment cells and the other migrates ventrolateral through the anterior sclerotome to become the epinephrine-producing cells of the adrenal gland and the neurons of the sympathetic nervous system. Some cells remain in the sclerotome to form the dorsal root ganglia [Wikipedia]. ISBN:0815318960 Wikipedia:Trunk_neural_crest Post-cranial portion of the neural crest. Exact anatomical derivations not experimentally resolved in amphibians.[AAO] 2012-06-20 AAO:0010582 AAO AAO:EJS We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] 2012-09-17 VHOG:0000062 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 http://bgee.unil.ch/ TNC XAO:0000319 Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. should probably be merged with heart rudiment. Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO] The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO] relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO] AAO:0011044 BTO:0001887 NCIT:C34276 TAO:0000028 UMLS:C1514450 XAO:0000336 ZFA:0000028 uberon cardiac field fused heart primordium UBERON:0003084 heart primordium Obol ZFA ZFA XAO Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. ZFIN:curator Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO] 2012-08-14 TAO:0000028 TAO ZFIN:curator The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO] 2012-06-20 AAO:0011044 AAO XAO:curator relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO] 2012-08-14 TAO:0000028 TAO UMLS:C1514450 ncithesaurus:Primordium_of_the_Heart cardiac field ZFA:0000028 Extension of the dorsal aorta in the tail. Extension of the dorsal aorta in the tail. Kimmel et al, 1995.[TAO] The posterior extension of the dorsal aorta to the tail region, which degenerates at metamorphosis.[AAO] AAO:0011023 EFO:0003472 TAO:0000011 VHOG:0000123 Wikipedia:Caudal_artery XAO:0000364 ZFA:0000011 uberon CA UBERON:0003086 caudal artery Extension of the dorsal aorta in the tail. Wikipedia:Caudal_artery ZFIN:curator Extension of the dorsal aorta in the tail. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000011 TAO ZFIN:curator The posterior extension of the dorsal aorta to the tail region, which degenerates at metamorphosis.[AAO] 2012-06-20 AAO:0011023 AAO ISBN:0-226-55763-4 Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. Skeletogenic portion of somites.[AAO] The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG] part_of somite in XAO AAO:0010571 AEO:0000212 EHDAA2:0003439 EMAPA:31159 FMA:295652 NCIT:C34287 TAO:0001080 UMLS:C0183176 VHOG:0000680 Wikipedia:Sclerotome XAO:0000397 ZFA:0001080 sclerotomes uberon sclerotomus UBERON:0003089 sclerotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png EHDAA2 EHDAA2 VHOG:0000680 ZFA Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. Wikipedia:Sclerotome XB:curator https://github.com/obophenotype/uberon/issues/316 Skeletogenic portion of somites.[AAO] 2012-06-20 AAO:0010571 AAO AAO:EJS The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG] 2012-09-17 VHOG:0000680 VHOG DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) http://bgee.unil.ch/ part_of somite in XAO XAO UMLS:C0183176 ncithesaurus:Sclerotome sclerotomes TAO:0001080 sclerotomus Wikipedia:Sclerotome neural crest cells (NCCs) originating in the anterior part of the developing embryo and residing between the mid-diencephalon and the forming hindbrain; cranial NCCs migrate dorsolaterally to form the craniofacial mesenchyme that differentiates into various craniofacial cartilages and bones, cranial neurons, glia, and connective tissues of the face; these cells enter the pharyngeal pouches and arches where they give rise to thymic cells, bones of the middle ear and jaw (mandible), and the odontoblasts of the tooth primordia; like their counterparts in the trunk, cranial NCCs also contribute to the developing peripheral nervous system, along with the pigmented cell (i.e. melanocyte) lineage. Anterior most portion of the neural crest. Migrates in three highly conserved streams: mandibular, hyoid and branchial.[AAO] Neural crest that is part of the head.[TAO] We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] AAO:0010580 EFO:0003645 EHDAA2:0004420 EMAPA:16091 TAO:0001194 VHOG:0000063 Wikipedia:Cranial_neural_crest XAO:0001001 ZFA:0001194 CNC cephalic neural crest cranial NCC population head NCC population uberon crista neuralis cranialis head crest head neural crest UBERON:0003099 cranial neural crest neural crest cells (NCCs) originating in the anterior part of the developing embryo and residing between the mid-diencephalon and the forming hindbrain; cranial NCCs migrate dorsolaterally to form the craniofacial mesenchyme that differentiates into various craniofacial cartilages and bones, cranial neurons, glia, and connective tissues of the face; these cells enter the pharyngeal pouches and arches where they give rise to thymic cells, bones of the middle ear and jaw (mandible), and the odontoblasts of the tooth primordia; like their counterparts in the trunk, cranial NCCs also contribute to the developing peripheral nervous system, along with the pigmented cell (i.e. melanocyte) lineage. MGI:anna Anterior most portion of the neural crest. Migrates in three highly conserved streams: mandibular, hyoid and branchial.[AAO] 2012-06-20 AAO:0010580 AAO AAO:EJS Neural crest that is part of the head.[TAO] 2012-08-14 TAO:0001194 TAO ZFIN:curator We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] 2012-09-17 VHOG:0000063 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 http://bgee.unil.ch/ CNC XAO:0001001 cephalic neural crest EMAPA:16091 crista neuralis cranialis Wikipedia:Cranial_neural_crest Gonochoristic organism that can produce female gametes. AAO:0010030 BILA:0000028 CARO:0000028 FBbt:00007011 FMA:67812 HAO:0000028 SCTID:362608006 TAO:0000303 TGMA:0001839 XAO:0003005 ZFA:0000303 female human body uberon female UBERON:0003100 female organism Gonochoristic organism that can produce female gametes. CARO:0000028 female human body FMA:67812 female TAO:0000303 Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism. consider obsoleting. See issue/1305 Organism subdivision which is the collection of anatomical structures on the body surface.[ZFA] AAO:0010337 AEO_RETIRED:0000010 EHDAA2_RETIRED:0003010 TAO:0000292 VSAO:0000001 Wikipedia:Surface_structure XAO:0003028 ZFA:0000292 galen:SurfaceRegion anatomical surface feature uberon surface feature surface region surface structures UBERON:0003102 surface structure Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism. http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/24 Organism subdivision which is the collection of anatomical structures on the body surface.[ZFA] 2012-08-14 TAO:0000292 TAO ZFIN:curator anatomical surface feature EHDAA2:0003010 surface structures ZFA:0000292 Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types. this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs AAO:0010015 AEO:0000024 BILA:0000024 CARO:0000024 EHDAA2:0003024 HAO:0000024 TADS:0000598 TAO:0000496 TGMA:0001837 VHOG:0001723 XAO:0003041 ZFA:0000496 uberon organ UBERON:0003103 compound organ Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types. CARO:0000024 Portion of tissue composed of mesenchymal cells (motile cells that develop from epthelia via an epithelial to mesenchymal transition) and surrounding extracellular material. Mesenchyme has different embryological origins in different metazoan taxa - in many invertebrates it derives in whole or part from ectoderm. In vertebrates it derives largely from mesoderm, and sometimes the terms are used interchangeably, e.g. lateral plate mesoderm/mesenchyme. the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO] Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO] mesenchymal AAO:0010427 AEO:0000145 BTO:0001393 CALOHA:TS-0620 EHDAA2:0003145 EV:0100007 NCIT:C13301 TAO:0000393 UMLS:C0162415 VHOG:0000170 Wikipedia:Mesenchyme XAO:0003046 ZFA:0000393 mesenchymal tissue mesenchyme tissue portion of mesenchymal tissue portion of mesenchyme tissue uberon mesenchyma UBERON:0003104 mesenchyme http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg Portion of tissue composed of mesenchymal cells (motile cells that develop from epthelia via an epithelial to mesenchymal transition) and surrounding extracellular material. Mesenchyme has different embryological origins in different metazoan taxa - in many invertebrates it derives in whole or part from ectoderm. In vertebrates it derives largely from mesoderm, and sometimes the terms are used interchangeably, e.g. lateral plate mesoderm/mesenchyme. https://archive.org/details/invertebratesnde00brus/page/n240/mode/2up https://en.wikipedia.org/wiki/Mesenchyme https://github.com/obophenotype/uberon/issues/1641 A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000393 TAO ZFIN:curator Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO] 2012-06-20 AAO:0010427 AAO AAO:EJS UMLS:C0162415 ncithesaurus:Mesenchyme mesenchyma Wikipedia:Mesenchyme Subdivision of skeleton that includes all dermal bones in the cranial skeleton[ZFA,modified]. wikipedia treats skull roof and dermatocranium as synonymous, but some sources treat the roof as being part of the dermatocranium - see UBERONREF:0000007 Anatomical cluster that is part of the cranium and composed of dermally derived bones.[TAO] Anatomical cluster that is part of the cranium which consists of dermally derived bones.[AAO] AAO:0010154 TAO:0000863 VHOG:0001665 Wikipedia:Skull_roof XAO:0003169 ZFA:0000863 dendrocranium exocranium dermal skull roof dermatocranial cover roof of skull skull roof uberon dermal bone cranium dermal part of skull dermal skull bones roofing bones of the skull skull exoskeleton UBERON:0003113 dermatocranium Subdivision of skeleton that includes all dermal bones in the cranial skeleton[ZFA,modified]. Wikipedia:Skull_roof ZFA:0000863 ISBN:0073040584 Anatomical cluster that is part of the cranium and composed of dermally derived bones.[TAO] 2012-08-14 TAO:0000863 TAO ZFIN:curator Anatomical cluster that is part of the cranium which consists of dermally derived bones.[AAO] 2012-06-20 AAO:0010154 AAO AAO:BJB dendrocranium TAO:0000863 exocranium UBERONREF:0000007 dermal skull roof PMID:11523816 Wikipedia:Skull_roof roof of skull Wikipedia:Skull_roof skull roof PMID:11523816 Wikipedia:Skull_roof dermal bone cranium ZFA:0000863 roofing bones of the skull Wikipedia:Skull_roof The third branchial arch contributes to the development of the hyoid bone, stylopharyngeus muscle, inferior parathyroid gland, and thymus. The most anterior, or first, pharygeal/branchial arch, composed of the mandibular process, forming the posterior border of the stomodeum, and the maxillary process anterior to the stomodeum, contains the first aortic arch.[AAO] A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] in XAO, called branchial arch 1 and df VP3 3 AAO:0010365 EHDAA2:0000069 EHDAA:1080 EMAPA:16399 FMA:293029 SCTID:308769006 TAO:0001598 VHOG:0000298 XAO:0000447 ZFA:0001606 3rd pharyngeal arch first gill arch gill arch 1 third pharyngeal arch third visceral arch visceral arch 3 uberon 3rd arch 3rd visceral arch branchial arch 1 first branchial arch UBERON:0003114 pharyngeal arch 3 The third branchial arch contributes to the development of the hyoid bone, stylopharyngeus muscle, inferior parathyroid gland, and thymus. MP:0006339 The most anterior, or first, pharygeal/branchial arch, composed of the mandibular process, forming the posterior border of the stomodeum, and the maxillary process anterior to the stomodeum, contains the first aortic arch.[AAO] 2012-06-20 AAO:0010365 AAO ISBN:0-02-377110-0 A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] 2012-09-17 VHOG:0000298 VHOG DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005) http://bgee.unil.ch/ in XAO, called branchial arch 1 and df VP3 XAO first gill arch ZFA:0001606 gill arch 1 ZFA:0001606 3rd arch EHDAA2:0000069 3rd visceral arch VHOG:0000298 branchial arch 1 AAO:0010365 ZFA:0001606 first branchial arch ZFA:0001606 contributes to development of the cartilage of the larynx, laryngeal, pharyngeal, and soft palate muscles, superior parathyroid gland, and C-cells of the thymus The second pharyngeal/branchial arch; arises as a thickening of the pharygeal wall between the first and second branchial clefts; contains the second aortic arch; forms part of the hyoid bone, tongue and facial musculature.[AAO] A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] in XAO, called branchial arch 2 and df VP4 4 AAO:0010366 EHDAA2:0000086 EHDAA:1663 EMAPA:16760 FMA:293035 SCTID:308770007 TAO:0001599 VHOG:0000299 XAO:0000449 ZFA:0001607 4th branchial arch 4th pharyngeal arch 4th visceral arch fourth pharyngeal arch gill arch 2 second gill arch visceral arch 4 uberon 4th arch branchial arch 2 fourth visceral arch second branchial arch UBERON:0003115 pharyngeal arch 4 contributes to development of the cartilage of the larynx, laryngeal, pharyngeal, and soft palate muscles, superior parathyroid gland, and C-cells of the thymus MP:0006340 The second pharyngeal/branchial arch; arises as a thickening of the pharygeal wall between the first and second branchial clefts; contains the second aortic arch; forms part of the hyoid bone, tongue and facial musculature.[AAO] 2012-06-20 AAO:0010366 AAO ISBN:0-02-377110-0 A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] 2012-09-17 VHOG:0000299 VHOG DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005) http://bgee.unil.ch/ in XAO, called branchial arch 2 and df VP4 XAO 4th branchial arch gill arch 2 ZFA:0001607 second gill arch ZFA:0001607 4th arch EHDAA2:0000086 branchial arch 2 AAO:0010366 ZFA:0001607 fourth visceral arch VHOG:0000299 second branchial arch ZFA:0001607 The 6th pharyngeal arch. contributes to the development of the sternocleidomastoid and trapezius muscles The forth in a series of paired bars in the wall of the pharynx, within which are formed the forth aortic arch and the cartilage bar of the visceral skeleton, forms and supports the gills.[AAO] A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] 6 UBERON:0004349 AAO:0010368 EHDAA2:0004075 EMAPA:32766 FMA:293047 SCTID:308772004 TAO:0001601 VHOG:0001205 XAO:0000453 ZFA:0001609 6th arch gill arch 4 sixth branchial arch visceral arch 6 uberon 6th pharyngeal arch 6th visceral arch branchial arch 4 fourth branchial arch sixth pharyngeal arch sixth visceral arch UBERON:0003117 pharyngeal arch 6 The 6th pharyngeal arch. contributes to the development of the sternocleidomastoid and trapezius muscles MP:0006347 The forth in a series of paired bars in the wall of the pharynx, within which are formed the forth aortic arch and the cartilage bar of the visceral skeleton, forms and supports the gills.[AAO] 2012-06-20 AAO:0010368 AAO ISBN:0-02-377110-0 A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] 2012-09-17 VHOG:0001205 VHOG DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M, Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005) http://bgee.unil.ch/ 6th arch EHDAA2:0004075 gill arch 4 ZFA:0001609 visceral arch 6 ZFA:0001609 6th pharyngeal arch VHOG:0001205 6th visceral arch VHOG:0001205 branchial arch 4 AAO:0010368 ZFA:0001609 fourth branchial arch sixth pharyngeal arch VHOG:0001205 sixth visceral arch XAO:0000453 The vessels formed within the first pair of branchial arches in embryogenesis Disappears early in development in tetrapods ZFA states that The paired aortic arch 1 arteries branch off of the ventral aorta, and empty into the right and left lateral dorsal aortas UBERON:0004371 AAO:0010415 EHDAA2:0000007 EMAPA:16202 EMAPA:16685 SCTID:308774003 TAO:0005005 VHOG:0000149 XAO:0000342 ZFA:0005005 1st arch artery AA1 aortic arch 1 first aortic arch first branchial arch artery mandibular aortic arch uberon 1st aortic arch artery 1st branchial arch artery 1st pharyngeal arch artery first arch artery UBERON:0003118 pharyngeal arch artery 1 The vessels formed within the first pair of branchial arches in embryogenesis MP:0010355 ZFA states that The paired aortic arch 1 arteries branch off of the ventral aorta, and empty into the right and left lateral dorsal aortas ZFA 1st arch artery EMAPA:16685 AA1 ZFA:0005005 aortic arch 1 ZFA:0005005 first aortic arch XAO:0000342 mandibular aortic arch ZFA:0005005 1st aortic arch artery EMAPA:16685 1st branchial arch artery EMAPA:16685 1st pharyngeal arch artery EMAPA:16685 first arch artery EMAPA:16685 The vessels formed within the third pair of branchial arches in embryogenesis Aortic arches 3 and 4 are not remodeled but are retained largely intact as the branchial arteries providing circulation through the gills. These areches are direct branches from the ventral aorta to the lateral dorsal aorta. Isogai et al. 2001.[TAO] The third aortic arch constitutes the commencement of the internal carotid artery, and is therefore named the carotid arch[WP][Wikipedia:Aortic_arches#Arch_3]. The third in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 3 lies within the 3rd branchial arch and branches directly from the ventral aorta to the lateral dorsal aorta, and are retained as the branchial arteries providing circulation through the gills in the adult.[AAO] UBERON:0004352 AAO:0010419 EHDAA2:0000070 EMAPA:16687 SCTID:308776001 TAO:0005007 VHOG:0000147 Wikipedia:Aortic_arches#Arch_3 XAO:0000344 ZFA:0005007 3rd arch artery AA3 aortic arch 3 carotid arch third aortic arch third branchial arch artery uberon 3rd aortic arch artery 3rd branchial arch artery 3rd pharyngeal arch artery UBERON:0003120 pharyngeal arch artery 3 The vessels formed within the third pair of branchial arches in embryogenesis MP:0006356 Aortic arches 3 and 4 are not remodeled but are retained largely intact as the branchial arteries providing circulation through the gills. These areches are direct branches from the ventral aorta to the lateral dorsal aorta. Isogai et al. 2001.[TAO] 2012-08-14 TAO:0005007 TAO ZFIN:curator The third aortic arch constitutes the commencement of the internal carotid artery, and is therefore named the carotid arch[WP][Wikipedia:Aortic_arches#Arch_3]. Wikipedia:Aortic_arches#Arch_3 The third in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 3 lies within the 3rd branchial arch and branches directly from the ventral aorta to the lateral dorsal aorta, and are retained as the branchial arteries providing circulation through the gills in the adult.[AAO] 2012-06-20 AAO:0010419 AAO ISBN:0-02-377110-0 3rd arch artery EHDAA2:0000070 AA3 ZFA:0005007 aortic arch 3 ZFA:0005007 carotid arch Wikipedia:Aortic_arches#Arch_3 third aortic arch XAO:0000344 3rd aortic arch artery EMAPA:16687 3rd branchial arch artery EMAPA:16687 3rd pharyngeal arch artery EMAPA:16687 The vessels formed within the fourth pair of branchial arches in embryogenesis Aortic arches 3 and 4 are not remodeled but are retained largely intact as the branchial arteries providing circulation through the gills. These areches are direct branches from the ventral aorta to the lateral dorsal aorta. Isogai et al. 2001.[TAO] The forth in a series paired arterial connections between the dorsal and ventral aortae, lies within the 4th branchial arch. The paired aortic arch 4 arteries branch directly from the ventral aorta to the lateral dorsal aorta, and are retained as the branchial arteries providing circulation through the gills in the adult.[AAO] The fourth right arch forms the right subclavian as far as the origin of its internal mammary branch; while the fourth left arch constitutes the arch of the aorta between the origin of the left carotid artery and the termination of the ductus arteriosus[WP][Wikipedia:Aortic_arches#Arch_4]. Normally, the left fourth arch becomes the aortic arch, the right fourth arch contributes to the innominate artery[http://emedicine.medscape.com/article/899609-overview] in birds it is the right fourth arch which forms the permanent aorta UBERON:0004350 AAO:0010420 EHDAA2:0000087 EMAPA:17004 SCTID:308777005 TAO:0005008 Wikipedia:Aortic_arches#Arch_4 XAO:0000355 ZFA:0005008 4th arch artery AA4 aortic arch 4 fourth aortic arch fourth branchial arch artery uberon 4th aortic arch artery 4th branchial arch artery 4th pharyngeal arch artery systemic arch UBERON:0003121 proximal right subclavian pharyngeal arch artery 4 The vessels formed within the fourth pair of branchial arches in embryogenesis MP:0006354 Aortic arches 3 and 4 are not remodeled but are retained largely intact as the branchial arteries providing circulation through the gills. These areches are direct branches from the ventral aorta to the lateral dorsal aorta. Isogai et al. 2001.[TAO] 2012-08-14 TAO:0005008 TAO ZFIN:curator The forth in a series paired arterial connections between the dorsal and ventral aortae, lies within the 4th branchial arch. The paired aortic arch 4 arteries branch directly from the ventral aorta to the lateral dorsal aorta, and are retained as the branchial arteries providing circulation through the gills in the adult.[AAO] 2012-06-20 AAO:0010420 AAO ISBN:0-02-377110-0 The fourth right arch forms the right subclavian as far as the origin of its internal mammary branch; while the fourth left arch constitutes the arch of the aorta between the origin of the left carotid artery and the termination of the ductus arteriosus[WP][Wikipedia:Aortic_arches#Arch_4]. Wikipedia:Aortic_arches#Arch_4 4th arch artery EHDAA2:0000087 AA4 ZFA:0005008 aortic arch 4 ZFA:0005008 fourth aortic arch XAO:0000355 4th aortic arch artery EMAPA:17004 4th branchial arch artery EMAPA:17004 4th pharyngeal arch artery EMAPA:17004 systemic arch ISBN:0073040584 XAO:0000355 The vessels formed within the sixth pair of branchial arches in embryogenesis The fifth and sixth arches, which come on-line at approximately 2.5 dpf, have a common trunk from the ventral aorta and drain to the midline dorsal aorta via an independent route. The fifth and sixth aortic arches supply the trunk and tail with oxigenated blood. Isogai et al. 2001.[TAO] The sixth in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 6 artery is paired and has a common trunk with aortic arch 5 from the ventral aorta, and drains via a separate branch of the lateral dorsal aorta. It forms part of the pulmonary arteries, and in the later embryo, the ductus arteriosis. Aortic arches 5 and 6 together supply the trunk and tail with oxygenated blood.[AAO] The sixth right arch disappears; the sixth left arch gives off the pulmonary arteries and forms the ductus arteriosus; this duct remains pervious during the whole of fetal life, but then closes within the first few days after birth due to increased O2 concentration. Oxygen concentration causes the production of bradykinin which causes the ductus to constrict occluding all flow. Within 1-3 months, the ductus is obliterated and becomes the ligamentum arteriosus. His showed that in the early embryo the right and left arches each gives a branch to the lungs, but that later both pulmonary arteries take origin from the left arch[WP][Wikipedia:Aortic_arches#Arch_6]. the distal left sixth arch becomes the ductus arteriosus, the proximal sixth arches bilaterally contribute to the proximal branch pulmonary arteries UBERON:0004351 AAO:0010422 EHDAA2:0000102 EMAPA:17005 SCTID:308779008 TAO:0005016 VHOG:0000144 Wikipedia:Aortic_arches#Arch_6 XAO:0000353 ZFA:0005016 6th arch artery AA6 aortic arch 6 sixth aortic arch sixth branchial arch artery uberon 6th aortic arch artery 6th branchial arch artery 6th pharyngeal arch artery pulmonary arch UBERON:0003123 pharyngeal arch artery 6 The vessels formed within the sixth pair of branchial arches in embryogenesis MP:0006355 The fifth and sixth arches, which come on-line at approximately 2.5 dpf, have a common trunk from the ventral aorta and drain to the midline dorsal aorta via an independent route. The fifth and sixth aortic arches supply the trunk and tail with oxigenated blood. Isogai et al. 2001.[TAO] 2012-08-14 TAO:0005016 TAO ZFIN:curator The sixth in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 6 artery is paired and has a common trunk with aortic arch 5 from the ventral aorta, and drains via a separate branch of the lateral dorsal aorta. It forms part of the pulmonary arteries, and in the later embryo, the ductus arteriosis. Aortic arches 5 and 6 together supply the trunk and tail with oxygenated blood.[AAO] 2012-06-20 AAO:0010422 AAO ISBN:0-02-377110-0 The sixth right arch disappears; the sixth left arch gives off the pulmonary arteries and forms the ductus arteriosus; this duct remains pervious during the whole of fetal life, but then closes within the first few days after birth due to increased O2 concentration. Oxygen concentration causes the production of bradykinin which causes the ductus to constrict occluding all flow. Within 1-3 months, the ductus is obliterated and becomes the ligamentum arteriosus. His showed that in the early embryo the right and left arches each gives a branch to the lungs, but that later both pulmonary arteries take origin from the left arch[WP][Wikipedia:Aortic_arches#Arch_6]. Wikipedia:Aortic_arches#Arch_6 the distal left sixth arch becomes the ductus arteriosus, the proximal sixth arches bilaterally contribute to the proximal branch pulmonary arteries http://emedicine.medscape.com/article/899609-overview 6th arch artery EMAPA:17005 AA6 ZFA:0005016 aortic arch 6 ZFA:0005016 sixth aortic arch XAO:0000353 6th aortic arch artery EMAPA:17005 6th branchial arch artery EMAPA:17005 6th pharyngeal arch artery EMAPA:17005 pulmonary arch ISBN:0073040584 Upper portion of the skull that excludes the mandible (when present in the organism). cranial the inclusion of the FMA class here is probably not quite correct, as this class includes as parts sutures, whereas this is not part of the bones of the cranium The term cranium can be ambiguous, in that it can refer to the neurocranium, or the neurocranium and the Facial skeleton BTO:0001328 EFO:0000831 EHDAA:6029 EMAPA:17680 FMA:71325 MA:0000316 MAT:0000340 MIAA:0000340 OpenCyc:Mx4rvVlEyJwpEbGdrcN5Y29ycA SCTID:181889008 VHOG:0000334 Wikipedia:Cranium_(anatomy) bones of cranium ossa cranii set of bones of cranium skull minus mandible upper part of skull uberon calvarium epicranial plate skeletal system of head UBERON:0003128 cranium FMA-inferred Upper portion of the skull that excludes the mandible (when present in the organism). Wikipedia:Cranium_(anatomy) http://orcid.org/0000-0002-6601-2165 the inclusion of the FMA class here is probably not quite correct, as this class includes as parts sutures, whereas this is not part of the bones of the cranium FMA The term cranium can be ambiguous, in that it can refer to the neurocranium, or the neurocranium and the Facial skeleton WP bones of cranium FMA:71325 ossa cranii FMA:71325 FMA:TA set of bones of cranium FMA:71325 calvarium BTO:0001328 Anatomical structure that is part of the head consisting entirely of cranium and mandible[WP]. in FMA the skull is divided into orbit, neurocranium (8 parts), viscerocranium (26 parts). Here we have a separate overlapping division into cranium and mandible. in many ontologies, the structure called the cranium is inclusive of the mandible/lower jaw skeleton A skull that is missing a mandible is only a cranium; this is the source of a very commonly made error in terminology. Those animals having skulls are called craniates BTO:0001295 CALOHA:TS-2344 EHDAA2:0000325 EMAPA:17680 FMA:46565 GAID:82 MESH:D012886 NCIT:C12789 OpenCyc:Mx4rvVjOsZwpEbGdrcN5Y29ycA SCTID:110530005 UMLS:C0037303 Wikipedia:Skull WikipediaCategory:Skull galen:Skull uberon cranial skeleton skeletal system of head UBERON:0003129 skull FMA Anatomical structure that is part of the head consisting entirely of cranium and mandible[WP]. PMID:11523816 Wikipedia:Skull http://sourceforge.net/tracker/?func=detail&aid=2962656&group_id=76834&atid=1205376 in FMA the skull is divided into orbit, neurocranium (8 parts), viscerocranium (26 parts). Here we have a separate overlapping division into cranium and mandible. FMA A skull that is missing a mandible is only a cranium; this is the source of a very commonly made error in terminology. Those animals having skulls are called craniates WP UMLS:C0037303 ncithesaurus:Skull An organ involved in reproduction GO uses genitalia for the singular organ EMAPA:17381 EMAPA:37731 MA:0001752 MESH:D005835 NCIT:C25177 OpenCyc:Mx4rwO39aJwpEbGdrcN5Y29ycA SCTID:128181006 TGMA:0000591 UMLS:C0017420 WBbt:0008422 genital organ reproductive system organ sex organ uberon genitalia UBERON:0003133 reproductive organ An organ involved in reproduction UBERON:xp GO uses genitalia for the singular organ GO EMAPA:37731 MA:th UMLS:C0017420 ncithesaurus:Genitalia genitalia A female organ involved in reproduction EMAPA:28540 MA:0000544 female organism reproductive organ female organism reproductive structure female organism reproductive system organ female organism sex organ female reproductive gland/organ female reproductive system organ female sex organ reproductive organ of female organism reproductive structure of female organism reproductive system organ of female organism sex organ of female organism uberon UBERON:0003134 female reproductive organ A female organ involved in reproduction UBERON:xp female organism reproductive organ OBOL:automatic female organism reproductive structure OBOL:automatic female organism reproductive system organ OBOL:automatic female organism sex organ OBOL:automatic female reproductive gland/organ MA:0000544 reproductive organ of female organism OBOL:automatic reproductive structure of female organism OBOL:automatic reproductive system organ of female organism OBOL:automatic sex organ of female organism OBOL:automatic Any sense organ that functions in (some) detection of chemical stimulus involved in sensory perception of taste (GO:0050912). FBbt:00005159 FMA:77853 gustatory organ system organ gustatory system organ organ of gustatory organ system organ of gustatory system organ of taste system taste organ taste system organ uberon UBERON:0003212 gustatory organ Any sense organ that functions in (some) detection of chemical stimulus involved in sensory perception of taste (GO:0050912). FBC:auto_generated_definition gustatory organ system organ OBOL:automatic gustatory system organ OBOL:automatic organ of gustatory organ system OBOL:automatic organ of gustatory system OBOL:automatic organ of taste system OBOL:automatic taste system organ OBOL:automatic Septum that divides the ovary, the basal portion of a carpel or group of fused carpels, that encloses the ovule(s)[GO]. uberon UBERON:0003218 ovary septum Septum that divides the ovary, the basal portion of a carpel or group of fused carpels, that encloses the ovule(s)[GO]. GO:0080126 An epithelium that is part of a lower jaw [Automatically generated definition]. EHDAA2:0001019 EHDAA:7999 EMAPA:35516 VHOG:0000802 epithelial tissue of lower jaw epithelial tissue of ventral mandibular arch epithelium of ventral mandibular arch lower jaw epithelial tissue lower jaw epithelium ventral mandibular arch epithelial tissue ventral mandibular arch epithelium uberon UBERON:0003236 epithelium of lower jaw An epithelium that is part of a lower jaw [Automatically generated definition]. OBOL:automatic epithelial tissue of lower jaw OBOL:automatic epithelial tissue of ventral mandibular arch OBOL:automatic epithelium of ventral mandibular arch OBOL:automatic lower jaw epithelial tissue OBOL:automatic lower jaw epithelium OBOL:automatic ventral mandibular arch epithelial tissue OBOL:automatic ventral mandibular arch epithelium OBOL:automatic An endoderm that is part of a foregut [Automatically generated definition]. TODO - check EHDAA2:0004568 EHDAA:524 foregut endoderm uberon UBERON:0003258 endoderm of foregut An endoderm that is part of a foregut [Automatically generated definition]. OBOL:automatic foregut endoderm OBOL:automatic An endoderm that is part of a midgut [Automatically generated definition]. TODO - check EHDAA:987 EMAPA:16257 RETIRED_EHDAA2:0001194 VHOG:0001080 midgut endoderm uberon UBERON:0003259 endoderm of midgut An endoderm that is part of a midgut [Automatically generated definition]. OBOL:automatic midgut endoderm OBOL:automatic An endoderm that is part of a hindgut [Automatically generated definition]. TODO - check EHDAA:979 RETIRED_EHDAA2:0000781 hindgut endoderm uberon UBERON:0003260 endoderm of hindgut An endoderm that is part of a hindgut [Automatically generated definition]. OBOL:automatic hindgut endoderm OBOL:automatic A portion of skeletal muscle tissue that is part of a eye [Automatically generated definition]. EHDAA2:0000486 EHDAA:2923 EMAPA:17844 eye skeletal muscle eye skeletal muscle tissue skeletal muscle tissue of eye uberon eye skeletal muscle group UBERON:0003269 skeletal muscle tissue of eye A portion of skeletal muscle tissue that is part of a eye [Automatically generated definition]. OBOL:automatic eye skeletal muscle OBOL:automatic eye skeletal muscle tissue OBOL:automatic skeletal muscle tissue of eye OBOL:automatic eye skeletal muscle group EHDAA2:0000486 A subdivision of the skeleton that corresponds to the lower part of the mouth. The lower jaw skeleton includes the following elements, when present: lower jaw teeth, the mandible and other lower jaw bones, and Meckel's cartilage. The ventral portion of the first pharyngeal arch, comprising the lower jaw.[TAO] The jaw joint of all jawed vertebrates, except for mammals, involves the quadrate and articular bones, or the posterior ends of the palatoquadrate and mandibular cartilages; A correlate of the conversion of the articular and quadrate bones to the malleus and incus is that all adult mammals have a jaw joint that lies between the dentary of the lower jaw and the squamosal bone of the skull roof.[well established][VHOG] Inclusion of the FMA class 'lower jaw' is debatable - this mostly corresponds to the lower jaw skeleton (with 'maxillary part of mouth' corresponding to the upper jaw region); however, the FMA class also includes gingiva. See also: https://github.com/obophenotype/mouse-anatomy-ontology/issues/102 lower jaw mandible AAO:0000274 EHDAA2:0004606 EHDAA:8005 EMAPA:17906 EMAPA:17910 FMA:54398 MA:0001906 TAO:0001273 VHOG:0000428 XAO:0003084 ZFA:0001273 lower jaw skeleton uberon mandibles mandibular series UBERON:0003278 skeleton of lower jaw EHDAA2 VHOG-modified A subdivision of the skeleton that corresponds to the lower part of the mouth. The lower jaw skeleton includes the following elements, when present: lower jaw teeth, the mandible and other lower jaw bones, and Meckel's cartilage. http://orcid.org/0000-0002-6601-2165 The ventral portion of the first pharyngeal arch, comprising the lower jaw.[TAO] 2012-08-14 TAO:0001273 TAO ZFIN:curator The jaw joint of all jawed vertebrates, except for mammals, involves the quadrate and articular bones, or the posterior ends of the palatoquadrate and mandibular cartilages; A correlate of the conversion of the articular and quadrate bones to the malleus and incus is that all adult mammals have a jaw joint that lies between the dentary of the lower jaw and the squamosal bone of the skull roof.[well established][VHOG] 2012-09-17 VHOG:0000428 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.241 and p.101 http://bgee.unil.ch/ Inclusion of the FMA class 'lower jaw' is debatable - this mostly corresponds to the lower jaw skeleton (with 'maxillary part of mouth' corresponding to the upper jaw region); however, the FMA class also includes gingiva. See also: https://github.com/obophenotype/mouse-anatomy-ontology/issues/102 FMA lower jaw MA:0001906 lower jaw ZFA:0001273 mandible ZFA:0001273 lower jaw skeleton AAO:0000274 mandibles TAO:0001273 mandibular series ZFA:0001273 A gland that is part of a foregut [Automatically generated definition]. EHDAA2:0000567 EHDAA:950 EMAPA:16557 VHOG:0000650 foregut gland uberon UBERON:0003294 gland of foregut A gland that is part of a foregut [Automatically generated definition]. OBOL:automatic foregut gland OBOL:automatic Racemose mucous glands beneath the mucous membrane of the pharynx. BTO:0004849 EHDAA2:0001461 EHDAA:2967 FMA:55075 pharynx gland uberon glandulae pharyngeae UBERON:0003295 pharyngeal gland BTO Racemose mucous glands beneath the mucous membrane of the pharynx. http://www.biology-online.org/dictionary/ pharynx gland EHDAA2:0001461 glandulae pharyngeae BTO:0004849 Any gland that is part of the diencephalon. Examples: pineal gland, neurohypophysis. EHDAA2:0000395 EHDAA:4475 EMAPA:16897 VHOG:0000653 diencephalon gland interbrain gland uberon UBERON:0003296 gland of diencephalon Any gland that is part of the diencephalon. Examples: pineal gland, neurohypophysis. http://orcid.org/0000-0002-6601-2165 diencephalon gland OBOL:automatic interbrain gland OBOL:automatic A gland that is part of a integumental system [Automatically generated definition]. EHDAA2:0000837 EHDAA:6522 EMAPA:17758 MA:0000144 VHOG:0000654 integumental gland integumental system gland integumentary gland uberon UBERON:0003297 gland of integumental system A gland that is part of a integumental system [Automatically generated definition]. OBOL:automatic integumental gland http://orcid.org/0000-0002-6601-2165 integumental system gland http://orcid.org/0000-0002-6601-2165 integumentary gland http://orcid.org/0000-0002-6601-2165 A blood island that is part of a mesoderm. in EHDAA2, gives rise to blood and dorsal aorta UBERON:0003305 EHDAA2:0003241 EHDAA:170 EMAPA:16115 mesoderm blood islands uberon mesenchyme blood island UBERON:0003304 mesoderm blood island EHDAA2 EHDAA2 A blood island that is part of a mesoderm. OBOL:automatic in EHDAA2, gives rise to blood and dorsal aorta EHDAA2 mesoderm blood islands EHDAA2:0003241 mesenchyme blood island OBOL:automatic Mesenchyme that is part of a developing camera-type eye. TODO - change mesenchyme relationships to precursor_of EHDAA2:0000485 EHDAA:2910 EMAPA:16673 VHOG:0001084 mesenchyme of eye uberon UBERON:0003314 eye mesenchyme EHDAA2 Mesenchyme that is part of a developing camera-type eye. OBOL:automatic mesenchyme of eye OBOL:automatic Mesenchyme that is part of a developing ovary [Automatically generated definition]. EHDAA2:0001362 EHDAA:8128 VHOG:0001441 female reproductive system gonad mesenchyme female reproductive system gonada mesenchyme gonad of female reproductive system mesenchyme gonada of female reproductive system mesenchyme mesenchyme of female reproductive system gonad mesenchyme of female reproductive system gonada mesenchyme of gonad of female reproductive system mesenchyme of gonada of female reproductive system ovary mesenchyme uberon UBERON:0003315 mesenchyme of ovary Mesenchyme that is part of a developing ovary [Automatically generated definition]. OBOL:automatic female reproductive system gonad mesenchyme OBOL:automatic female reproductive system gonada mesenchyme OBOL:automatic gonad of female reproductive system mesenchyme OBOL:automatic gonada of female reproductive system mesenchyme OBOL:automatic mesenchyme of female reproductive system gonad OBOL:automatic mesenchyme of female reproductive system gonada OBOL:automatic mesenchyme of gonad of female reproductive system OBOL:automatic mesenchyme of gonada of female reproductive system OBOL:automatic ovary mesenchyme OBOL:automatic Mesenchyme that is part of a developing lower jaw [Automatically generated definition]. EHDAA2:0001024 EHDAA:8003 EMAPA:17916 VHOG:0001069 lower jaw mesenchyme mesenchyme of ventral mandibular arch ventral mandibular arch mesenchyme uberon UBERON:0003324 mesenchyme of lower jaw EHDAA2 Mesenchyme that is part of a developing lower jaw [Automatically generated definition]. OBOL:automatic lower jaw mesenchyme OBOL:automatic mesenchyme of ventral mandibular arch OBOL:automatic ventral mandibular arch mesenchyme OBOL:automatic A submucosa that is part of an anal canal [Automatically generated definition]. EMAPA:27217 EMAPA:27227 EMAPA:27535 FMA:85399 SCTID:7892006 anal canal submucosa anal canal viewed anatomically submucosa anal region submucosa anatomical anal canal submucosa submucosa of anal canal viewed anatomically submucosa of anal region submucosa of anatomical anal canal uberon UBERON:0003329 submucosa of anal canal A submucosa that is part of an anal canal [Automatically generated definition]. OBOL:automatic anal canal submucosa OBOL:automatic anal canal viewed anatomically submucosa OBOL:automatic anal region submucosa OBOL:automatic anatomical anal canal submucosa OBOL:automatic submucosa of anal canal viewed anatomically OBOL:automatic submucosa of anal region OBOL:automatic submucosa of anatomical anal canal OBOL:automatic The submucous layer of the wall of the rectum. BTO:0002114 EMAPA:27083 FMA:15034 SCTID:71683001 rectal submucosa rectum submucosa tela submucosa recti uberon UBERON:0003330 submucosa of rectum The submucous layer of the wall of the rectum. BTO:0002114 rectal submucosa FMA:15034 rectum submucosa OBOL:automatic tela submucosa recti BTO:0002114 A submucosa that is part of a colon [Automatically generated definition]. EMAPA:27379 FMA:14985 MA:0003200 SCTID:61647009 colon submucosa colonic submucosa large bowel submucosa submucosa of large bowel uberon UBERON:0003331 submucosa of colon A submucosa that is part of a colon [Automatically generated definition]. OBOL:automatic colon submucosa OBOL:automatic colonic submucosa FMA:14985 large bowel submucosa OBOL:automatic submucosa of large bowel OBOL:automatic A serous membrane that is part of a rectum [Automatically generated definition]. EMAPA:27087 FMA:15039 rectal serosa rectum serosa rectum serous membrane serous membrane of rectum visceral peritoneum of rectum uberon UBERON:0003334 serosa of rectum A serous membrane that is part of a rectum [Automatically generated definition]. OBOL:automatic rectal serosa FMA:15039 rectum serosa OBOL:automatic rectum serous membrane OBOL:automatic serous membrane of rectum OBOL:automatic visceral peritoneum of rectum FMA:15039 A serous membrane that is part of a colon [Automatically generated definition]. EMAPA:27387 FMA:14990 MA:0003199 SCTID:90132000 colon serosa colon serous membrane colonic serosa large bowel serosa large bowel serous membrane serosa of large bowel serous membrane of colon serous membrane of large bowel visceral peritoneum of colon uberon UBERON:0003335 serosa of colon A serous membrane that is part of a colon [Automatically generated definition]. OBOL:automatic colon serosa OBOL:automatic colon serous membrane OBOL:automatic colonic serosa FMA:14990 large bowel serosa OBOL:automatic large bowel serous membrane OBOL:automatic serosa of large bowel OBOL:automatic serous membrane of colon OBOL:automatic serous membrane of large bowel OBOL:automatic visceral peritoneum of colon FMA:14990 A spatially aggregated collection of nerve cell bodies in the PNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections. (CUMBO). we follow MA in including separate classes for ganglion and peripheral nervous system, even though for vertebrates gangia are always in the PNS BIRNLEX:2548 BTO:0001123 EMAPA:32814 MA:0001161 peripheral nervous system ganglion uberon UBERON:0003338 ganglion of peripheral nervous system A spatially aggregated collection of nerve cell bodies in the PNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections. (CUMBO). BIRNLEX:2548 we follow MA in including separate classes for ganglion and peripheral nervous system, even though for vertebrates gangia are always in the PNS MA peripheral nervous system ganglion OBOL:automatic A ganglion that is part of a central nervous system [Automatically generated definition]. this has no subclasses in FMA. In EHDAA2 and EMAPA it has only the cranial ganglia EHDAA2:0000227 EMAPA:16658 FMA:83843 central nervous system ganglion ganglion of neuraxis neuraxis ganglion uberon UBERON:0003339 ganglion of central nervous system A ganglion that is part of a central nervous system [Automatically generated definition]. OBOL:automatic this has no subclasses in FMA. In EHDAA2 and EMAPA it has only the cranial ganglia FMA central nervous system ganglion OBOL:automatic ganglion of neuraxis OBOL:automatic neuraxis ganglion OBOL:automatic A mucosa that is part of an anal canal [Automatically generated definition]. EMAPA:27531 FMA:74654 NCIT:C60784 SCTID:362170004 UMLS:C0227414 anal canal mucosa anal canal mucosa of organ anal canal mucous membrane anal canal organ mucosa anal canal viewed anatomically mucosa anal canal viewed anatomically mucosa of organ anal canal viewed anatomically mucous membrane anal canal viewed anatomically organ mucosa anal mucosa anal mucous membrane anal region mucosa anal region mucosa of organ anal region mucous membrane anal region organ mucosa anatomical anal canal mucosa anatomical anal canal mucosa of organ anatomical anal canal mucous membrane anatomical anal canal organ mucosa mucosa of anal canal viewed anatomically mucosa of anal region mucosa of anatomical anal canal mucosa of organ of anal canal mucosa of organ of anal canal viewed anatomically mucosa of organ of anal region mucosa of organ of anatomical anal canal mucous membrane of anal canal mucous membrane of anal canal viewed anatomically mucous membrane of anal region mucous membrane of anatomical anal canal organ mucosa of anal canal organ mucosa of anal canal viewed anatomically organ mucosa of anal region organ mucosa of anatomical anal canal uberon UBERON:0003342 mucosa of anal canal A mucosa that is part of an anal canal [Automatically generated definition]. OBOL:automatic UMLS:C0227414 ncithesaurus:Anal_Mucosa anal canal mucosa OBOL:automatic anal canal mucosa of organ OBOL:automatic anal canal mucous membrane OBOL:automatic anal canal organ mucosa OBOL:automatic anal canal viewed anatomically mucosa OBOL:automatic anal canal viewed anatomically mucosa of organ OBOL:automatic anal canal viewed anatomically mucous membrane OBOL:automatic anal canal viewed anatomically organ mucosa OBOL:automatic anal mucosa FMA:74654 anal mucous membrane FMA:74654 anal region mucosa OBOL:automatic anal region mucosa of organ OBOL:automatic anal region mucous membrane OBOL:automatic anal region organ mucosa OBOL:automatic anatomical anal canal mucosa OBOL:automatic anatomical anal canal mucosa of organ OBOL:automatic anatomical anal canal mucous membrane OBOL:automatic anatomical anal canal organ mucosa OBOL:automatic mucosa of anal canal viewed anatomically OBOL:automatic mucosa of anal region OBOL:automatic mucosa of anatomical anal canal OBOL:automatic mucosa of organ of anal canal OBOL:automatic mucosa of organ of anal canal viewed anatomically OBOL:automatic mucosa of organ of anal region OBOL:automatic mucosa of organ of anatomical anal canal OBOL:automatic mucous membrane of anal canal OBOL:automatic mucous membrane of anal canal viewed anatomically OBOL:automatic mucous membrane of anal region OBOL:automatic mucous membrane of anatomical anal canal OBOL:automatic organ mucosa of anal canal OBOL:automatic organ mucosa of anal canal viewed anatomically OBOL:automatic organ mucosa of anal region OBOL:automatic organ mucosa of anatomical anal canal OBOL:automatic A mucosa that is part of a oral opening [Automatically generated definition]. EMAPA:26937 SCTID:362083000 mucosa of oral opening mucosa of oral part of face mucosa of organ of oral opening mucosa of organ of oral part of face mucosa of organ of oral region mucosa of organ of subdivision of mouth mucosa of subdivision of mouth mucous membrane of oral opening mucous membrane of oral part of face mucous membrane of oral region mucous membrane of subdivision of mouth oral opening mucosa oral opening mucosa of organ oral opening mucous membrane oral opening organ mucosa oral part of face mucosa oral part of face mucosa of organ oral part of face mucous membrane oral part of face organ mucosa oral region mucosa oral region mucosa of organ oral region mucous membrane oral region organ mucosa organ mucosa of oral opening organ mucosa of oral part of face organ mucosa of oral region organ mucosa of subdivision of mouth subdivision of mouth mucosa subdivision of mouth mucosa of organ subdivision of mouth mucous membrane subdivision of mouth organ mucosa uberon UBERON:0003343 mucosa of oral region A mucosa that is part of a oral opening [Automatically generated definition]. OBOL:automatic mucosa of oral opening OBOL:automatic mucosa of oral part of face OBOL:automatic mucosa of organ of oral opening OBOL:automatic mucosa of organ of oral part of face OBOL:automatic mucosa of organ of oral region OBOL:automatic mucosa of organ of subdivision of mouth OBOL:automatic mucosa of subdivision of mouth OBOL:automatic mucous membrane of oral opening OBOL:automatic mucous membrane of oral part of face OBOL:automatic mucous membrane of oral region OBOL:automatic mucous membrane of subdivision of mouth OBOL:automatic oral opening mucosa OBOL:automatic oral opening mucosa of organ OBOL:automatic oral opening mucous membrane OBOL:automatic oral opening organ mucosa OBOL:automatic oral part of face mucosa OBOL:automatic oral part of face mucosa of organ OBOL:automatic oral part of face mucous membrane OBOL:automatic oral part of face organ mucosa OBOL:automatic oral region mucosa OBOL:automatic oral region mucosa of organ OBOL:automatic oral region mucous membrane OBOL:automatic oral region organ mucosa OBOL:automatic organ mucosa of oral opening OBOL:automatic organ mucosa of oral part of face OBOL:automatic organ mucosa of oral region OBOL:automatic organ mucosa of subdivision of mouth OBOL:automatic subdivision of mouth mucosa OBOL:automatic subdivision of mouth mucosa of organ OBOL:automatic subdivision of mouth mucous membrane OBOL:automatic subdivision of mouth organ mucosa OBOL:automatic A mucosa that is part of a rectum [Automatically generated definition]. CALOHA:TS-2107 EMAPA:27081 FMA:15033 MA:0003218 SCTID:362167003 mucosa of organ of rectum mucous membrane of rectum organ mucosa of rectum rectal mucosa rectal mucous membrane rectum mucosa rectum mucosa of organ rectum mucous membrane rectum organ mucosa uberon UBERON:0003346 mucosa of rectum A mucosa that is part of a rectum [Automatically generated definition]. OBOL:automatic mucosa of organ of rectum OBOL:automatic mucous membrane of rectum OBOL:automatic organ mucosa of rectum OBOL:automatic rectal mucosa FMA:15033 rectal mucous membrane FMA:15033 rectum mucosa OBOL:automatic rectum mucosa of organ OBOL:automatic rectum mucous membrane OBOL:automatic rectum organ mucosa OBOL:automatic A layer of epithelial cells on the surface of the mucosa. BTO:0003752 uberon lamina epithelialis mucosa lamina epithelialis mucosae UBERON:0003350 lies on top of lamina propria epithelium of mucosa A layer of epithelial cells on the surface of the mucosa. BTO:0003752 lamina epithelialis mucosa BTO:0003752 lamina epithelialis mucosae BTO:0003752 An epithelium that is part of a pharynx [Automatically generated definition]. Epithelium lining the pharynx consisting largely of simple columnar epithelium with a short segment (1mm) of stratified squamous epithelium on the ventral side. Chen et al, 2007.[TAO] BSA:0000112 BTO:0005240 EMAPA:16708 MA:0002725 RETIRED_EHDAA2:0001460 TAO:0001174 XAO:0003202 ZFA:0001174 epithelial tissue of pharynx epithelium of pharynx pharynx epithelial tissue pharynx epithelium uberon UBERON:0003351 pharyngeal epithelium ZFA ZFA An epithelium that is part of a pharynx [Automatically generated definition]. OBOL:automatic Epithelium lining the pharynx consisting largely of simple columnar epithelium with a short segment (1mm) of stratified squamous epithelium on the ventral side. Chen et al, 2007.[TAO] 2012-08-14 TAO:0001174 TAO ZFIN:curator epithelial tissue of pharynx OBOL:automatic epithelium of pharynx OBOL:automatic pharynx epithelial tissue OBOL:automatic pharynx epithelium OBOL:automatic An epithelium that is part of a midgut. BTO:0005053 EHDAA2:0001195 EMAPA:16569 MA:0003205 epithelial tissue of midgut midgut epithelial tissue midgut epithelium uberon UBERON:0003352 epithelium of midgut BTO An epithelium that is part of a midgut. OBOL:automatic epithelial tissue of midgut OBOL:automatic midgut epithelial tissue OBOL:automatic midgut epithelium BTO:0005053 midgut epithelium OBOL:automatic An epithelium that is part of a hindgut [Automatically generated definition]. EHDAA2:0000782 EMAPA:16717 MA:0003206 epithelial tissue of hindgut hindgut epithelial tissue hindgut epithelium uberon UBERON:0003353 epithelium of hindgut An epithelium that is part of a hindgut [Automatically generated definition]. OBOL:automatic epithelial tissue of hindgut OBOL:automatic hindgut epithelial tissue OBOL:automatic hindgut epithelium OBOL:automatic An epithelium that is part of a rectum [Automatically generated definition]. CALOHA:TS-2066 EHDAA2:0001594 EMAPA:17898 FMA:17510 MA:0003219 VHOG:0001037 epithelial tissue of rectum rectal epithelium rectum epithelial tissue rectum epithelium uberon UBERON:0003354 epithelium of rectum An epithelium that is part of a rectum [Automatically generated definition]. OBOL:automatic epithelial tissue of rectum OBOL:automatic rectal epithelium FMA:17510 rectum epithelial tissue OBOL:automatic rectum epithelium OBOL:automatic An epithelium that is part of a right lung [Automatically generated definition]. EMAPA:17663 MA:0003132 epithelial tissue of right lung right lung epithelial tissue right lung epithelium uberon UBERON:0003364 epithelium of right lung An epithelium that is part of a right lung [Automatically generated definition]. OBOL:automatic epithelial tissue of right lung OBOL:automatic right lung epithelial tissue OBOL:automatic right lung epithelium OBOL:automatic An epithelium that is part of a left lung [Automatically generated definition]. EMAPA:17655 MA:0003131 epithelial tissue of left lung left lung epithelial tissue left lung epithelium uberon UBERON:0003365 epithelium of left lung An epithelium that is part of a left lung [Automatically generated definition]. OBOL:automatic epithelial tissue of left lung OBOL:automatic left lung epithelial tissue OBOL:automatic left lung epithelium OBOL:automatic An unilaminar epithelium that surrounds a pelvic appendage bud. UBERON:0005232 EHDAA2:0001034 EMAPA:16780 VHOG:0001048 hindlimb ectoderm hindlimb bud ectoderm hindlimb ectoderm lower limb bud ectoderm pelvic fin bud ectoderm uberon leg ectoderm UBERON:0003371 pelvic appendage bud ectoderm EHDAA2 EHDAA2 An unilaminar epithelium that surrounds a pelvic appendage bud. OBOL:automatic hindlimb ectoderm VHOG:0001048 hindlimb bud ectoderm EMAPA:16780 hindlimb bud ectoderm hindlimb ectoderm VHOG:0001048 lower limb bud ectoderm EHDAA2:0001034 pelvic fin bud ectoderm leg ectoderm OBOL:automatic A portion of cardiac muscle tissue that is part of a right atrium [Automatically generated definition]. EHDAA2:0004155 EMAPA:17326 FMA:7282 SCTID:362018002 VHOG:0001227 cardiac muscle of cardiac right atrium cardiac muscle of heart right atrium cardiac muscle tissue of heart right atrium cardiac muscle tissue of right atrium cardiac muscle tissue of right atrium of heart myocardium of right atrium right atrium heart muscle right atrium myocardium textus muscularis of myocardium of right atrium textus muscularis of myocardium of right atrium of heart textus muscularis of myocardium of right cardiac atrium uberon UBERON:0003379 cardiac muscle of right atrium A portion of cardiac muscle tissue that is part of a right atrium [Automatically generated definition]. OBOL:automatic cardiac muscle of cardiac right atrium OBOL:automatic cardiac muscle of heart right atrium OBOL:automatic cardiac muscle tissue of heart right atrium OBOL:automatic cardiac muscle tissue of right atrium OBOL:automatic cardiac muscle tissue of right atrium of heart OBOL:automatic right atrium heart muscle EHDAA2:0004155 right atrium myocardium VHOG:0001227 textus muscularis of myocardium of right atrium OBOL:automatic textus muscularis of myocardium of right atrium of heart OBOL:automatic textus muscularis of myocardium of right cardiac atrium OBOL:automatic A portion of cardiac muscle tissue that is part of a left atrium [Automatically generated definition]. EHDAA2:0004154 EMAPA:17320 FMA:7285 SCTID:189936008 VHOG:0001225 cardiac left atrium cardiac muscle cardiac left atrium cardiac muscle tissue cardiac muscle of cardiac left atrium cardiac muscle of heart left atrium cardiac muscle of left atrium of heart left atrium heart muscle left atrium myocardium myocardium of left atrium textus muscularis of myocardium of cardiac left atrium textus muscularis of myocardium of heart left atrium textus muscularis of myocardium of left atrium textus muscularis of myocardium of left atrium of heart textus muscularis of myocardium of left cardiac atrium uberon UBERON:0003380 cardiac muscle of left atrium A portion of cardiac muscle tissue that is part of a left atrium [Automatically generated definition]. OBOL:automatic cardiac left atrium cardiac muscle OBOL:automatic cardiac left atrium cardiac muscle tissue OBOL:automatic cardiac muscle of cardiac left atrium OBOL:automatic cardiac muscle of heart left atrium OBOL:automatic cardiac muscle of left atrium of heart OBOL:automatic left atrium heart muscle EHDAA2:0004154 left atrium myocardium VHOG:0001225 textus muscularis of myocardium of cardiac left atrium OBOL:automatic textus muscularis of myocardium of heart left atrium OBOL:automatic textus muscularis of myocardium of left atrium OBOL:automatic textus muscularis of myocardium of left atrium of heart OBOL:automatic textus muscularis of myocardium of left cardiac atrium OBOL:automatic A portion of cardiac muscle tissue that is part of a right ventricle [Automatically generated definition]. EMAPA:17342 FMA:83452 VHOG:0001236 cardiac muscle tissue of right ventricle right ventricular cardiac muscle tissue uberon right ventricle cardiac muscle UBERON:0003381 cardiac muscle of right ventricle A portion of cardiac muscle tissue that is part of a right ventricle [Automatically generated definition]. OBOL:automatic cardiac muscle tissue of right ventricle FMA:83452 right ventricular cardiac muscle tissue GO:0003221 right ventricle cardiac muscle VHOG:0001236 A portion of cardiac muscle tissue that is part of a left ventricle [Automatically generated definition]. EMAPA:17339 FMA:83453 VHOG:0001234 cardiac muscle tissue of left ventricle left ventricular cardiac muscle tissue uberon left ventricle cardiac muscle UBERON:0003382 cardiac muscle of left ventricle A portion of cardiac muscle tissue that is part of a left ventricle [Automatically generated definition]. OBOL:automatic cardiac muscle tissue of left ventricle FMA:83453 left ventricular cardiac muscle tissue GO:0003220 left ventricle cardiac muscle VHOG:0001234 A portion of cardiac muscle tissue that is part of an interventricular septum [Automatically generated definition]. EHDAA2:0004158 EMAPA:17335 FMA:84084 VHOG:0000999 cardiac muscle of interventricular septum cardiac muscle tissue of interventricular septum interventricular septum cardiac muscle interventricular septum heart muscle interventricular septum myocardium uberon interventricular septum muscle UBERON:0003383 cardiac muscle tissue of interventricular septum A portion of cardiac muscle tissue that is part of an interventricular septum [Automatically generated definition]. OBOL:automatic cardiac muscle tissue of interventricular septum FMA:84084 interventricular septum cardiac muscle VHOG:0000999 interventricular septum heart muscle EHDAA2:0004158 interventricular septum myocardium VHOG:0000999 interventricular septum muscle http://orcid.org/0000-0002-6601-2165 A portion of skeletal muscle tissue that is part of a pharynx [Automatically generated definition]. EMAPA:18963 pharynx skeletal muscle pharynx skeletal muscle tissue skeletal muscle tissue of pharynx uberon UBERON:0003384 skeletal muscle tissue of pharynx A portion of skeletal muscle tissue that is part of a pharynx [Automatically generated definition]. OBOL:automatic pharynx skeletal muscle OBOL:automatic pharynx skeletal muscle tissue OBOL:automatic skeletal muscle tissue of pharynx OBOL:automatic any of the striated muscles that move the eye and include: superior rectus, inferior rectus, medial rectus, lateral rectus, superior oblique, inferior oblique, retractor bulbi Not clear if we need this and intra-ocular muscle. See issue #331. MA includes ciliary and iris smooth muscle EMAPA:18807 MA:0001268 ocular smooth muscle uberon UBERON:0003386 smooth muscle of eye any of the striated muscles that move the eye and include: superior rectus, inferior rectus, medial rectus, lateral rectus, superior oblique, inferior oblique, retractor bulbi MGI:cwg MP:0005247 ocular smooth muscle MA:0001268 A mesothelium that is part of a pericardium [Automatically generated definition]. RETIRED_EHDAA2:0001436 cavity of pericardial sac meso-epithelium cavity of pericardial sac mesothelium meso-epithelium of cavity of pericardial sac meso-epithelium of pericardial cavity mesothelium of cavity of pericardial sac pericardial cavity meso-epithelium pericardial cavity mesothelium uberon UBERON:0003388 mesothelium of pericardial cavity A mesothelium that is part of a pericardium [Automatically generated definition]. OBOL:automatic cavity of pericardial sac meso-epithelium OBOL:automatic cavity of pericardial sac mesothelium OBOL:automatic meso-epithelium of cavity of pericardial sac OBOL:automatic meso-epithelium of pericardial cavity OBOL:automatic mesothelium of cavity of pericardial sac OBOL:automatic pericardial cavity meso-epithelium OBOL:automatic pericardial cavity mesothelium OBOL:automatic A mesothelium that is part of a diaphragm [Automatically generated definition]. EMAPA:18429 diaphragm meso-epithelium diaphragm mesothelium meso-epithelium of diaphragm meso-epithelium of thoracic diaphragm mesothelium of thoracic diaphragm thoracic diaphragm meso-epithelium thoracic diaphragm mesothelium uberon UBERON:0003389 mesothelium of diaphragm A mesothelium that is part of a diaphragm [Automatically generated definition]. OBOL:automatic diaphragm meso-epithelium OBOL:automatic diaphragm mesothelium OBOL:automatic meso-epithelium of diaphragm OBOL:automatic meso-epithelium of thoracic diaphragm OBOL:automatic mesothelium of thoracic diaphragm OBOL:automatic thoracic diaphragm meso-epithelium OBOL:automatic thoracic diaphragm mesothelium OBOL:automatic A mesothelium that is part of a pleural cavity [Automatically generated definition]. BTO:0003155 EHDAA2:0001476 EMAPA:16775 FMA:18148 meso-epithelium of pleural cavity mesothelium of pleura pleural cavity meso-epithelium pleural cavity mesothelium pleural mesothelium uberon pleura UBERON:0003390 mesothelium of pleural cavity A mesothelium that is part of a pleural cavity [Automatically generated definition]. OBOL:automatic meso-epithelium of pleural cavity OBOL:automatic mesothelium of pleura FMA:18148 pleural cavity meso-epithelium OBOL:automatic pleural cavity mesothelium OBOL:automatic pleural mesothelium EMAPA:16775 pleura EMAPA:16775 A cartilage element that is part of a respiratory system [Automatically generated definition]. EMAPA:18694 MA:0001818 apparatus respiratorius cartilage cartilage of apparatus respiratorius respiratory system cartilage uberon UBERON:0003406 cartilage of respiratory system A cartilage element that is part of a respiratory system [Automatically generated definition]. OBOL:automatic apparatus respiratorius cartilage OBOL:automatic cartilage of apparatus respiratorius OBOL:automatic respiratory system cartilage OBOL:automatic A gland that is part of a digestive tract [Automatically generated definition]. EMAPA:18815 MA:0003202 digestive tract gland gland of digestive tract gland of lower gastrointestinal tract gut gland lower gastrointestinal tract gland uberon UBERON:0003408 gland of digestive tract A gland that is part of a digestive tract [Automatically generated definition]. OBOL:automatic digestive tract gland OBOL:automatic gland of digestive tract OBOL:automatic gland of lower gastrointestinal tract OBOL:automatic gut gland MA:0003202 lower gastrointestinal tract gland OBOL:automatic Mesenchyme that is part of a pelvic appendage bud. Mesoderm part of pelvic fin bud.[TAO] EHDAA2:0001035 EMAPA:16781 TAO:0001386 ZFA:0001386 leg mesenchyme lower limb bud mesenchyme hindlimb bud mesenchyme mesoderm pelvic fin bud pelvic fin bud mesenchyme uberon UBERON:0003412 pelvic appendage bud mesenchyme Mesenchyme that is part of a pelvic appendage bud. OBOL:automatic Mesoderm part of pelvic fin bud.[TAO] 2012-08-14 TAO:0001386 TAO ZFIN:curator leg mesenchyme OBOL:automatic lower limb bud mesenchyme EHDAA2:0001035 hindlimb bud mesenchyme EMAPA:16781 mesoderm pelvic fin bud ZFA:0001386 pelvic fin bud mesenchyme An adipose tissue that is part of a dermis [Automatically generated definition]. MA:0000798 adipose tissue of dermis dermis fat tissue dermis fatty tissue fat tissue of dermis fatty tissue of dermis uberon UBERON:0003426 dermis adipose tissue An adipose tissue that is part of a dermis [Automatically generated definition]. OBOL:automatic adipose tissue of dermis OBOL:automatic dermis fat tissue OBOL:automatic dermis fatty tissue OBOL:automatic fat tissue of dermis OBOL:automatic fatty tissue of dermis OBOL:automatic A nerve that is part of an abdomen [Automatically generated definition]. MA:0000521 nerve of abdomen uberon UBERON:0003429 abdomen nerve A nerve that is part of an abdomen [Automatically generated definition]. OBOL:automatic nerve of abdomen OBOL:automatic A nerve that is part of a neck [Automatically generated definition]. EMAPA:37263 MA:0000588 neck (volume) nerve nerve of neck nerve of neck (volume) uberon UBERON:0003430 neck nerve A nerve that is part of a neck [Automatically generated definition]. OBOL:automatic EMAPA:37263 MA:th neck (volume) nerve OBOL:automatic nerve of neck OBOL:automatic nerve of neck (volume) OBOL:automatic Any nerve that innervates the iris. added for consistency with mouse ontologies. The term 'ciliary nerve' is usually used to denote either of the two nerves (with different origins) that innervate the iris, as well as ciliary muscles and cornea EMAPA:35449 MA:0001291 nerve of iris ciliary nerve uberon UBERON:0003438 iris nerve Any nerve that innervates the iris. UBERON:cjm nerve of iris OBOL:automatic A nerve that is part of the trunk region of the body (not to be confused with a nerve trunk). EMAPA:37264 MA:0000515 nerve of torso nerve of trunk torso nerve uberon trunk nerve UBERON:0003439 nerve of trunk region A nerve that is part of the trunk region of the body (not to be confused with a nerve trunk). http://orcid.org/0000-0002-6601-2165 EMAPA:37264 MA:th nerve of torso OBOL:automatic nerve of trunk OBOL:automatic torso nerve OBOL:automatic trunk nerve MA:0000515 A nerve that is located in a thoracic cavity [Automatically generated definition]. consider merging with thoracic nerve. In MA the only subclass is the phrenic nerve, which arises from a cervical nerve EMAPA:37267 MA:0000556 cavity of chest nerve cavity of thorax nerve chest cavity nerve nerve of cavity of chest nerve of cavity of thorax nerve of chest cavity nerve of pectoral cavity nerve of thoracic cavity pectoral cavity nerve uberon UBERON:0003443 thoracic cavity nerve A nerve that is located in a thoracic cavity [Automatically generated definition]. OBOL:automatic EMAPA:37267 MA:th cavity of chest nerve OBOL:automatic cavity of thorax nerve OBOL:automatic chest cavity nerve OBOL:automatic nerve of cavity of chest OBOL:automatic nerve of cavity of thorax OBOL:automatic nerve of chest cavity OBOL:automatic nerve of pectoral cavity OBOL:automatic nerve of thoracic cavity OBOL:automatic pectoral cavity nerve OBOL:automatic A nerve that is part of a pelvis [Automatically generated definition]. EMAPA:37269 MA:0000542 nerve of pelvis uberon UBERON:0003444 pelvis nerve A nerve that is part of a pelvis [Automatically generated definition]. OBOL:automatic EMAPA:37269 MA:th nerve of pelvis OBOL:automatic A bone that is part of a head [Automatically generated definition]. EMAPA:35996 MA:0000576 SCTID:118646007 adult head bone adult head bone organ bone of adult head bone of head bone organ of adult head bone organ of head head bone organ uberon craniofacial bone UBERON:0003457 Different sources vary regarding which bones are craniofacial; e.g. hyoid bone head bone A bone that is part of a head [Automatically generated definition]. OBOL:automatic adult head bone OBOL:automatic adult head bone organ OBOL:automatic bone of adult head OBOL:automatic bone of head OBOL:automatic bone organ of adult head OBOL:automatic bone organ of head OBOL:automatic head bone organ OBOL:automatic craniofacial bone http://orcid.org/0000-0002-6601-2165 A bone that is part of a neck [Automatically generated definition]. EMAPA:37246 MA:0000584 OpenCyc:Mx4rvnpJSJwpEbGdrcN5Y29ycA bone of neck bone of neck (volume) bone organ of neck bone organ of neck (volume) neck (volume) bone neck (volume) bone organ neck bone organ uberon UBERON:0003458 neck bone A bone that is part of a neck [Automatically generated definition]. OBOL:automatic EMAPA:37246 MA:th bone of neck OBOL:automatic bone of neck (volume) OBOL:automatic bone organ of neck OBOL:automatic bone organ of neck (volume) OBOL:automatic neck (volume) bone OBOL:automatic neck (volume) bone organ OBOL:automatic neck bone organ OBOL:automatic A bone that is part of a facial skeleton [Automatically generated definition]. test whether 'facial bone' is an exact synonym EMAPA:19019 EMAPA:35924 MA:0001482 MA:0003159 NCIT:C63706 SCTID:181799005 UMLS:C0015455 bone of facial skeleton facial bone facial skeleton bone uberon bone of viscerocranium viscerocranium bone UBERON:0003462 facial bone MA A bone that is part of a facial skeleton [Automatically generated definition]. OBOL:automatic UMLS:C0015455 ncithesaurus:Facial_Bone bone of facial skeleton OBOL:automatic facial bone EMAPA:19019 facial skeleton bone OBOL:automatic bone of viscerocranium OBOL:automatic viscerocranium bone OBOL:automatic A bone that is part of a trunk [Automatically generated definition]. EMAPA:36583 MA:0000512 SCTID:427358002 bone of torso bone of trunk bone organ of torso bone organ of trunk torso bone torso bone organ trunk bone organ uberon UBERON:0003463 trunk bone A bone that is part of a trunk [Automatically generated definition]. OBOL:automatic bone of torso OBOL:automatic bone of trunk OBOL:automatic bone organ of torso OBOL:automatic bone organ of trunk OBOL:automatic torso bone OBOL:automatic torso bone organ OBOL:automatic trunk bone organ OBOL:automatic An artery that is part of a respiratory system [Automatically generated definition]. EMAPA:37569 MA:0001804 uberon UBERON:0003469 respiratory system artery An artery that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37569 MA:th The Iinferior labial artery (inferior labial branch of facial artery) arises near the angle of the mouth; it passes upward and forward beneath the Triangularis and, penetrating the Orbicularis oris, runs in a tortuous course along the edge of the lower lip between this muscle and the mucous membrane. It supplies the labial glands, the mucous membrane, and the muscles of the lower lip; and anastomoses with the artery of the opposite side, and with the mental branch of the inferior alveolar artery. EMAPA:37429 FMA:49567 MA:0001916 SCTID:145036002 Wikipedia:Inferior_labial_artery arteria labialis inferior inferior labial artery inferior labial branch of facial artery ramus labialis inferior (arteria facialis) ramus labialis inferior arteriae facialis uberon UBERON:0003471 artery of lower lip FMA The Iinferior labial artery (inferior labial branch of facial artery) arises near the angle of the mouth; it passes upward and forward beneath the Triangularis and, penetrating the Orbicularis oris, runs in a tortuous course along the edge of the lower lip between this muscle and the mucous membrane. It supplies the labial glands, the mucous membrane, and the muscles of the lower lip; and anastomoses with the artery of the opposite side, and with the mental branch of the inferior alveolar artery. Wikipedia:Inferior_labial_artery EMAPA:37429 MA:th arteria labialis inferior Wikipedia:Inferior_labial_artery inferior labial artery FMA:49567 inferior labial branch of facial artery FMA:49567 ramus labialis inferior (arteria facialis) FMA:TA ramus labialis inferior arteriae facialis Wikipedia:Inferior_labial_artery An artery that is part of a thoracic cavity[cjm]. in MA, aorta is classified here - but this is problematic because the abdominal aorta is not in the thoracic cavity EMAPA:37241 MA:0001902 MESH:D013895 uberon thoracic artery UBERON:0003473 thoracic cavity artery An artery that is part of a thoracic cavity[cjm]. https://sourceforge.net/tracker/index.php?func=detail&aid=3317815&group_id=76834&atid=1205376 in MA, aorta is classified here - but this is problematic because the abdominal aorta is not in the thoracic cavity MA EMAPA:37241 MA:th thoracic artery MESH:A07.231.114.891 A vein that is part of a respiratory system [Automatically generated definition]. EMAPA:37584 MA:0001809 MA:0001810 apparatus respiratorius vein respiratory system vein vein of apparatus respiratorius vein of respiratory system uberon UBERON:0003476 respiratory system venous blood vessel A vein that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37584 MA:th apparatus respiratorius vein OBOL:automatic respiratory system vein OBOL:automatic vein of apparatus respiratorius OBOL:automatic vein of respiratory system OBOL:automatic The inferior labial vein is the vein receiving blood from the lower lip. EMAPA:37202 FMA:52541 MA:0002253 SCTID:422955002 Wikipedia:Inferior_labial_vein inferior labial vein lower lip vein vena labialis inferior uberon venae labiales inferiores UBERON:0003478 vein of lower lip http://upload.wikimedia.org/wikipedia/commons/8/8c/Gray557.png The inferior labial vein is the vein receiving blood from the lower lip. Wikipedia:Inferior_labial_vein EMAPA:37202 MA:th inferior labial vein FMA:52541 lower lip vein OBOL:automatic vena labialis inferior venae labiales inferiores Wikipedia:Inferior_labial_vein A vein that is part of a thoracic cavity [Automatically generated definition]. EMAPA:37242 MA:0001903 cavity of chest vein cavity of thorax vein chest cavity vein pectoral cavity vein vein of cavity of chest vein of cavity of thorax vein of chest cavity vein of pectoral cavity vein of thoracic cavity uberon UBERON:0003479 thoracic cavity vein A vein that is part of a thoracic cavity [Automatically generated definition]. OBOL:automatic EMAPA:37242 MA:th cavity of chest vein OBOL:automatic cavity of thorax vein OBOL:automatic chest cavity vein OBOL:automatic pectoral cavity vein OBOL:automatic vein of cavity of chest OBOL:automatic vein of cavity of thorax OBOL:automatic vein of chest cavity OBOL:automatic vein of pectoral cavity OBOL:automatic vein of thoracic cavity OBOL:automatic A vein that is part of a tail [Automatically generated definition]. see also caudal vein AAO:0011105 EMAPA:37761 MA:0002233 Wikipedia:Tail_vein XAO:0000393 post-vent region vein vein of post-vent region vein of tail uberon caudal vein UBERON:0003481 tail vein A vein that is part of a tail [Automatically generated definition]. OBOL:automatic Wikipedia:Tail_vein EMAPA:37761 MA:th post-vent region vein OBOL:automatic vein of post-vent region OBOL:automatic vein of tail OBOL:automatic caudal vein Wikipedia:Tail_vein An endothelium of capillary that is part of a respiratory system [Automatically generated definition]. EMAPA:37575 MA:0001808 apparatus respiratorius blood capillary endothelium apparatus respiratorius capillary endothelium apparatus respiratorius capillary vessel endothelium apparatus respiratorius endothelium of blood capillary apparatus respiratorius endothelium of capillary apparatus respiratorius endothelium of capillary vessel blood capillary endothelium of apparatus respiratorius blood capillary endothelium of respiratory system capillary endothelium of apparatus respiratorius capillary endothelium of respiratory system capillary vessel endothelium of apparatus respiratorius capillary vessel endothelium of respiratory system endothelium of blood capillary of apparatus respiratorius endothelium of blood capillary of respiratory system endothelium of capillary of apparatus respiratorius endothelium of capillary of respiratory system endothelium of capillary vessel of apparatus respiratorius endothelium of capillary vessel of respiratory system respiratory system blood capillary endothelium respiratory system capillary vessel endothelium respiratory system endothelium of blood capillary respiratory system endothelium of capillary respiratory system endothelium of capillary vessel uberon UBERON:0003489 respiratory system capillary endothelium true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships An endothelium of capillary that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37575 MA:th apparatus respiratorius blood capillary endothelium OBOL:automatic apparatus respiratorius capillary endothelium OBOL:automatic apparatus respiratorius capillary vessel endothelium OBOL:automatic apparatus respiratorius endothelium of blood capillary OBOL:automatic apparatus respiratorius endothelium of capillary OBOL:automatic apparatus respiratorius endothelium of capillary vessel OBOL:automatic blood capillary endothelium of apparatus respiratorius OBOL:automatic blood capillary endothelium of respiratory system OBOL:automatic capillary endothelium of apparatus respiratorius OBOL:automatic capillary endothelium of respiratory system OBOL:automatic capillary vessel endothelium of apparatus respiratorius OBOL:automatic capillary vessel endothelium of respiratory system OBOL:automatic endothelium of blood capillary of apparatus respiratorius OBOL:automatic endothelium of blood capillary of respiratory system OBOL:automatic endothelium of capillary of apparatus respiratorius OBOL:automatic endothelium of capillary of respiratory system OBOL:automatic endothelium of capillary vessel of apparatus respiratorius OBOL:automatic endothelium of capillary vessel of respiratory system OBOL:automatic respiratory system blood capillary endothelium OBOL:automatic respiratory system capillary vessel endothelium OBOL:automatic respiratory system endothelium of blood capillary OBOL:automatic respiratory system endothelium of capillary OBOL:automatic respiratory system endothelium of capillary vessel OBOL:automatic A venule that is part of a respiratory system [Automatically generated definition]. EMAPA:37587 MA:0001813 apparatus respiratorius venule venule of apparatus respiratorius venule of respiratory system uberon UBERON:0003494 respiratory system venule A venule that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37587 MA:th apparatus respiratorius venule OBOL:automatic venule of apparatus respiratorius OBOL:automatic venule of respiratory system OBOL:automatic An arteriole that is part of a respiratory system [Automatically generated definition]. EMAPA:37568 MA:0001803 uberon UBERON:0003495 respiratory system arteriole true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships An arteriole that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37568 MA:th A blood vessel that is part of a head [Automatically generated definition]. EMAPA:36610 MA:0000575 SCTID:127865000 adult head blood vessel blood vessel of adult head blood vessel of head uberon UBERON:0003496 head blood vessel true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships A blood vessel that is part of a head [Automatically generated definition]. OBOL:automatic adult head blood vessel OBOL:automatic blood vessel of adult head OBOL:automatic blood vessel of head OBOL:automatic A blood vessel that is part of an abdomen [Automatically generated definition]. MA:0000518 blood vessel of abdomen uberon UBERON:0003497 abdomen blood vessel UBERON:0012254 A blood vessel that is part of an abdomen [Automatically generated definition]. OBOL:automatic blood vessel of abdomen OBOL:automatic UBERON:0012254 abdominal aorta artery A blood vessel that is part of a heart [Automatically generated definition]. EMAPA:35397 MA:0002483 blood vessel of heart uberon cardiac blood vessel UBERON:0003498 heart blood vessel A blood vessel that is part of a heart [Automatically generated definition]. OBOL:automatic blood vessel of heart OBOL:automatic cardiac blood vessel EMAPA:35397 A blood vessel that is part of a brain [Automatically generated definition]. EMAPA:35182 MA:0002769 blood vessel of brain uberon UBERON:0003499 brain blood vessel A blood vessel that is part of a brain [Automatically generated definition]. OBOL:automatic blood vessel of brain OBOL:automatic A blood vessel that is part of a cornea [Automatically generated definition]. follow up on tracker item EMAPA:36611 MA:0001241 blood vessel of cornea cornea blood vessel uberon UBERON:0003500 corneal blood vessel A blood vessel that is part of a cornea [Automatically generated definition]. https://orcid.org/0000-0002-6601-2165 https://sourceforge.net/tracker/index.php?func=detail&aid=3564332&group_id=36855&atid=440764 PMID:17051153 blood vessel of cornea OBOL:automatic cornea blood vessel OBOL:automatic A blood vessel that is part of a retina [Automatically generated definition]. EMAPA:36520 GAID:509 MA:0001317 MESH:D012171 SCTID:280692003 XAO:0004153 blood vessel of inner layer of eyeball blood vessel of retina blood vessel of tunica interna of eyeball inner layer of eyeball blood vessel retinal blood vessel tunica interna of eyeball blood vessel uberon UBERON:0003501 retina blood vessel A blood vessel that is part of a retina [Automatically generated definition]. OBOL:automatic blood vessel of inner layer of eyeball OBOL:automatic blood vessel of retina OBOL:automatic blood vessel of tunica interna of eyeball OBOL:automatic inner layer of eyeball blood vessel OBOL:automatic retinal blood vessel OBOL:automatic tunica interna of eyeball blood vessel OBOL:automatic A blood vessel that is part of a neck [Automatically generated definition]. EMAPA:37236 MA:0000583 blood vessel of neck blood vessel of neck (volume) neck (volume) blood vessel uberon UBERON:0003502 neck blood vessel A blood vessel that is part of a neck [Automatically generated definition]. OBOL:automatic EMAPA:37236 MA:th blood vessel of neck OBOL:automatic blood vessel of neck (volume) OBOL:automatic neck (volume) blood vessel OBOL:automatic A blood vessel that is part of a respiratory system [Automatically generated definition]. EMAPA:35731 EMAPA:35995 MA:0001799 apparatus respiratorius blood vessel blood vessel of apparatus respiratorius blood vessel of respiratory system uberon UBERON:0003504 respiratory system blood vessel A blood vessel that is part of a respiratory system [Automatically generated definition]. OBOL:automatic apparatus respiratorius blood vessel OBOL:automatic blood vessel of apparatus respiratorius OBOL:automatic blood vessel of respiratory system OBOL:automatic A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta. EMAPA:35144 MA:0000061 uberon UBERON:0003509 only in MA - supertype of artery, arteriole, aorta. arterial blood vessel A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta. https://orcid.org/0000-0002-6601-2165 A blood vessel that is part of a iris [Automatically generated definition]. EMAPA:37387 MA:0001290 ZFA:0005568 blood vessel of iris uberon UBERON:0003511 iris blood vessel A blood vessel that is part of a iris [Automatically generated definition]. OBOL:automatic EMAPA:37387 MA:th blood vessel of iris OBOL:automatic A blood vessel that is part of a lung [Automatically generated definition]. EMAPA:32867 MA:0002457 blood vessel of lung uberon pulmonary vascular element UBERON:0003512 lung blood vessel A blood vessel that is part of a lung [Automatically generated definition]. OBOL:automatic blood vessel of lung OBOL:automatic pulmonary vascular element EMAPA:32867 A blood vessel that is part of a trunk [Automatically generated definition]. EMAPA:37237 MA:0000511 blood vessel of torso blood vessel of trunk torso blood vessel uberon UBERON:0003513 trunk blood vessel A blood vessel that is part of a trunk [Automatically generated definition]. OBOL:automatic EMAPA:37237 MA:th blood vessel of torso OBOL:automatic blood vessel of trunk OBOL:automatic torso blood vessel OBOL:automatic A blood vessel that is part of a thoracic cavity [Automatically generated definition]. EMAPA:37240 MA:0000554 blood vessel of cavity of chest blood vessel of cavity of thorax blood vessel of chest cavity blood vessel of pectoral cavity blood vessel of thoracic cavity cavity of chest blood vessel cavity of thorax blood vessel chest cavity blood vessel pectoral cavity blood vessel uberon UBERON:0003519 thoracic cavity blood vessel A blood vessel that is part of a thoracic cavity [Automatically generated definition]. OBOL:automatic EMAPA:37240 MA:th blood vessel of cavity of chest OBOL:automatic blood vessel of cavity of thorax OBOL:automatic blood vessel of chest cavity OBOL:automatic blood vessel of pectoral cavity OBOL:automatic blood vessel of thoracic cavity OBOL:automatic cavity of chest blood vessel OBOL:automatic cavity of thorax blood vessel OBOL:automatic chest cavity blood vessel OBOL:automatic pectoral cavity blood vessel OBOL:automatic A blood vessel that is part of a pelvis [Automatically generated definition]. EMAPA:37244 MA:0000531 blood vessel of pelvis uberon UBERON:0003520 pelvis blood vessel A blood vessel that is part of a pelvis [Automatically generated definition]. OBOL:automatic EMAPA:37244 MA:th blood vessel of pelvis OBOL:automatic A blood vessel that is part of a tail [Automatically generated definition]. EMAPA:35848 MA:0000695 blood vessel of post-vent region blood vessel of tail post-vent region blood vessel uberon UBERON:0003524 tail blood vessel A blood vessel that is part of a tail [Automatically generated definition]. OBOL:automatic blood vessel of post-vent region OBOL:automatic blood vessel of tail OBOL:automatic post-vent region blood vessel OBOL:automatic A capillary that is part of a respiratory system [Automatically generated definition]. EMAPA:37574 MA:0001807 apparatus respiratorius blood capillary apparatus respiratorius capillary apparatus respiratorius capillary vessel blood capillary of apparatus respiratorius blood capillary of respiratory system capillary of apparatus respiratorius capillary of respiratory system capillary vessel of apparatus respiratorius capillary vessel of respiratory system respiratory system blood capillary respiratory system capillary vessel uberon UBERON:0003526 respiratory system capillary A capillary that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37574 MA:th apparatus respiratorius blood capillary OBOL:automatic apparatus respiratorius capillary OBOL:automatic apparatus respiratorius capillary vessel OBOL:automatic blood capillary of apparatus respiratorius OBOL:automatic blood capillary of respiratory system OBOL:automatic capillary of apparatus respiratorius OBOL:automatic capillary of respiratory system OBOL:automatic capillary vessel of apparatus respiratorius OBOL:automatic capillary vessel of respiratory system OBOL:automatic respiratory system blood capillary OBOL:automatic respiratory system capillary vessel OBOL:automatic A gray matter that is part of a brain [Automatically generated definition]. EMAPA:35184 MA:0000810 NCIT:C49333 UMLS:C1707348 brain grey matter brain grey substance gray matter of brain grey matter of brain grey substance of brain uberon UBERON:0003528 brain gray matter A gray matter that is part of a brain [Automatically generated definition]. OBOL:automatic UMLS:C1707348 ncithesaurus:Cerebral_Gray_Matter brain grey matter MA:0000810 brain grey substance OBOL:automatic gray matter of brain OBOL:automatic grey matter of brain OBOL:automatic grey substance of brain OBOL:automatic A zone of skin that is part of a tail [Automatically generated definition]. EMAPA:36502 MA:0000700 SCTID:67214004 post-vent region skin skin of post-vent region skin of tail uberon UBERON:0003534 tail skin A zone of skin that is part of a tail [Automatically generated definition]. OBOL:automatic post-vent region skin OBOL:automatic skin of post-vent region OBOL:automatic skin of tail OBOL:automatic A portion of connective tissue that is part of a head [Automatically generated definition]. EMAPA:16098 MA:0000577 adult head connective tissue adult head portion of connective tissue adult head textus connectivus connective tissue of adult head connective tissue of head head portion of connective tissue head textus connectivus portion of connective tissue of adult head portion of connective tissue of head textus connectivus of adult head textus connectivus of head uberon UBERON:0003566 head connective tissue A portion of connective tissue that is part of a head [Automatically generated definition]. OBOL:automatic adult head connective tissue OBOL:automatic adult head portion of connective tissue OBOL:automatic adult head textus connectivus OBOL:automatic connective tissue of adult head OBOL:automatic connective tissue of head OBOL:automatic head portion of connective tissue OBOL:automatic head textus connectivus OBOL:automatic portion of connective tissue of adult head OBOL:automatic portion of connective tissue of head OBOL:automatic textus connectivus of adult head OBOL:automatic textus connectivus of head OBOL:automatic A portion of connective tissue that is part of an abdomen [Automatically generated definition]. MA:0000519 abdomen portion of connective tissue abdomen textus connectivus connective tissue of abdomen portion of connective tissue of abdomen textus connectivus of abdomen uberon UBERON:0003567 abdomen connective tissue A portion of connective tissue that is part of an abdomen [Automatically generated definition]. OBOL:automatic abdomen portion of connective tissue OBOL:automatic abdomen textus connectivus OBOL:automatic connective tissue of abdomen OBOL:automatic portion of connective tissue of abdomen OBOL:automatic textus connectivus of abdomen OBOL:automatic A portion of connective tissue that is part of a neck [Automatically generated definition]. EMAPA:37250 MA:0000585 connective tissue of neck connective tissue of neck (volume) neck (volume) connective tissue neck (volume) portion of connective tissue neck (volume) textus connectivus neck portion of connective tissue neck textus connectivus portion of connective tissue of neck portion of connective tissue of neck (volume) textus connectivus of neck textus connectivus of neck (volume) uberon UBERON:0003568 neck connective tissue A portion of connective tissue that is part of a neck [Automatically generated definition]. OBOL:automatic EMAPA:37250 MA:th connective tissue of neck OBOL:automatic connective tissue of neck (volume) OBOL:automatic neck (volume) connective tissue OBOL:automatic neck (volume) portion of connective tissue OBOL:automatic neck (volume) textus connectivus OBOL:automatic neck portion of connective tissue OBOL:automatic neck textus connectivus OBOL:automatic portion of connective tissue of neck OBOL:automatic portion of connective tissue of neck (volume) OBOL:automatic textus connectivus of neck OBOL:automatic textus connectivus of neck (volume) OBOL:automatic A portion of connective tissue that is part of a respiratory system [Automatically generated definition]. EMAPA:35968 EMAPA:35977 MA:0001814 apparatus respiratorius connective tissue apparatus respiratorius portion of connective tissue apparatus respiratorius textus connectivus connective tissue of apparatus respiratorius connective tissue of respiratory system portion of connective tissue of apparatus respiratorius portion of connective tissue of respiratory system respiratory system portion of connective tissue respiratory system textus connectivus textus connectivus of apparatus respiratorius textus connectivus of respiratory system uberon UBERON:0003570 respiratory system connective tissue A portion of connective tissue that is part of a respiratory system [Automatically generated definition]. OBOL:automatic apparatus respiratorius connective tissue OBOL:automatic apparatus respiratorius portion of connective tissue OBOL:automatic apparatus respiratorius textus connectivus OBOL:automatic connective tissue of apparatus respiratorius OBOL:automatic connective tissue of respiratory system OBOL:automatic portion of connective tissue of apparatus respiratorius OBOL:automatic portion of connective tissue of respiratory system OBOL:automatic respiratory system portion of connective tissue OBOL:automatic respiratory system textus connectivus OBOL:automatic textus connectivus of apparatus respiratorius OBOL:automatic textus connectivus of respiratory system OBOL:automatic A portion of connective tissue that is part of a lower respiratory tract [Automatically generated definition]. EMAPA:37548 MA:0002409 connective tissue of lower respiratory tract lower respiratory tract portion of connective tissue lower respiratory tract textus connectivus portion of connective tissue of lower respiratory tract textus connectivus of lower respiratory tract uberon UBERON:0003580 lower respiratory tract connective tissue A portion of connective tissue that is part of a lower respiratory tract [Automatically generated definition]. OBOL:automatic EMAPA:37548 MA:th connective tissue of lower respiratory tract OBOL:automatic lower respiratory tract portion of connective tissue OBOL:automatic lower respiratory tract textus connectivus OBOL:automatic portion of connective tissue of lower respiratory tract OBOL:automatic textus connectivus of lower respiratory tract OBOL:automatic A portion of connective tissue that is part of a larynx [Automatically generated definition]. EMAPA:35471 MA:0001754 NCIT:C49245 UMLS:C1708651 connective tissue of larynx larynx portion of connective tissue larynx textus connectivus portion of connective tissue of larynx textus connectivus of larynx uberon laryngeal connective tissue UBERON:0003583 larynx connective tissue A portion of connective tissue that is part of a larynx [Automatically generated definition]. OBOL:automatic UMLS:C1708651 ncithesaurus:Laryngeal_Connective_Tissue connective tissue of larynx OBOL:automatic larynx portion of connective tissue OBOL:automatic larynx textus connectivus OBOL:automatic portion of connective tissue of larynx OBOL:automatic textus connectivus of larynx OBOL:automatic laryngeal connective tissue EMAPA:35471 A portion of connective tissue that is part of a dermis [Automatically generated definition]. EMAPA:36509 MA:0000799 connective tissue of dermis dermis portion of connective tissue dermis textus connectivus portion of connective tissue of dermis textus connectivus of dermis uberon UBERON:0003585 dermis connective tissue A portion of connective tissue that is part of a dermis [Automatically generated definition]. OBOL:automatic connective tissue of dermis OBOL:automatic dermis portion of connective tissue OBOL:automatic dermis textus connectivus OBOL:automatic portion of connective tissue of dermis OBOL:automatic textus connectivus of dermis OBOL:automatic A portion of connective tissue that is part of a trunk [Automatically generated definition]. EMAPA:37252 MA:0000513 connective tissue of torso connective tissue of trunk portion of connective tissue of torso portion of connective tissue of trunk textus connectivus of torso textus connectivus of trunk torso connective tissue torso portion of connective tissue torso textus connectivus trunk portion of connective tissue trunk textus connectivus uberon UBERON:0003586 trunk connective tissue A portion of connective tissue that is part of a trunk [Automatically generated definition]. OBOL:automatic EMAPA:37252 MA:th connective tissue of torso OBOL:automatic connective tissue of trunk OBOL:automatic portion of connective tissue of torso OBOL:automatic portion of connective tissue of trunk OBOL:automatic textus connectivus of torso OBOL:automatic textus connectivus of trunk OBOL:automatic torso connective tissue OBOL:automatic torso portion of connective tissue OBOL:automatic torso textus connectivus OBOL:automatic trunk portion of connective tissue OBOL:automatic trunk textus connectivus OBOL:automatic A portion of connective tissue that is part of a thoracic cavity [Automatically generated definition]. EMAPA:37255 MA:0000555 cavity of chest connective tissue cavity of chest portion of connective tissue cavity of chest textus connectivus cavity of thorax connective tissue cavity of thorax portion of connective tissue cavity of thorax textus connectivus chest cavity connective tissue chest cavity portion of connective tissue chest cavity textus connectivus connective tissue of cavity of chest connective tissue of cavity of thorax connective tissue of chest cavity connective tissue of pectoral cavity connective tissue of thoracic cavity pectoral cavity connective tissue pectoral cavity portion of connective tissue pectoral cavity textus connectivus portion of connective tissue of cavity of chest portion of connective tissue of cavity of thorax portion of connective tissue of chest cavity portion of connective tissue of pectoral cavity portion of connective tissue of thoracic cavity textus connectivus of cavity of chest textus connectivus of cavity of thorax textus connectivus of chest cavity textus connectivus of pectoral cavity textus connectivus of thoracic cavity thoracic cavity portion of connective tissue thoracic cavity textus connectivus uberon UBERON:0003593 thoracic cavity connective tissue A portion of connective tissue that is part of a thoracic cavity [Automatically generated definition]. OBOL:automatic EMAPA:37255 MA:th cavity of chest connective tissue OBOL:automatic cavity of chest portion of connective tissue OBOL:automatic cavity of chest textus connectivus OBOL:automatic cavity of thorax connective tissue OBOL:automatic cavity of thorax portion of connective tissue OBOL:automatic cavity of thorax textus connectivus OBOL:automatic chest cavity connective tissue OBOL:automatic chest cavity portion of connective tissue OBOL:automatic chest cavity textus connectivus OBOL:automatic connective tissue of cavity of chest OBOL:automatic connective tissue of cavity of thorax OBOL:automatic connective tissue of chest cavity OBOL:automatic connective tissue of pectoral cavity OBOL:automatic connective tissue of thoracic cavity OBOL:automatic pectoral cavity connective tissue OBOL:automatic pectoral cavity portion of connective tissue OBOL:automatic pectoral cavity textus connectivus OBOL:automatic portion of connective tissue of cavity of chest OBOL:automatic portion of connective tissue of cavity of thorax OBOL:automatic portion of connective tissue of chest cavity OBOL:automatic portion of connective tissue of pectoral cavity OBOL:automatic portion of connective tissue of thoracic cavity OBOL:automatic textus connectivus of cavity of chest OBOL:automatic textus connectivus of cavity of thorax OBOL:automatic textus connectivus of chest cavity OBOL:automatic textus connectivus of pectoral cavity OBOL:automatic textus connectivus of thoracic cavity OBOL:automatic thoracic cavity portion of connective tissue OBOL:automatic thoracic cavity textus connectivus OBOL:automatic A portion of connective tissue that is part of a pelvis [Automatically generated definition]. EMAPA:37257 MA:0000533 connective tissue of pelvis pelvis portion of connective tissue pelvis textus connectivus portion of connective tissue of pelvis textus connectivus of pelvis uberon UBERON:0003594 pelvis connective tissue A portion of connective tissue that is part of a pelvis [Automatically generated definition]. OBOL:automatic EMAPA:37257 MA:th connective tissue of pelvis OBOL:automatic pelvis portion of connective tissue OBOL:automatic pelvis textus connectivus OBOL:automatic portion of connective tissue of pelvis OBOL:automatic textus connectivus of pelvis OBOL:automatic A portion of connective tissue that is part of a tail [Automatically generated definition]. EMAPA:16749 MA:0000697 connective tissue of post-vent region connective tissue of tail portion of connective tissue of post-vent region portion of connective tissue of tail post-vent region connective tissue post-vent region portion of connective tissue post-vent region textus connectivus tail portion of connective tissue tail textus connectivus textus connectivus of post-vent region textus connectivus of tail uberon UBERON:0003599 tail connective tissue A portion of connective tissue that is part of a tail [Automatically generated definition]. OBOL:automatic connective tissue of post-vent region OBOL:automatic connective tissue of tail OBOL:automatic portion of connective tissue of post-vent region OBOL:automatic portion of connective tissue of tail OBOL:automatic post-vent region connective tissue OBOL:automatic post-vent region portion of connective tissue OBOL:automatic post-vent region textus connectivus OBOL:automatic tail portion of connective tissue OBOL:automatic tail textus connectivus OBOL:automatic textus connectivus of post-vent region OBOL:automatic textus connectivus of tail OBOL:automatic A cartilage that is part of a neck [Automatically generated definition]. EMAPA:37251 MA:0000586 cartilage of neck cartilage of neck (volume) neck (volume) cartilage uberon UBERON:0003601 neck cartilage A cartilage that is part of a neck [Automatically generated definition]. OBOL:automatic EMAPA:37251 MA:th cartilage of neck OBOL:automatic cartilage of neck (volume) OBOL:automatic neck (volume) cartilage OBOL:automatic A cartilage that is part of a lower respiratory tract [Automatically generated definition]. EMAPA:37547 MA:0001819 NCIT:C49256 UMLS:C1708759 cartilage of lower respiratory tract uberon UBERON:0003603 lower respiratory tract cartilage A cartilage that is part of a lower respiratory tract [Automatically generated definition]. OBOL:automatic EMAPA:37547 MA:th UMLS:C1708759 ncithesaurus:Lower_Respiratory_Tract_Cartilage cartilage of lower respiratory tract OBOL:automatic A skin gland that is part of a camera-type eye [Automatically generated definition]. EMAPA:37530 MA:0002451 camera-type eye skin gland camera-type eye skin glands camera-type eye skin glands set skin gland of camera-type eye skin gland of vertebrate eye skin glands of camera-type eye skin glands of vertebrate eye skin glands set of camera-type eye skin glands set of vertebrate eye vertebrate eye skin gland vertebrate eye skin glands vertebrate eye skin glands set uberon UBERON:0003605 eye skin gland A skin gland that is part of a camera-type eye [Automatically generated definition]. OBOL:automatic EMAPA:37530 MA:th camera-type eye skin gland OBOL:automatic camera-type eye skin glands OBOL:automatic camera-type eye skin glands set OBOL:automatic skin gland of camera-type eye OBOL:automatic skin gland of vertebrate eye OBOL:automatic skin glands of camera-type eye OBOL:automatic skin glands of vertebrate eye OBOL:automatic skin glands set of camera-type eye OBOL:automatic skin glands set of vertebrate eye OBOL:automatic vertebrate eye skin gland OBOL:automatic vertebrate eye skin glands OBOL:automatic vertebrate eye skin glands set OBOL:automatic The dense connective tissue which contains predominantly elastic fibers and is found in the tunica media of the aorta wall. MA:0002859 adult aorta elastic connective tissue adult aorta elastic tissue adult aorta textus connectivus elasticus aorta elastic connective tissue aorta elastic lamina aorta elastic laminae aorta textus connectivus elasticus dorsal aorta elastic connective tissue dorsal aorta elastic tissue dorsal aorta textus connectivus elasticus elastic connective tissue of adult aorta elastic connective tissue of aorta elastic connective tissue of dorsal aorta elastic connective tissue of trunk of aortic tree elastic tissue of adult aorta elastic tissue of aorta elastic tissue of dorsal aorta elastic tissue of trunk of aortic tree textus connectivus elasticus of adult aorta textus connectivus elasticus of aorta textus connectivus elasticus of dorsal aorta textus connectivus elasticus of trunk of aortic tree trunk of aortic tree elastic connective tissue trunk of aortic tree elastic tissue trunk of aortic tree textus connectivus elasticus uberon UBERON:0003609 aorta elastic tissue The dense connective tissue which contains predominantly elastic fibers and is found in the tunica media of the aorta wall. MP:0009862 adult aorta elastic connective tissue OBOL:automatic adult aorta elastic tissue OBOL:automatic adult aorta textus connectivus elasticus OBOL:automatic aorta elastic connective tissue OBOL:automatic aorta elastic lamina MP:0009862 aorta elastic laminae MP:0009862 aorta textus connectivus elasticus OBOL:automatic dorsal aorta elastic connective tissue OBOL:automatic dorsal aorta elastic tissue OBOL:automatic dorsal aorta textus connectivus elasticus OBOL:automatic elastic connective tissue of adult aorta OBOL:automatic elastic connective tissue of aorta OBOL:automatic elastic connective tissue of dorsal aorta OBOL:automatic elastic connective tissue of trunk of aortic tree OBOL:automatic elastic tissue of adult aorta OBOL:automatic elastic tissue of aorta OBOL:automatic elastic tissue of dorsal aorta OBOL:automatic elastic tissue of trunk of aortic tree OBOL:automatic textus connectivus elasticus of adult aorta OBOL:automatic textus connectivus elasticus of aorta OBOL:automatic textus connectivus elasticus of dorsal aorta OBOL:automatic textus connectivus elasticus of trunk of aortic tree OBOL:automatic trunk of aortic tree elastic connective tissue OBOL:automatic trunk of aortic tree elastic tissue OBOL:automatic trunk of aortic tree textus connectivus elasticus OBOL:automatic The type of heart connective tissue found in the endocardial layer that consists mainly of elastic fibers. MA:0002858 cardiac elastic tissue elastic connective tissue of heart elastic tissue of heart heart elastic connective tissue heart textus connectivus elasticus textus connectivus elasticus of heart uberon UBERON:0003610 heart elastic tissue The type of heart connective tissue found in the endocardial layer that consists mainly of elastic fibers. MP:0009863 cardiac elastic tissue MP:0009863 elastic connective tissue of heart OBOL:automatic elastic tissue of heart OBOL:automatic heart elastic connective tissue OBOL:automatic heart textus connectivus elasticus OBOL:automatic textus connectivus elasticus of heart OBOL:automatic An elastic tissue that is part of a respiratory system [Automatically generated definition]. EMAPA:37579 MA:0001820 apparatus respiratorius elastic connective tissue apparatus respiratorius elastic tissue apparatus respiratorius textus connectivus elasticus elastic connective tissue of apparatus respiratorius elastic connective tissue of respiratory system elastic tissue of apparatus respiratorius elastic tissue of respiratory system respiratory system elastic connective tissue respiratory system textus connectivus elasticus textus connectivus elasticus of apparatus respiratorius textus connectivus elasticus of respiratory system uberon UBERON:0003611 respiratory system elastic tissue An elastic tissue that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37579 MA:th apparatus respiratorius elastic connective tissue OBOL:automatic apparatus respiratorius elastic tissue OBOL:automatic apparatus respiratorius textus connectivus elasticus OBOL:automatic elastic connective tissue of apparatus respiratorius OBOL:automatic elastic connective tissue of respiratory system OBOL:automatic elastic tissue of apparatus respiratorius OBOL:automatic elastic tissue of respiratory system OBOL:automatic respiratory system elastic connective tissue OBOL:automatic respiratory system textus connectivus elasticus OBOL:automatic textus connectivus elasticus of apparatus respiratorius OBOL:automatic textus connectivus elasticus of respiratory system OBOL:automatic An elastic tissue that is part of a circulatory system [Automatically generated definition]. MA:0002857 cardiovascular system elastic connective tissue cardiovascular system textus connectivus elasticus circulatory system elastic connective tissue circulatory system elastic tissue circulatory system textus connectivus elasticus elastic connective tissue of cardiovascular system elastic connective tissue of circulatory system elastic tissue of cardiovascular system elastic tissue of circulatory system textus connectivus elasticus of cardiovascular system textus connectivus elasticus of circulatory system uberon UBERON:0003613 cardiovascular system elastic tissue An elastic tissue that is part of a circulatory system [Automatically generated definition]. OBOL:automatic cardiovascular system elastic connective tissue OBOL:automatic cardiovascular system textus connectivus elasticus OBOL:automatic circulatory system elastic connective tissue OBOL:automatic circulatory system elastic tissue OBOL:automatic circulatory system textus connectivus elasticus OBOL:automatic elastic connective tissue of cardiovascular system OBOL:automatic elastic connective tissue of circulatory system OBOL:automatic elastic tissue of cardiovascular system OBOL:automatic elastic tissue of circulatory system OBOL:automatic textus connectivus elasticus of cardiovascular system OBOL:automatic textus connectivus elasticus of circulatory system OBOL:automatic Elastic tissue layer that lines a blood vessel layer. elastic lamina elastic laminae EMAPA:36300 MA:0002856 blood vessel elastic connective tissue blood vessel textus connectivus elasticus elastic connective tissue of blood vessel elastic tissue of blood vessel textus connectivus elasticus of blood vessel vascular elastic lamina vascular elastic laminae vascular elastic tissue uberon UBERON:0003614 blood vessel elastic tissue Elastic tissue layer that lines a blood vessel layer. http://orcid.org/0000-0002-6601-2165 https://sourceforge.net/p/obo/mammalian-phenotype-requests/2026/ elastic lamina MP:0006083 elastic laminae MP:0006083 blood vessel elastic connective tissue OBOL:automatic blood vessel textus connectivus elasticus OBOL:automatic elastic connective tissue of blood vessel OBOL:automatic elastic tissue of blood vessel OBOL:automatic textus connectivus elasticus of blood vessel OBOL:automatic vascular elastic lamina http://orcid.org/0000-0002-6601-2165 vascular elastic laminae http://orcid.org/0000-0002-6601-2165 vascular elastic tissue MP:0006083 Elastic tissue that is part of a lung [Automatically generated definition]. MA:0002860 elastic connective tissue of lung elastic tissue of lung lung elastic connective tissue lung textus connectivus elasticus textus connectivus elasticus of lung pulmonary elastic fiber uberon UBERON:0003615 lung elastic tissue Elastic tissue that is part of a lung [Automatically generated definition]. OBOL:automatic elastic connective tissue of lung OBOL:automatic elastic tissue of lung OBOL:automatic lung elastic connective tissue OBOL:automatic lung textus connectivus elasticus OBOL:automatic textus connectivus elasticus of lung OBOL:automatic pulmonary elastic fiber http://orcid.org/0000-0002-6601-2165 The middle layer of the aorta wall, containing the smooth muscle layer and elastic fibers. EMAPA:35138 FMA:74433 MA:0002903 SCTID:48467007 adult aorta tunica media dorsal aorta tunica media trunk of aortic tree tunica media tunica media of adult aorta tunica media of aorta tunica media of dorsal aorta tunica media of trunk of aortic tree uberon UBERON:0003618 aorta tunica media The middle layer of the aorta wall, containing the smooth muscle layer and elastic fibers. MP:0009873 adult aorta tunica media OBOL:automatic dorsal aorta tunica media OBOL:automatic trunk of aortic tree tunica media OBOL:automatic tunica media of adult aorta OBOL:automatic tunica media of aorta OBOL:automatic tunica media of dorsal aorta OBOL:automatic tunica media of trunk of aortic tree OBOL:automatic The innermost layer of the aorta, containing the endothelium and an inner elastic membrane. BTO:0005553 EMAPA:35137 FMA:74419 MA:0002904 SCTID:362031007 adult aorta tunica intima dorsal aorta tunica intima trunk of aortic tree tunica intima tunica intima of adult aorta tunica intima of aorta tunica intima of dorsal aorta tunica intima of trunk of aortic tree uberon UBERON:0003619 aorta tunica intima The innermost layer of the aorta, containing the endothelium and an inner elastic membrane. MP:0009872 adult aorta tunica intima OBOL:automatic dorsal aorta tunica intima OBOL:automatic trunk of aortic tree tunica intima OBOL:automatic tunica intima of adult aorta OBOL:automatic tunica intima of aorta OBOL:automatic tunica intima of dorsal aorta OBOL:automatic tunica intima of trunk of aortic tree OBOL:automatic An arterial blood vessel that is part of a respiratory system [Automatically generated definition]. EMAPA:37565 MA:0001800 uberon UBERON:0003643 respiratory system arterial blood vessel An arterial blood vessel that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37565 MA:th A muscle organ that attaches to a tail vertebra [Automatically generated definition]. the BTO class may possibly refer to an invertebrate structure AAO:0000081 BTO:0001905 EMAPA:37759 MA:0000699 SCTID:113230005 caudal muscle muscle organ of post-vent region muscle organ of tail post-vent region muscle organ tail muscle tail muscle organ uberon UBERON:0003665 post-anal tail muscle A muscle organ that attaches to a tail vertebra [Automatically generated definition]. OBOL:automatic the BTO class may possibly refer to an invertebrate structure BTO EMAPA:37759 MA:th muscle organ of post-vent region OBOL:automatic muscle organ of tail OBOL:automatic post-vent region muscle organ OBOL:automatic tail muscle MA:0000699 tail muscle organ OBOL:automatic The part of the ventral body cavity that is within the abdomen proper (excluding the pelvic cavity). in FMA this contains the pelvic cavity, but this is inconsistent with the concept of abdominopelvic cavity EFO:0000213 EMAPA:36505 FMA:12266 GAID:17 MA:0003057 MESH:A01.047.025 NCIT:C12664 OpenCyc:Mx4rvZR1TJwpEbGdrcN5Y29ycA SCTID:361294009 UMLS:C0230168 Wikipedia:Abdominal_cavity galen:AbdominalCavity cavity of abdominal compartment cavity of compartment of abdomen space of abdominal compartment uberon cavitas abdominis UBERON:0003684 abdominal cavity http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg The part of the ventral body cavity that is within the abdomen proper (excluding the pelvic cavity). UBERON:cjm in FMA this contains the pelvic cavity, but this is inconsistent with the concept of abdominopelvic cavity FMA UMLS:C0230168 ncithesaurus:Abdominal_Cavity cavity of abdominal compartment FMA:12266 cavity of compartment of abdomen FMA:12266 space of abdominal compartment FMA:12266 cavitas abdominis GAID:17 cavitas abdominis Wikipedia:Abdominal_cavity In anatomy, in the occipital bone, the foramen magnum is one of the several oval or circular apertures in the base of the skull, through which the medulla oblongata (an extension of the spinal cord) enters and exits the skull vault. Apart from the transmission of the medulla oblongata and its membranes, the foramen magnum transmits the Spinal Accessory nerve, vertebral arteries, the anterior and posterior spinal arteries, the membrana tectoria and alar ligaments. [WP,unvetted]. Foramen in the occipital region of neurocranium to allow passage of spinal cord.[TAO] AAO:0010826 EMAPA:37868 FMA:75306 GAID:228 MESH:D005539 NCIT:C12495 OpenCyc:Mx4rwOm-FpwpEbGdrcN5Y29ycA SCTID:244679008 TAO:0002045 UMLS:C0016519 Wikipedia:Foramen_magnum ZFA:0005387 uberon UBERON:0003687 Design pattern notes: check whether this fits the foramen design pattern foramen magnum http://upload.wikimedia.org/wikipedia/commons/3/39/Gray130.png In anatomy, in the occipital bone, the foramen magnum is one of the several oval or circular apertures in the base of the skull, through which the medulla oblongata (an extension of the spinal cord) enters and exits the skull vault. Apart from the transmission of the medulla oblongata and its membranes, the foramen magnum transmits the Spinal Accessory nerve, vertebral arteries, the anterior and posterior spinal arteries, the membrana tectoria and alar ligaments. [WP,unvetted]. Wikipedia:Foramen_magnum Foramen in the occipital region of neurocranium to allow passage of spinal cord.[TAO] 2012-08-14 TAO:0002045 TAO TAO:wd EMAPA:37868 MA:th UMLS:C0016519 ncithesaurus:Foramen_Magnum The tissues that surround the organs that are present within the abdominal cavity. The abdominal wall tissue is composed of layers of fat, parietal peritoneum, fascia, and muscles. EMAPA:37064 FMA:10429 FMA:259054 GAID:26 MESH:A01.047.050 NCIT:C77608 SCTID:181613000 UMLS:C0836916 Wikipedia:Abdominal_wall paries abdominalis wall of abdomen wall of abdomen proper uberon abdominal wall proper layers of the abdominal wall paries abdominalis UBERON:0003697 abdominal wall http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg The tissues that surround the organs that are present within the abdominal cavity. The abdominal wall tissue is composed of layers of fat, parietal peritoneum, fascia, and muscles. ncithesaurus:Abdominal_Wall EMAPA:37064 MA:th UMLS:C0836916 ncithesaurus:Abdominal_Wall paries abdominalis Wikipedia:Abdominal_wall wall of abdomen FMA:259054 wall of abdomen proper FMA:10429 abdominal wall proper FMA:10429 layers of the abdominal wall Wikipedia:Abdominal_wall paries abdominalis Wikipedia:Abdominal_wall A circle of arteries that supply blood to the brain. The Circle of Willis comprises the following arteries: Anterior cerebral artery (left and right); Anterior communicating artery; Internal carotid artery (left and right); Posterior cerebral artery (left and right); Posterior communicating artery (left and right).The basilar artery and middle cerebral arteries, supplying the brain, are also considered part of the circle In zebrafish, the circle of vessels comprised of the basal communicating artery (BCA) and posterior communicating segments (PCS) superficially resemble but are not homologous to the human circle of Willis arterial circle EHDAA2:0000252 EHDAA:9758 EMAPA:37829 FMA:50454 GAID:486 MESH:D002941 OpenCyc:Mx4rwSrCwJwpEbGdrcN5Y29ycA SCTID:362047009 Wikipedia:Circle_of_Willis http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1468 arterial circle of Willis cerebral arterial circle uberon Willis circle circulus arteriosus cerebri UBERON:0003709 circle of Willis http://upload.wikimedia.org/wikipedia/commons/2/2e/Circle_of_Willis_en.svg FMA-modified FMA-modified A circle of arteries that supply blood to the brain. The Circle of Willis comprises the following arteries: Anterior cerebral artery (left and right); Anterior communicating artery; Internal carotid artery (left and right); Posterior cerebral artery (left and right); Posterior communicating artery (left and right).The basilar artery and middle cerebral arteries, supplying the brain, are also considered part of the circle Wikipedia:Circle_of_Willis In zebrafish, the circle of vessels comprised of the basal communicating artery (BCA) and posterior communicating segments (PCS) superficially resemble but are not homologous to the human circle of Willis http://zfish.nichd.nih.gov/zfatlas/Intro%20Page/comparative.html arterial circle Wikipedia:Circle_of_Willis EMAPA:37829 MA:th cerebral arterial circle GAID:486 Willis circle GAID:486 circulus arteriosus cerebri Wikipedia:Circle_of_Willis A vein arising from the splenic trabecular vein in the hilum of the spleen that drains into the portal vein. EMAPA:37226 FMA:14331 GAID:541 MA:0002164 MESH:D013162 NCIT:C33608 OpenCyc:Mx4rwCt0eZwpEbGdrcN5Y29ycA SCTID:278029005 UMLS:C0038001 Wikipedia:Splenic_vein galen:SplenicVein vena splenica uberon lienal vein vena lienalis UBERON:0003713 splenic vein http://upload.wikimedia.org/wikipedia/commons/5/5b/Gray1189.png http://upload.wikimedia.org/wikipedia/commons/e/e4/Bilebladder.png A vein arising from the splenic trabecular vein in the hilum of the spleen that drains into the portal vein. ncithesaurus:Splenic_Vein EMAPA:37226 MA:th UMLS:C0038001 ncithesaurus:Splenic_Vein vena splenica FMA:14331 FMA:TA lienal vein MA:0002164 Wikipedia:Splenic_vein vena lienalis Wikipedia:Splenic_vein Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature. One of the four types of tissue in traditional classifications. Cells forming the brain, spinal cord and peripheral nervous system.[AAO] FMA definition includes vasculature AAO:0000325 AEO:0000123 EHDAA2:0003123 FMA:9642 GAID:609 MESH:D009417 NCIT:C13052 OpenCyc:Mx4rVmfYCsQ_QdeM_bFAeS8NRQ SCTID:91728009 UMLS:C0027757 nerve tissue nervous tissue portion of neural tissue uberon UBERON:0003714 neural tissue Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature. FMA:9642 One of the four types of tissue in traditional classifications. Cells forming the brain, spinal cord and peripheral nervous system.[AAO] 2012-06-20 AAO:0000325 AAO AAO:LAP FMA definition includes vasculature FMA UMLS:C0027757 ncithesaurus:Nervous_Tissue nerve tissue FMA:9642 nervous tissue FMA:9642 portion of neural tissue FMA:9642 The major nerves supplying sympathetic innervation to the abdomen, including the greater, lesser, and lowest (or smallest) splanchnic nerves that are formed by preganglionic fibers from the spinal cord which pass through the paravertebral ganglia and then to the celiac ganglia and plexuses and the lumbar splanchnic nerves carry fibers which pass through the lumbar paravertebral ganglia to the mesenteric and hypogastric ganglia. All carry sympathetic fibers except for the pelvic splanchnic nerves, which carry parasympathetic fibers BAMS:spn EMAPA:37959 FMA:5883 GAID:800 MESH:D013153 SCTID:264198001 Wikipedia:Splanchnic_nerves uberon splanchnic nerves visceral nerve UBERON:0003715 splanchnic nerve The major nerves supplying sympathetic innervation to the abdomen, including the greater, lesser, and lowest (or smallest) splanchnic nerves that are formed by preganglionic fibers from the spinal cord which pass through the paravertebral ganglia and then to the celiac ganglia and plexuses and the lumbar splanchnic nerves carry fibers which pass through the lumbar paravertebral ganglia to the mesenteric and hypogastric ganglia. MP:0008318 EMAPA:37959 MA:th splanchnic nerves BAMS:spn visceral nerve Wikipedia:Splanchnic_nerves A branch of the vagus nerve that supplies motor function and sensation to the larynx (voice box). It travels within the endoneurium. It is the nerve of the 6th Branchial Arch. Branch of the vagus nerve that separates from the vagus well postcranially, then continues anteriorly to innervate the larynx[AAO:0010754]. recurrent nerve AAO:0010754 FMA:6246 GAID:804 MESH:D012009 SCTID:24227007 VHOG:0001347 Wikipedia:Recurrent_laryngeal_nerve nervus laryngeus recurrens recurrent laryngeal nerve from vagus nerve vagus X nerve recurrent laryngeal branch uberon inferior laryngeal nerve ramus recurrens UBERON:0003716 recurrent laryngeal nerve Wikipedia A branch of the vagus nerve that supplies motor function and sensation to the larynx (voice box). It travels within the endoneurium. It is the nerve of the 6th Branchial Arch. Wikipedia:Recurrent_laryngeal_nerve Branch of the vagus nerve that separates from the vagus well postcranially, then continues anteriorly to innervate the larynx[AAO:0010754]. AAO:0010754 recurrent nerve Wikipedia:Recurrent_laryngeal_nerve nervus laryngeus recurrens Wikipedia:Recurrent_laryngeal_nerve vagus X nerve recurrent laryngeal branch VHOG:0001347 inferior laryngeal nerve GAID:804 ramus recurrens AAO:0010754 The twelve spinal nerves on each side of the thorax. They include eleven INTERCOSTAL NERVES and one subcostal nerve. Both sensory and motor, they supply the muscles and skin of the thoracic and abdominal walls. FMA:5860 GAID:857 MESH:D013900 OpenCyc:Mx4rwSJp_ZwpEbGdrcN5Y29ycA SCTID:360498003 Wikipedia:Thoracic_nerves http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1725 nervus thoracis thoracic spinal nerve uberon nervi thoracici pectoral nerve UBERON:0003726 thoracic nerve The twelve spinal nerves on each side of the thorax. They include eleven INTERCOSTAL NERVES and one subcostal nerve. Both sensory and motor, they supply the muscles and skin of the thoracic and abdominal walls. MESH:A08.800.800.720.800 nervus thoracis FMA:5860 FMA:TA thoracic spinal nerve FMA:5860 nervi thoracici Wikipedia:Thoracic_nerves pectoral nerve GAID:857 The intercostal nerves are the anterior divisions (rami anteriores; ventral divisions) of the thoracic spinal nerves from T1 to T11. Each nerve is connected with the adjoining ganglion of the sympathetic trunk by a gray and a white ramus communicans. The intercostal nerves are distributed chiefly to the thoracic pleura and abdominal peritoneum and differ from the anterior divisions of the other spinal nerves in that each pursues an independent course without plexus formation. The first two nerves supply fibers to the upper limb in addition to their thoracic branches; the next four are limited in their distribution to the parietes of the thorax; the lower five supply the parietes of the thorax and abdomen. The 7th intercostal nerve terminates at the xyphoid process, at the lower end of the sternum. The 10th intercostal nerve terminates at the umbilicus. The twelfth thoracic is distributed to the abdominal wall and groin. [WP,unvetted]. EMAPA:18227 FMA:6028 GAID:858 MESH:D007367 NCIT:C32825 SCTID:279568001 UMLS:C1285089 Wikipedia:Intercostal_nerves anterior ramus of thoracic nerve anterior ramus of thoracic spinal nerve ramus anterior, nervus thoracicus thoracic anterior ramus ventral ramus of thoracic spinal nerve uberon nervi intercostales UBERON:0003727 intercostal nerve http://upload.wikimedia.org/wikipedia/commons/b/b1/Gray819.png The intercostal nerves are the anterior divisions (rami anteriores; ventral divisions) of the thoracic spinal nerves from T1 to T11. Each nerve is connected with the adjoining ganglion of the sympathetic trunk by a gray and a white ramus communicans. The intercostal nerves are distributed chiefly to the thoracic pleura and abdominal peritoneum and differ from the anterior divisions of the other spinal nerves in that each pursues an independent course without plexus formation. The first two nerves supply fibers to the upper limb in addition to their thoracic branches; the next four are limited in their distribution to the parietes of the thorax; the lower five supply the parietes of the thorax and abdomen. The 7th intercostal nerve terminates at the xyphoid process, at the lower end of the sternum. The 10th intercostal nerve terminates at the umbilicus. The twelfth thoracic is distributed to the abdominal wall and groin. [WP,unvetted]. Wikipedia:Intercostal_nerves UMLS:C1285089 ncithesaurus:Intercostal_Nerve anterior ramus of thoracic nerve FMA:6028 anterior ramus of thoracic spinal nerve FMA:6028 ramus anterior, nervus thoracicus FMA:6028 thoracic anterior ramus FMA:6028 ventral ramus of thoracic spinal nerve FMA:6028 nervi intercostales Wikipedia:Intercostal_nerves A mucous membrane that lines the mouth. this is defined as any mucous membrane of the mouth - including palate, lips, uvula, etc. ncit split mouth/oral mucosa into lip and buccal. In future we may split into masticatory/keratinized (gingiva + hard palate) vs lining/non-keratinized (lips, cheeks, floor of mouth, soft palate). FMA distinguishes between mucosa of mouth and region of mouth (the latter including the buccal mucosa) the mucous membrane epithelium of the mouth. It can be divided into three categories: masticatory, lining, and specialized[Wikipedia:Oral_mucosa]. BTO:0002860 CALOHA:TS-0716 EMAPA:26937 FMA:59660 GAID:951 MA:0002794 MESH:D009061 NCIT:C77637 UMLS:C0026639 Wikipedia:Oral_mucosa mouth mucosa mouth mucous membrane mouth organ mucosa mucosa of mouth mucous membrane of mouth oral mucous membrane oral part of viscerocranial mucosa tunica mucosa oris uberon buccal mucosa mucosal lining of mouth oral mucosa tunica mucosa oris UBERON:0003729 mouth mucosa A mucous membrane that lines the mouth. http://orcid.org/0000-0002-6601-2165 the mucous membrane epithelium of the mouth. It can be divided into three categories: masticatory, lining, and specialized[Wikipedia:Oral_mucosa]. Wikipedia:Oral_mucosa UMLS:C0026639 ncithesaurus:Oral_Mucosa mouth mucosa FMA:59660 mouth mucous membrane OBOL:accepted mouth organ mucosa OBOL:accepted mucosa of mouth OBOL:accepted mucous membrane of mouth FMA:59660 oral part of viscerocranial mucosa FMA:59660 tunica mucosa oris FMA:59660 FMA:TA buccal mucosa GAID:951 mucosal lining of mouth MA:0002794 oral mucosa GAID:951 tunica mucosa oris Wikipedia:Oral_mucosa A nerve that is part of a thorax [Automatically generated definition]. EMAPA:37265 MA:0000562 MESH:D013900 SCTID:359876006 nerve of thorax thoracic segment nerve thorax nerve uberon upper body nerve UBERON:0003824 nerve of thoracic segment A nerve that is part of a thorax [Automatically generated definition]. OBOL:automatic EMAPA:37265 MA:th nerve of thorax OBOL:automatic thoracic segment nerve MA:0000562 thorax nerve OBOL:automatic upper body nerve MA:0000562 A nerve that is part of an abdominal segment of trunk [Automatically generated definition]. EMAPA:37061 MA:0000528 abdominal segment nerve uberon UBERON:0003825 nerve of abdominal segment A nerve that is part of an abdominal segment of trunk [Automatically generated definition]. OBOL:automatic EMAPA:37061 MA:th abdominal segment nerve MA:0000528 A bone that is part of a thorax [Automatically generated definition]. EMAPA:37247 MA:0000559 SCTID:426649006 bone of thorax bone organ of thorax thorax bone thorax bone organ uberon upper body bone UBERON:0003827 thoracic segment bone A bone that is part of a thorax [Automatically generated definition]. OBOL:automatic EMAPA:37247 MA:th bone of thorax OBOL:automatic bone organ of thorax OBOL:automatic thorax bone OBOL:automatic thorax bone organ OBOL:automatic upper body bone MA:0000559 A bone that is part of an abdominal segment of trunk [Automatically generated definition]. EMAPA:37058 MA:0000525 abdominal segment of trunk bone abdominal segment of trunk bone organ bone of abdominal segment of trunk bone organ of abdominal segment of trunk uberon UBERON:0003828 abdominal segment bone A bone that is part of an abdominal segment of trunk [Automatically generated definition]. OBOL:automatic EMAPA:37058 MA:th abdominal segment of trunk bone OBOL:automatic abdominal segment of trunk bone organ OBOL:automatic bone of abdominal segment of trunk OBOL:automatic bone organ of abdominal segment of trunk OBOL:automatic Any muscle organ that is part of a thorax [Automatically generated definition]. MA:0000561 muscle organ of thorax thorax muscle organ uberon upper body muscle UBERON:0003830 thoracic segment muscle prolog Any muscle organ that is part of a thorax [Automatically generated definition]. OBOL:automatic muscle organ of thorax OBOL:automatic thorax muscle organ OBOL:automatic upper body muscle MA:0000561 Any muscle organ that is part of a respiratory system [Automatically generated definition]. EMAPA:35733 MA:0001828 apparatus respiratorius muscle organ muscle organ of apparatus respiratorius muscle organ of respiratory system respiratory system muscle organ uberon UBERON:0003831 respiratory system muscle Any muscle organ that is part of a respiratory system [Automatically generated definition]. OBOL:automatic apparatus respiratorius muscle organ OBOL:automatic muscle organ of apparatus respiratorius OBOL:automatic muscle organ of respiratory system OBOL:automatic respiratory system muscle organ OBOL:automatic Any muscle organ that is part of a esophagus [Automatically generated definition]. merge muscle and muscle layer? EMAPA:26983 MA:0002682 SCTID:360961009 esophageal muscle esophagus muscle organ gullet muscle organ muscle organ of esophagus muscle organ of gullet muscle organ of oesophagus oesophagus muscle organ uberon UBERON:0003832 esophagus muscle MA Any muscle organ that is part of a esophagus [Automatically generated definition]. OBOL:automatic esophagus muscle organ OBOL:automatic gullet muscle organ OBOL:automatic muscle organ of esophagus OBOL:automatic muscle organ of gullet OBOL:automatic muscle organ of oesophagus OBOL:automatic oesophagus muscle organ OBOL:automatic A muscle organ that is part of an abdominal segment of trunk [Automatically generated definition]. EMAPA:37060 MA:0000527 abdominal segment of trunk muscle organ muscle organ of abdominal segment of trunk uberon UBERON:0003833 abdominal segment muscle A muscle organ that is part of an abdominal segment of trunk [Automatically generated definition]. OBOL:automatic EMAPA:37060 MA:th abdominal segment of trunk muscle organ OBOL:automatic muscle organ of abdominal segment of trunk OBOL:automatic A blood vessel that is part of a thorax [Automatically generated definition]. EMAPA:37238 MA:0000558 blood vessel of thorax thorax blood vessel uberon upper body blood vessel UBERON:0003834 thoracic segment blood vessel A blood vessel that is part of a thorax [Automatically generated definition]. OBOL:automatic EMAPA:37238 MA:th blood vessel of thorax OBOL:automatic thorax blood vessel OBOL:automatic upper body blood vessel MA:0000558 A blood vessel that is part of an abdominal segment of trunk [Automatically generated definition]. EMAPA:37057 MA:0000524 abdominal segment of trunk blood vessel blood vessel of abdominal segment of trunk uberon UBERON:0003835 abdominal segment blood vessel A blood vessel that is part of an abdominal segment of trunk [Automatically generated definition]. OBOL:automatic EMAPA:37057 MA:th abdominal segment of trunk blood vessel OBOL:automatic blood vessel of abdominal segment of trunk OBOL:automatic A skin of body that is part of an abdominal segment of trunk [Automatically generated definition]. EMAPA:37063 FMA:264898 MA:0000530 abdominal segment of trunk skin skin of abdominal segment of trunk uberon UBERON:0003836 abdominal segment skin A skin of body that is part of an abdominal segment of trunk [Automatically generated definition]. OBOL:automatic EMAPA:37063 MA:th abdominal segment of trunk skin OBOL:automatic skin of abdominal segment of trunk OBOL:automatic A portion of connective tissue that is part of a thorax [Automatically generated definition]. EMAPA:37253 MA:0000560 connective tissue of thorax portion of connective tissue of thorax textus connectivus of thorax thorax connective tissue thorax portion of connective tissue thorax textus connectivus uberon upper body connective tissue UBERON:0003837 thoracic segment connective tissue A portion of connective tissue that is part of a thorax [Automatically generated definition]. OBOL:automatic EMAPA:37253 MA:th connective tissue of thorax OBOL:automatic portion of connective tissue of thorax OBOL:automatic textus connectivus of thorax OBOL:automatic thorax connective tissue OBOL:automatic thorax portion of connective tissue OBOL:automatic thorax textus connectivus OBOL:automatic upper body connective tissue MA:0000560 A portion of connective tissue that is part of an abdominal segment of trunk [Automatically generated definition]. EMAPA:37059 MA:0000526 abdominal segment of trunk connective tissue abdominal segment of trunk portion of connective tissue abdominal segment of trunk textus connectivus connective tissue of abdominal segment of trunk portion of connective tissue of abdominal segment of trunk textus connectivus of abdominal segment of trunk uberon UBERON:0003838 abdominal segment connective tissue A portion of connective tissue that is part of an abdominal segment of trunk [Automatically generated definition]. OBOL:automatic EMAPA:37059 MA:th abdominal segment of trunk connective tissue OBOL:automatic abdominal segment of trunk portion of connective tissue OBOL:automatic abdominal segment of trunk textus connectivus OBOL:automatic connective tissue of abdominal segment of trunk OBOL:automatic portion of connective tissue of abdominal segment of trunk OBOL:automatic textus connectivus of abdominal segment of trunk OBOL:automatic An anatomical space that surrounded_by a neural tube. (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] UBERON:0005713 AAO:0011073 EHDAA2:0001269 EHDAA:2889 EHDAA:914 EMAPA:16167 VHOG:0001119 XAO:0000252 cavity of neural tube lumen of neural tube neural tube neural lumen prosencoel uberon central lumen neural lumen neurocoel UBERON:0003842 neural tube lumen An anatomical space that surrounded_by a neural tube. OBOL:automatic (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] 2012-09-17 VHOG:0001119 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 http://bgee.unil.ch/ cavity of neural tube https://orcid.org/0000-0002-6601-2165 lumen of neural tube https://orcid.org/0000-0002-6601-2165 neural tube neural lumen EHDAA2:0001269 neural lumen EHDAA:2889 neurocoel VHOG:0001119 In medicine, gonadal vein refers to the blood vessel that carrying blood away from the gonad (testis, ovary) toward the heart. Females : ovarian vein Males : testicular vein [WP,unvetted]. EHDAA2:0000719 EHDAA:8703 OpenCyc:Mx4rvlWYh5wpEbGdrcN5Y29ycA SCTID:278192008 VHOG:0001340 Wikipedia:Gonadal_vein gonad vein gonada vein vein of gonad vein of gonada uberon UBERON:0003848 gonadal vein http://upload.wikimedia.org/wikipedia/commons/d/da/Gray1120.png In medicine, gonadal vein refers to the blood vessel that carrying blood away from the gonad (testis, ovary) toward the heart. Females : ovarian vein Males : testicular vein [WP,unvetted]. Wikipedia:Gonadal_vein gonad vein OBOL:automatic gonada vein OBOL:automatic vein of gonad OBOL:automatic vein of gonada OBOL:automatic A neural crest that has_potential_to_developmentally_contribute_to a midbrain. We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] EFO:0003591 EHDAA2:0001101 EHDAA:360 TAO:0000935 VHOG:0000796 ZFA:0000935 mesencephalic neural crest neural crest midbrain uberon UBERON:0003849 mesencephalic neural crest ZFA A neural crest that has_potential_to_developmentally_contribute_to a midbrain. OBOL:automatic We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] 2012-09-17 VHOG:0000796 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 http://bgee.unil.ch/ mesencephalic neural crest ZFA:0000935 neural crest midbrain ZFA:0000935 A neural crest that has_potential_to_developmentally_contribute_to a telencephalon. Cranial neural crest that is part of the telencephalon.[TAO] We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] EFO:0003574 RETIRED_EHDAA2:0001991 TAO:0000812 VHOG:0000799 ZFA:0000812 neural crest telencephalon uberon UBERON:0003850 telencephalon neural crest A neural crest that has_potential_to_developmentally_contribute_to a telencephalon. OBOL:automatic Cranial neural crest that is part of the telencephalon.[TAO] 2012-08-14 TAO:0000812 TAO ZFIN:curator We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] 2012-09-17 VHOG:0000799 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 http://bgee.unil.ch/ neural crest telencephalon ZFA:0000812 A neural crest that has_potential_to_developmentally_contribute_to a diencephalon. We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] EFO:0003573 EHDAA2:0000603 EMAPA:16518 TAO:0000811 VHOG:0000798 ZFA:0000811 diencephalic neural crest future diencephalon neural crest neural crest diencephalon neural crest of future diencephalon uberon UBERON:0003851 diencephalon neural crest A neural crest that has_potential_to_developmentally_contribute_to a diencephalon. OBOL:automatic We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] 2012-09-17 VHOG:0000798 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 http://bgee.unil.ch/ diencephalic neural crest ZFA:0000811 future diencephalon neural crest EHDAA2:0000603 neural crest diencephalon ZFA:0000811 neural crest of future diencephalon EMAPA:16518 A neural crest that has_potential_to_developmentally_contribute_to a hindbrain. Cranial neural crest that is part of the hindbrain.[TAO] We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] EHDAA2:0001628 EHDAA:362 EMAPA:35747 TAO:0007063 VHOG:0001210 ZFA:0007063 neural crest hindbrain rhombencephalic neural crest uberon rhombomere neural crest UBERON:0003852 rhombencephalon neural crest ZFA A neural crest that has_potential_to_developmentally_contribute_to a hindbrain. OBOL:automatic Cranial neural crest that is part of the hindbrain.[TAO] 2012-08-14 TAO:0007063 TAO ZFIN:curator We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] 2012-09-17 VHOG:0001210 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 http://bgee.unil.ch/ neural crest hindbrain ZFA:0007063 rhombencephalic neural crest ZFA:0007063 rhombomere neural crest EMAPA:35747 A neural crest that has_potential_to_developmentally_contribute_to a spinal cord. We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)[well established][VHOG] EHDAA:696 EMAPA:16163 EMAPA:16881 VHOG:0001006 neural crest spinal cord uberon spinal neural crest UBERON:0003853 spinal cord neural crest A neural crest that has_potential_to_developmentally_contribute_to a spinal cord. OBOL:automatic We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)[well established][VHOG] 2012-09-17 VHOG:0001006 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 http://bgee.unil.ch/ neural crest spinal cord VHOG:0001006 spinal neural crest VHOG:0001006 A neural plate that develops_from a future spinal cord. Neural plate that is part of the spinal cord. [Bgee_curator][VHOG] (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...)[well established][VHOG] FMA:312957 TAO:0007021 VHOG:0000439 ZFA:0007021 neural plate of spinal cord uberon UBERON:0003854 spinal cord neural plate ZFA A neural plate that develops_from a future spinal cord. OBOL:automatic Neural plate that is part of the spinal cord. [Bgee_curator][VHOG] 2012-09-17 VHOG:0000439 VHOG http://bgee.unil.ch/ (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...)[well established][VHOG] 2012-09-17 VHOG:0000439 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 http://bgee.unil.ch/ neural plate of spinal cord OBOL:automatic Mesenchyme that is part of a developing gonad [Automatically generated definition]. EHDAA:5012 EMAPA:16858 EMAPA:17385 VHOG:0001090 gonada mesenchyme mesenchyme of gonad mesenchyme of gonada uberon UBERON:0003855 gonad mesenchyme Mesenchyme that is part of a developing gonad [Automatically generated definition]. OBOL:automatic gonada mesenchyme OBOL:automatic mesenchyme of gonad OBOL:automatic mesenchyme of gonada OBOL:automatic A presumptive structure that has the potential to develop into a ganglion. uberon UBERON:0003869 presumptive ganglion A presumptive structure that has the potential to develop into a ganglion. OBOL:automatic An anatomical cavity that has the potential to develop into a coelemic cavity lumen. uberon body cavity precursor UBERON:0003886 future coelemic cavity lumen An anatomical cavity that has the potential to develop into a coelemic cavity lumen. OBOL:automatic The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults (...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG] EHDAA:251 EMAPA:16088 NCIT:C34195 UMLS:C1512940 VHOG:0000316 Wikipedia:Intraembryonic_coelom somatic coelom uberon UBERON:0003887 intraembryonic coelom Wikipedia The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom MGI:anna MP:0012187 (...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG] 2012-09-17 VHOG:0000316 VHOG ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.166 http://bgee.unil.ch/ UMLS:C1512940 ncithesaurus:Intraembryonic_Coelom somatic coelom Wikipedia:Intraembryonic_coelom Connective, non-functional supportive framework of a biological cell, tissue, or organ. Contrast with parenchyma. stromal FMA:81494 NCIT:C67387 UMLS:C0927195 uberon stromal connective tissue UBERON:0003891 stroma Connective, non-functional supportive framework of a biological cell, tissue, or organ. Contrast with parenchyma. http://orcid.org/0000-0002-6601-2165 UMLS:C0927195 ncithesaurus:Stroma_Connective_Tissue One of the skeletal muscles of the head and neck, spine, and ribs. EHDAA:5982 EMAPA:18167 MA:0003153 RETIRED_EHDAA2:0000160 TAO:0001954 uberon UBERON:0003897 axial muscle One of the skeletal muscles of the head and neck, spine, and ribs. HP:0003327 A portion of skeletal muscle tissue in the trunk. SCTID:244848007 skeletal muscle of torso skeletal muscle tissue of torso skeletal muscle tissue of trunk torso skeletal muscle torso skeletal muscle tissue trunk skeletal muscle trunk skeletal muscle tissue uberon UBERON:0003898 skeletal muscle tissue of trunk https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships A portion of skeletal muscle tissue in the trunk. http://orcid.org/0000-0002-6601-2165 skeletal muscle of torso OBOL:automatic skeletal muscle tissue of torso OBOL:automatic skeletal muscle tissue of trunk OBOL:automatic torso skeletal muscle OBOL:automatic torso skeletal muscle tissue OBOL:automatic trunk skeletal muscle OBOL:automatic trunk skeletal muscle tissue OBOL:automatic The part of the retina that contains neurons and photoreceptor cells[GO]. (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] AAO:0011095 BTO:0000929 CALOHA:TS-0685 EHDAA2:0001253 EHDAA:4763 EMAPA:17171 EMAPA:18590 FMA:58628 MA:0000277 NCIT:C33166 TAO:0000046 UMLS:C1518263 VHOG:0000535 XAO:0003216 ZFA:0000046 neural layer of retina neural retina neuroretina stratum nervosum (retina) stratum nervosum retinae uberon neural retinal epithelium UBERON:0003902 retinal neural layer Bgee:AN The part of the retina that contains neurons and photoreceptor cells[GO]. GO:0003407 (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] 2012-09-17 VHOG:0000535 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 http://bgee.unil.ch/ UMLS:C1518263 ncithesaurus:Neural_Retina neural layer of retina FMA:58628 neural retina XAO:0003216 ZFA:0000046 neuroretina ZFA:0000046 stratum nervosum (retina) FMA:58628 stratum nervosum retinae FMA:58628 FMA:TA neural retinal epithelium MA:000027 small blood vessel similar to a capillary but with a fenestrated endothelium. Sinusoids are found in the liver, lymphoid tissue, endocrine organs, and hematopoietic organs such as the bone marrow and the spleen. Sinusoids found within terminal villi of the placenta are not comparable to these; they possess a continuous endothelium and complete basal lamina[WP]. Fenestrated blood vessel endothelium with pores that are large enough for blood cells to pass. The basal lamina and gap junctions may be discontinuous.[TAO] sinusoidal some sources give discontinuous capillary as synonym but this may be a subtype - see FMA:63198 discontinuous sinusoid (undefined). FMA:63131 SCTID:340163004 TAO:0005261 Wikipedia:Sinusoid_(blood_vessel) ZFA:0005261 sinusoidal blood vessel sinusoidal blood vessel endothelium uberon endothelium of irregular blood filled space sinusoidal capillary sinusoidal endothelium UBERON:0003909 sinusoid Wikipedia ZFA small blood vessel similar to a capillary but with a fenestrated endothelium. Sinusoids are found in the liver, lymphoid tissue, endocrine organs, and hematopoietic organs such as the bone marrow and the spleen. Sinusoids found within terminal villi of the placenta are not comparable to these; they possess a continuous endothelium and complete basal lamina[WP]. Wikipedia:Sinusoid_(blood_vessel) Fenestrated blood vessel endothelium with pores that are large enough for blood cells to pass. The basal lamina and gap junctions may be discontinuous.[TAO] 2012-08-14 TAO:0005261 TAO ZFIN:curator some sources give discontinuous capillary as synonym but this may be a subtype - see FMA:63198 discontinuous sinusoid (undefined). FMA sinusoidal blood vessel endothelium ZFA:0005261 sinusoidal capillary http://www.medilexicon.com/medicaldictionary.php?t=13986 Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system. contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers AEO:0000114 EHDAA2:0003114 FBbt:00007474 epithelial or endothelial tube uberon UBERON:0003914 epithelial tube Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system. GO:0060562 PMID:12526790 Any endothelium that has the quality of being cylindrical [Automatically generated definition]. uberon UBERON:0003915 endothelial tube Any endothelium that has the quality of being cylindrical [Automatically generated definition]. OBOL:automatic A blood vessel that carries blood from the capillaries toward the heart EMAPA:35932 FMA:86188 MA:0000066 segment of venous tree organ venous tree organ segment uberon UBERON:0003920 Compare to: vein venous blood vessel A blood vessel that carries blood from the capillaries toward the heart http://www.thefreedictionary.com/venous+blood+vessel segment of venous tree organ FMA:86188 venous tree organ segment FMA:86188 A duct that is part of a digestive system [Automatically generated definition]. TAO:0005162 ZFA:0005162 duct of digestive system duct of gastrointestinal system gastrointestinal system duct uberon UBERON:0003928 digestive system duct A duct that is part of a digestive system [Automatically generated definition]. OBOL:automatic duct of digestive system OBOL:automatic duct of gastrointestinal system OBOL:automatic gastrointestinal system duct OBOL:automatic An epithelium that lines the lumen of the digestive tract. Epithelium lining the lumen of the gut.[TAO] BTO:0000956 EHDAA2:0004567 EMAPA:32928 MA:0003201 NCIT:C12963 TAO:0005123 UMLS:C0836205 XAO:0003200 ZFA:0005123 digestive tract epithelial tissue epithelial tissue of digestive tract epithelial tissue of gut epithelium of digestive tract epithelium of gut gastrodermis gut epithelial tissue gut epithelium uberon alimentary tract epithelium UBERON:0003929 digestive tract epithelium An epithelium that lines the lumen of the digestive tract. http://orcid.org/0000-0002-6601-2165 Epithelium lining the lumen of the gut.[TAO] 2012-08-14 TAO:0005123 TAO ZFIN:curator UMLS:C0836205 ncithesaurus:Gut_Epithelium digestive tract epithelial tissue OBOL:automatic epithelial tissue of digestive tract OBOL:automatic epithelial tissue of gut OBOL:automatic epithelium of digestive tract OBOL:automatic epithelium of gut OBOL:automatic gastrodermis BGEE:ANN NCBITaxon:6073 gut epithelial tissue OBOL:automatic gut epithelium EHDAA2:0004567 MA:0003201 ZFA:0005123 alimentary tract epithelium OBOL:automatic A cartilage element of chondrocranium. Example: neurocranial trabecula. EFO:0003690 TAO:0001461 ZFA:0001461 cartilage of chondrocranium cartilaginous element of chondrocranium chondrocranium cartilage neurocranium cartilage uberon UBERON:0003932 cartilage element of chondrocranium A cartilage element of chondrocranium. Example: neurocranial trabecula. https://orcid.org/0000-0002-6601-2165 cartilage of chondrocranium OBOL:accepted cartilaginous element of chondrocranium OBOL:accepted chondrocranium cartilage ZFA:0001461 neurocranium cartilage ZFA:0001461 A cartilage element that is part of the cranial skeleton. Cartilage which is part of the cranium.[TAO] TAO:0001458 ZFA:0001458 cartilage of cranium cranium cartilage uberon cranial cartilages UBERON:0003933 cranial cartilage A cartilage element that is part of the cranial skeleton. ZFA:0001458 https://orcid.org/0000-0002-6601-2165 Cartilage which is part of the cranium.[TAO] 2012-08-14 TAO:0001458 TAO ZFIN:curator cartilage of cranium OBOL:automatic cranium cartilage OBOL:automatic cranial cartilages ZFA:0001458 Any of the organized aggregations of cells that function as secretory or excretory organs and are associated with reproduction. MA:0001751 genitalia gland gland of genitalia gland of reproductive system reproductive gland reproductive system gland sex gland uberon UBERON:0003937 reproductive gland Any of the organized aggregations of cells that function as secretory or excretory organs and are associated with reproduction. MP:0000653 genitalia gland OBOL:automatic gland of genitalia MP:0000653 gland of reproductive system OBOL:automatic reproductive gland MA:0001751 reproductive system gland OBOL:automatic sex gland MP:0000653 The sensory system for the sense of touch and pain. The neural tissue involved in the transmission of sensory signals MP defines this in a may more appropriate to somatosensory cortex UBERON:0014511 EMAPA:37954 NLXANAT:090818 Wikipedia:Somatosensory_system http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=2887 somatic sensory system somatosensory system system for detection of somatic senses uberon UBERON:0003942 somatic sensory system The sensory system for the sense of touch and pain. NLXANAT:090818 The neural tissue involved in the transmission of sensory signals MP:0000959 MP defines this in a may more appropriate to somatosensory cortex MP EMAPA:37954 MA:th somatosensory system NLXANAT:090818 The anterior segment of the lamellated connective tissue layer of the cornea anterior stroma EMAPA:37414 cornea anterior stroma uberon UBERON:0003952 anterior stroma of cornea lexical The anterior segment of the lamellated connective tissue layer of the cornea MP:0003093 anterior stroma MP:0003093 EMAPA:37414 MA:th cornea anterior stroma MP:0003093 The posterior segment of the lamellated connective tissue layer of the cornea posterior stroma EMAPA:37415 cornea posterior stroma uberon UBERON:0003953 posterior stroma of cornea lexical The posterior segment of the lamellated connective tissue layer of the cornea MP:0003094 posterior stroma MP:0003094 EMAPA:37415 MA:th cornea posterior stroma MP:0003094 The slender connective tissue fiber in the extracellular matrix of skin tissue that is composed of microfibrils and amorphous elastin and is characterized by great elasticity EMAPA:37841 cutaneous elastic fiber dermal elastic fiber uberon UBERON:0003967 cutaneous elastic tissue The slender connective tissue fiber in the extracellular matrix of skin tissue that is composed of microfibrils and amorphous elastin and is characterized by great elasticity MP:0008418 EMAPA:37841 MA:th cutaneous elastic fiber MP:0008418 dermal elastic fiber MP:0008418 The internal feminine genital organs, including the ovaries, uterine tubes, uterus, uterine cervix, and vagina. BTO:0003099 FMA:45654 SCTID:303518005 female internal genitalia internal female genital organ internal genitalia of female reproductive system uberon organa genitalia feminina interna UBERON:0003975 TODO: Relabel. Make distinct organ class. See https://github.com/obophenotype/uberon/issues/547 internal female genitalia The internal feminine genital organs, including the ovaries, uterine tubes, uterus, uterine cervix, and vagina. MP:0009209 female internal genitalia FMA:45654 internal female genital organ BTO:0003099 internal genitalia of female reproductive system OBOL:automatic organa genitalia feminina interna BTO:0003099 The connection between the embryo proper and extraembryonic tissues uberon UBERON:0004015 embryonic-extraembryonic boundary The connection between the embryo proper and extraembryonic tissues MP:0003890 A transitional population of migrating mesenchymal cells that derive from somites and that will become dermal cells. Not to be confused with 'dermatome segment of skin'. AAO:0011028 AEO:0001017 EHDAA2_RETIRED:0003428 EHDAA:1719 EHDAA:1725 EHDAA:1731 EHDAA:1737 EMAPA:32838 FMA:295656 NCIT:C61572 UMLS:C0180383 Wikipedia:Dermatome_(embryology) XAO:0000220 cutis plate dermatomal mesenchyme uberon epimere mesoderm mesenchyma dermatomiale UBERON:0004016 dermatome http://upload.wikimedia.org/wikipedia/commons/f/f3/Gray64.png AEO EHDAA2-abduced A transitional population of migrating mesenchymal cells that derive from somites and that will become dermal cells. AEO:0001017 AEO:JB UMLS:C0180383 ncithesaurus:Dermatome cutis plate Wikipedia:Cutis_plate dermatomal mesenchyme Wikipedia:Cutis_plate mesenchyma dermatomiale Wikipedia:Dermatomal_mesenchyme The single layer of epithelial cells that lines the early neural tube and develops into the nervous system and into the neural crest cells As the cells adjacent to the lumen continue to divide, the migrating cells form a second layer around the original neural tube. This layer becomes progressively thicker as more cells are added to it from the germinal neuroepithelium. This new layer is called the mantle (or intermediate) zone, and the germinal epithelium is now called the ventricular zone (and, later, the ependyma)[NCBIBook:NBK10047] germinal neuroepithelial layer germinal neuroepithelium original neural tube uberon UBERON:0004022 germinal neuroepithelium NCBIBook:NBK10047 The single layer of epithelial cells that lines the early neural tube and develops into the nervous system and into the neural crest cells MP:0004261 http://www.ncbi.nlm.nih.gov/books/NBK10047 germinal neuroepithelial layer http://orcid.org/0000-0002-6601-2165 germinal neuroepithelium NCBIBook:NBK10047 original neural tube NCBIBook:NBK10047 The transient outer neural tube region that contains the first generated post-mitotic neurons that receive synaptic input from thalamic axons and in turn project axons to the developing cortical plate The transient fetal subplate zone, together with the marginal zone and the cortical plate, represents the developmental anlage of the mammalian cerebral cortex. It serves as a waiting compartment for growing cortical afferents; its cells are involved in the establishment of pioneering cortical efferent projections and transient fetal circuitry, and apparently have a number of other developmental roles. The subplate zone is a phylogenetically recent structure and it is most developed in the human brain. Subplate neurons are among the first generated neurons in the mammalian cerebral cortex [1]. These neurons disappear during postnatal development and are important in establishing the correct wiring [2][3] and functional maturation [4] of the cerebral cortex. Subplate neurons appear to be selectively sensitive to injury (such as hypoxia) which in humans are associated with motor and cognitive defects SP DHBA:10522 EMAPA:32703 PBA:294021932 Wikipedia:Subplate http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=3233 https://upload.wikimedia.org/wikipedia/commons/thumb/a/ac/Corticogenesis_in_a_wild-type_mouse_with_captions_in_english_copy.png/360px-Corticogenesis_in_a_wild-type_mouse_with_captions_in_english_copy.png cerebral cortex subplate subplate subplate zone uberon UBERON:0004035 cortical subplate The transient outer neural tube region that contains the first generated post-mitotic neurons that receive synaptic input from thalamic axons and in turn project axons to the developing cortical plate MP:0008440 Wikipedia:Subplate https://github.com/obophenotype/mouse-anatomy-ontology/issues/1 The transient fetal subplate zone, together with the marginal zone and the cortical plate, represents the developmental anlage of the mammalian cerebral cortex. It serves as a waiting compartment for growing cortical afferents; its cells are involved in the establishment of pioneering cortical efferent projections and transient fetal circuitry, and apparently have a number of other developmental roles. The subplate zone is a phylogenetically recent structure and it is most developed in the human brain. Subplate neurons are among the first generated neurons in the mammalian cerebral cortex [1]. These neurons disappear during postnatal development and are important in establishing the correct wiring [2][3] and functional maturation [4] of the cerebral cortex. Subplate neurons appear to be selectively sensitive to injury (such as hypoxia) which in humans are associated with motor and cognitive defects WP SP BRAINSPAN:BRAINSPAN cerebral cortex subplate EMAPA:32833 subplate zone DHBA:10522 The region of the developing mammalian cortex that extends between the ventricular zone and the cortical plate (CP); normally, the IZ is a region of tangential migration of cells, and at midgestation, the lower part of the IZ develops into the subventricular zone IZ EMAPA:17545 EMAPA:32712 uberon cerebral cortex mantle layer cerebral cortex mantle zone cortical mantle layer UBERON:0004040 cortical intermediate zone Wikipedia The region of the developing mammalian cortex that extends between the ventricular zone and the cortical plate (CP); normally, the IZ is a region of tangential migration of cells, and at midgestation, the lower part of the IZ develops into the subventricular zone MP:0008457 IZ BRAINSPAN:BRAINSPAN cerebral cortex mantle layer EMAPA:17545 The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium consider merging with 'ventricular zone'; note that the MA class probably does not belong here, as this is an embryonic structure The layer of undifferentiated, proliferating cells that line the neural tube lumen ependymal layer EMAPA:17152 EMAPA:35362 EMAPA_RETIRED:16783 MA:0003193 neural tube ependymal layer neural tube ventricular germinal zone neural tube ventricular zone neural tube ependymal zone uberon UBERON:0004060 neural tube ventricular layer NCBIBook:NBK10047 NCBIBook:NBK10047 The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium MP:0009689 http://www.ncbi.nlm.nih.gov/books/NBK10047 The layer of undifferentiated, proliferating cells that line the neural tube lumen MP:0009689 ependymal layer NCBIBook:NBK10047 neural tube ependymal layer NCBIBook:NBK10047 neural tube ventricular germinal zone NCBIBook:NBK10047 neural tube ventricular zone MP:0009689 neural tube ependymal zone MP:0009689 The layer of glia and differentiating neurons that forms as a second layer around the germinal neuroepithium; as this develops it comes to lie between the ventricular and marginal layers and includes the basal and alar plates. Develops into neurons and glia forming a gray matter layer. EMAPA:17148 EMAPA:35360 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1367 neural tube intermediate zone uberon future brain marginal layer UBERON:0004061 neural tube mantle layer NCBIBook:NBK10047 by division NCBIBook:NBK10047 The layer of glia and differentiating neurons that forms as a second layer around the germinal neuroepithium; as this develops it comes to lie between the ventricular and marginal layers and includes the basal and alar plates. Develops into neurons and glia forming a gray matter layer. MP:0009690 http://www.ncbi.nlm.nih.gov/books/NBK10047 neural tube intermediate zone MP:0009690 http://www.ncbi.nlm.nih.gov/books/NBK10047 future brain marginal layer EMAPA:35360 The outermost layer of the neural tube that consists of axons from the developing mantle layer and will form the white matter EMAPA:17151 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1368 neural tube marginal zone uberon brain marginal zone UBERON:0004062 neural tube marginal layer forms from axons The outermost layer of the neural tube that consists of axons from the developing mantle layer and will form the white matter MP:0009691 http://www.ncbi.nlm.nih.gov/books/NBK10047 neural tube marginal zone MP:0009691 The region of the mantle layer of the neural tube that lies ventral to the sulcus limitans and contains primarily motor neurons and interneurons. AAO:0010561 EFO:0001904 NCIT:C34111 UMLS:C1511061 Wikipedia:Basal_plate_(neural_tube) http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1372 basal plate basal plate of neural tube spinal cord basal plate uberon motor part of neural tube ventral part of neural tube UBERON:0004064 neural tube basal plate Shh Swenson The region of the mantle layer of the neural tube that lies ventral to the sulcus limitans and contains primarily motor neurons and interneurons. MP:0009693 Wikipedia:Basal_plate_(neural_tube) http://www.ncbi.nlm.nih.gov/books/NBK10047 UMLS:C1511061 ncithesaurus:Basal_Plate basal plate of neural tube Wikipedia:Basal_plate_(neural_tube) spinal cord basal plate MP:0009693 The subdivision of the face that includes the eye (eyeball plus adnexa such as eyelids) and the orbit of the skull and associated parts of the face such as the eyebrows, if present note the FMA class is more narrow though, and is more like eye + muscles + vasculature. The FMA also has FMA:72951 orbital part of eye in HP covers eyelid, eyebrow. FMA:260119 content of orbital part of eye eye region orbital part of face uberon ocular and peri-ocular region ocular region orbital content orbital part of eye UBERON:0004088 orbital region The subdivision of the face that includes the eye (eyeball plus adnexa such as eyelids) and the orbit of the skull and associated parts of the face such as the eyebrows, if present http://orcid.org/0000-0002-6601-2165 in HP covers eyelid, eyebrow. HP:0000284 content of orbital part of eye FMA:260119 eye region http://orcid.org/0000-0002-6601-2165 orbital part of face http://orcid.org/0000-0002-6601-2165 orbital content FMA:260119 orbital part of eye FMA:72951 2 2 Any tube, opening or passage that connects two distinct anatomical spaces. FMA has both conduit and conduit space. In EHDAA2 this is a surface feature AEO:0000080 EHDAA2:0003080 FMA:242873 SCTID:346902003 Wikipedia:Foramen foramen foramina uberon opening ostia ostium UBERON:0004111 anatomical conduit Any tube, opening or passage that connects two distinct anatomical spaces. http://orcid.org/0000-0002-6601-2165 FMA has both conduit and conduit space. In EHDAA2 this is a surface feature FMA foramen EHDAA2:0003080 foramina https://orcid.org/0000-0002-6601-2165 ostia A vasculature that is part of a iris [Automatically generated definition]. ZFA:0005568 iris blood vessels iris vascular network iris vasculature vascular network of iris uberon UBERON:0004118 vasculature of iris A vasculature that is part of a iris [Automatically generated definition]. OBOL:automatic iris blood vessels ZFA:0005568 iris vascular network OBOL:automatic vascular network of iris OBOL:automatic An anatomical structure that develops (entirely or partially) from the endoderm. Grouping term for query purposes uberon UBERON:0004119 endoderm-derived structure An anatomical structure that develops (entirely or partially) from the endoderm. https://orcid.org/0000-0002-6601-2165 An anatomical structure that develops (entirely or partially) from the mesoderm. Grouping term for query purposes FBbt:00025998 mesodermal derivative uberon UBERON:0004120 mesoderm-derived structure An anatomical structure that develops (entirely or partially) from the mesoderm. https://orcid.org/0000-0002-6601-2165 mesodermal derivative FBbt:00025998 An anatomical structure that develops (entirely or partially) from the ectoderm. Grouping term for query purposes FBbt:00025990 ectodermal deriviative uberon UBERON:0004121 ectoderm-derived structure An anatomical structure that develops (entirely or partially) from the ectoderm. https://orcid.org/0000-0002-6601-2165 ectodermal deriviative FBbt:00025990 Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction. Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.[AAO] relationship type change: differentiates_from intermediate mesoderm (AAO:0010575) CHANGED TO: develops_from intermediate mesoderm (UBERON:0003064)[AAO] Kidneys and gonads (of vertebrates) develop from adjacent tissues, and after the excretory or urinary ducts have developed, the reproductive system usually taps into them or their derivatives.[well established][VHOG] genitourinary urogenital AAO:0000624 BILA:0000122 BTO:0003091 EFO:0003864 EHDAA:1013 EMAPA:16367 EV:0100094 FMA:280610 GAID:362 MESH:D014566 NCIT:C12810 OpenCyc:Mx4rQRpVMgAKEdyHxgDggVfs8g SCTID:278861008 UMLS:C0042066 VHOG:0000286 XAO:0000140 galen:GenitoUrinarySystem urogenital system uberon GU tract UG tract Urogenitalsystem genito-urinary system genitourinary tract urogenital tract UBERON:0004122 genitourinary system Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction. VHOG:0000286 Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.[AAO] 2012-06-20 AAO:0000624 AAO AAO:EJS relationship type change: differentiates_from intermediate mesoderm (AAO:0010575) CHANGED TO: develops_from intermediate mesoderm (UBERON:0003064)[AAO] 2012-06-20 AAO:0000624 AAO Kidneys and gonads (of vertebrates) develop from adjacent tissues, and after the excretory or urinary ducts have developed, the reproductive system usually taps into them or their derivatives.[well established][VHOG] 2012-09-17 VHOG:0000286 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.633 http://bgee.unil.ch/ UMLS:C0042066 ncithesaurus:Genitourinary_System Urogenitalsystem BTO:0003091 genito-urinary system FMA:280610 urogenital tract BTO:0003091 The optic vesicle is the evagination of neurectoderm that precedes formation of the optic cup[GO]. Portion of tissue that is comprised of neuroepitheium which has pinched off from the anterior neural keel and will form the optic cup[ZFA]. (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles.[well established][VHOG] AAO:0011039 EHDAA2:0001320 EMAPA:16540 FMA:293357 NCIT:C34236 SCTID:362864008 TAO:0000050 UMLS:C0231106 VHOG:0000165 Wikipedia:Optic_vesicles XAO:0000228 ZFA:0000050 uberon evagination eye vesicle ocular vesicle optic vesicles UBERON:0004128 Genes: Six3, Pax6, Rx1 are expressed together in the tip of the neural plate [ISBN:9780878932504 "Developmental Biology"]. Development notes: During subsequent develop- ment, the optic vesicle invaginates and becomes a two-layered structure with an inner neural retina and outer retinal pigment epithelium. As soon as the developing optic vesicle makes contact with the overlying ectoderm, it induces the ectoderm to thicken and form the lens placode [PMID:16496288] optic vesicle http://upload.wikimedia.org/wikipedia/commons/e/e0/Gray863.png ZFA GO-def ZFA The optic vesicle is the evagination of neurectoderm that precedes formation of the optic cup[GO]. Portion of tissue that is comprised of neuroepitheium which has pinched off from the anterior neural keel and will form the optic cup[ZFA]. GO:0003404 Wikipedia:Optic_vesicles (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles.[well established][VHOG] 2012-09-17 VHOG:0000165 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 http://bgee.unil.ch/ UMLS:C0231106 ncithesaurus:Optic_Vesicle eye vesicle XAO:0000228 ocular vesicle VHOG:0000165 optic vesicles ZFA:0000050 . salivary nucleus uberon UBERON:0004133 salivatory nucleus . GO:0021751 salivary nucleus GO:0021751 The first recognizable structure derived from the heart field TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO (In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG] EHDAA2:0000215 EMAPA:16106 VHOG:0000975 myocardial plate uberon cardiac crescent cardiogenic crescent heart rudiment UBERON:0004139 cardiogenic plate The first recognizable structure derived from the heart field GO:0003142 (In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG] 2012-09-17 VHOG:0000975 VHOG PMID:15611355 Gittenberger-de Groot AC, Bartelings MM, Deruiter MC, Poelmann RE, Basics of cardiac development for the understanding of congenital heart malformations. Pediatric Research (2005) http://bgee.unil.ch/ myocardial plate EHDAA2:0000215 cardiac crescent EMAPA:16106 cardiogenic crescent GO:0003142 A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle. this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138] XAO:0004185 first heart field primary heart field uberon FHF PHF heart field UBERON:0004140 primary heart field GO:0003128 BGEE:ann A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle. GO:0003138 GOC:mtg_heart GOC:rl this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138] GO first heart field XAO:0004185 primary heart field PMID:17276708 XAO:0004185 FHF XAO:0004185 PHF XAO:0004185 heart field XAO:0004185 An epithelial tube that will give rise to the mature heart. the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube. AAO:0010411 EFO:0003526 EMAPA:32685 NCIT:C34161 TAO:0000360 XAO:0000337 ZFA:0000360 embryonic heart tube endocardial heart tube endocardial tube uberon UBERON:0004141 heart tube ZFA-modified An epithelial tube that will give rise to the mature heart. GO:0003143 GOC:mtg_heart the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube. MP:0012700 embryonic heart tube GO:0003143 endocardial heart tube MP:0012700 endocardial tube XAO:0000337 The outflow tract septum is a partition in the outflow tract XAO:0004141 uberon UBERON:0004142 outflow tract septum The outflow tract septum is a partition in the outflow tract GO:0003148 The outflow tract is the portion of the heart through which blood flows into the arteries Depending on the species, attached at the cardiac outflow are described the conus arteriosus, the truncus arteriosus and, or the bulbus arteriosus. At the distal limit of these outflow structures, but lying outside the pericardial cavity, is the ventral aorta[PMID:20735616] EHDAA2:0001351 EHDAA:464 EHDAA:798 EMAPA:16346 MA:0000100 VHOG:0000670 XAO:0004139 cardiac outflow tract heart outflow tract uberon arterial (outflow) pole UBERON:0004145 outflow tract The outflow tract is the portion of the heart through which blood flows into the arteries GO:0003151 cardiac outflow tract PMID:20735616 arterial (outflow) pole PMID:20735616 Vein of heart that drains the myocardium EHDAA2:0004507 EMAPA:37137 FMA:12846 NCIT:C12878 NCIT:C12882 SCTID:277726009 UMLS:C0226654 UMLS:C0226737 Wikipedia:Coronary_circulation ZFA:0005814 galen:CoronaryVein cardiac vein coronary vein heart vein vein of heart uberon coronary vein UBERON:0004148 cardiac vein FMA Vein of heart that drains the myocardium http://orcid.org/0000-0002-6601-2165 EMAPA:37137 MA:th UMLS:C0226654 ncithesaurus:Cardiac_Vein UMLS:C0226737 ncithesaurus:Coronary_Vein cardiac vein FMA:12846 coronary vein ZFA:0005814 heart vein OBOL:automatic vein of heart OBOL:automatic coronary vein Wikipedia:Coronary_circulation A cardiac chamber surrounds an enclosed cavity within the heart FMA:7095 OpenCyc:Mx4rmexpjPdAEduAAAAOpmP6tw SCTID:276456008 chamber of heart heart chamber uberon UBERON:0004151 generic enough to cover FBbt:00003156 heart chamber but this is a cavity. GO defines it as the cavity. TODO - move subclasses. Note this also includes sinus venosus cardiac chamber A cardiac chamber surrounds an enclosed cavity within the heart GO:0003205 An embryonic group of progenitor cells that forms from an outpouching of the septum transversum near the venous pole of the heart and gives rise to the epicardium propepicardial Proepicardial clusters in Zebrafish form on the pericardial wall, adjacent to the atrioventricular (AV) junction and near the venous pole[ZFA] EMAPA:36025 ZFA:0005808 proepicardial cluster proepicardial organ uberon UBERON:0004160 proepicardium todo check other taxa ZFA An embryonic group of progenitor cells that forms from an outpouching of the septum transversum near the venous pole of the heart and gives rise to the epicardium GO:0003342 http://en.wiktionary.org/wiki/proepicardium proepicardial cluster ZFA:0005808 proepicardial organ ZFIN:ZDB-PUB-080218-16 A thick plate of mesodermal tissue that occupies the space between the thoracic cavity and yolk stalk in the early embryo, forming a transverse partition partially separating the coelomic cavity into thoracic and abdominal portions. It gives rise to the central tendon of the diaphragm[VHOG]. A thick plate of mesodermal tissue that occupies the space between the thoracic cavity and yolk stalk in the early embryo, forming a transverse partition partially separating the coelomic cavity into thoracic and abdominal portions. It gives rise to the central tendon of the diaphragm. [TFD][VHOG] In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart (of other tetrapods) is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes) Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG] The cranial part of the septum transversum gives rise to the central tendon of the diaphragm and is the origin of the myoblasts that invade the pleuroperitoneal folds resulting in the formation of the muscular diaphragm. The caudal part of the septum transversum is invaded by the hepatic diverticulum which divides within it to form the liver and thus gives rise to the ventral mesentery of the foregut. in EHDAA2 this is divided into mesenchymal portion and hepatic diverticulum EHDAA2:0001829 EHDAA:736 EMAPA:16318 FMA:295593 NCIT:C34296 SCTID:308819008 UMLS:C0231004 VHOG:0000019 Wikipedia:Septum_transversum transverse septum uberon UBERON:0004161 septum transversum A thick plate of mesodermal tissue that occupies the space between the thoracic cavity and yolk stalk in the early embryo, forming a transverse partition partially separating the coelomic cavity into thoracic and abdominal portions. It gives rise to the central tendon of the diaphragm[VHOG]. VHOG:0000019 Wikipedia:Septum_transversum A thick plate of mesodermal tissue that occupies the space between the thoracic cavity and yolk stalk in the early embryo, forming a transverse partition partially separating the coelomic cavity into thoracic and abdominal portions. It gives rise to the central tendon of the diaphragm. [TFD][VHOG] 2012-09-17 VHOG:0000019 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/transverse+septum In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart (of other tetrapods) is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes) Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG] 2012-09-17 VHOG:0000019 VHOG ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206 http://bgee.unil.ch/ in EHDAA2 this is divided into mesenchymal portion and hepatic diverticulum EHDAA2 UMLS:C0231004 ncithesaurus:Septum_Transversum transverse septum https://orcid.org/0000-0002-6601-2165 The internal genitalia are the internal sex organs such as the uterine tube, the uterus and the vagina in female mammals, and the testis, seminal vesicle, ejaculatory duct and prostate in male mammals FMA:45652 internal genitalia internal genitals uberon internal reproductive organ internal sex organ UBERON:0004175 TODO: make a subdivision of reproductive system. Relabel. See https://github.com/obophenotype/uberon/issues/547 internal genitalia The internal genitalia are the internal sex organs such as the uterine tube, the uterus and the vagina in female mammals, and the testis, seminal vesicle, ejaculatory duct and prostate in male mammals GO:0035260 The external genitalia are the outer sex organs, such as the penis or vulva in mammals FMA:45643 SCTID:362207005 external genitalia uberon external reproductive organ external sex organ UBERON:0004176 TODO: make a subdivision of reproductive system. Relabel. See https://github.com/obophenotype/uberon/issues/547 external genitalia The external genitalia are the outer sex organs, such as the penis or vulva in mammals GO:0035261 Organ that is part of the hematopoietic system. consider splitting out lymph organ, compare with lymph node the organs in which the formed elements of the blood and lymph are produced[http://encyclopedia2.thefreedictionary.com/Hematopoietic+Organs]. the FMA class 'lymphoid organ' is a general anatomical term BTO:0004605 EMAPA:37665 FMA:7143 MA:0000747 SCTID:361338006 haematological system organ haemopoietic system organ hematopoeitic organ hematopoietic system organ organ of haematological system organ of haemopoietic system organ of hematopoietic system organ of organa haemopoietica organa haemopoietica organ hematopoeitic or lymphoid organ lymph organ lymphoid organ uberon UBERON:0004177 hemopoietic organ Organ that is part of the hematopoietic system. GOC:Obol the organs in which the formed elements of the blood and lymph are produced[http://encyclopedia2.thefreedictionary.com/Hematopoietic+Organs]. http://encyclopedia2.thefreedictionary.com/Hematopoietic+Organs the FMA class 'lymphoid organ' is a general anatomical term FMA EMAPA:37665 MA:th haematological system organ OBOL:automatic haemopoietic system organ OBOL:automatic hematopoietic system organ OBOL:automatic organ of haematological system OBOL:automatic organ of haemopoietic system OBOL:automatic organ of hematopoietic system OBOL:automatic organ of organa haemopoietica OBOL:automatic organa haemopoietica organ OBOL:automatic lymph organ MA:0000747 lymphoid organ BTO:0004605 FMA:7143 the nonstriated, involuntary muscle tissue located in the wall of the aorta BTO:0001685 CALOHA:TS-0048 EFO:0002775 EMAPA:35135 MA:0000702 NCIT:C49191 UMLS:C1706825 aorta non-striated muscle aorta smooth muscle aortic smooth muscle uberon UBERON:0004178 aorta smooth muscle tissue the nonstriated, involuntary muscle tissue located in the wall of the aorta MGI:csmith MP:0009865 UMLS:C1706825 ncithesaurus:Aorta_Smooth_Muscle_Tissue aorta non-striated muscle OBOL:automatic aorta smooth muscle OBOL:automatic aortic smooth muscle BTO:0001685 A portions of the gut that is derived from endoderm. EMAPA:32930 endodermal gut gut endoderm uberon UBERON:0004185 endodermal part of digestive tract A portions of the gut that is derived from endoderm. GO:0061031 gut endoderm EMAPA:32930 A nerve that is part of a back [Automatically generated definition]. EMAPA:37268 MA:0000497 nerve of back uberon UBERON:0004215 back nerve A nerve that is part of a back [Automatically generated definition]. OBOL:automatic EMAPA:37268 MA:th nerve of back OBOL:automatic A portion of smooth muscle tissue that is part of a large intestine [Automatically generated definition]. MA class may specifically mean muscle layer, but we treat as the sum of smooth muscle in both muscle layer and muscularis mucosa EMAPA:35469 MA:0001547 involuntary muscle of large intestine large intestine involuntary muscle large intestine non-striated muscle large intestine smooth muscle tissue non-striated muscle of large intestine smooth muscle of large intestine smooth muscle tissue of large intestine uberon UBERON:0004220 large intestine smooth muscle MA consider merging A portion of smooth muscle tissue that is part of a large intestine [Automatically generated definition]. OBOL:automatic MA class may specifically mean muscle layer, but we treat as the sum of smooth muscle in both muscle layer and muscularis mucosa MA involuntary muscle of large intestine OBOL:automatic large intestine involuntary muscle OBOL:automatic large intestine non-striated muscle OBOL:automatic large intestine smooth muscle tissue OBOL:automatic non-striated muscle of large intestine OBOL:automatic smooth muscle of large intestine OBOL:automatic smooth muscle tissue of large intestine OBOL:automatic A portion of smooth muscle tissue that is part of a intestine [Automatically generated definition]. MA class may specifically mean muscle layer, but we treat as the sum of smooth muscle in both muscle layer and muscularis mucosa BTO:0000643 EMAPA:35441 EMAPA:35443 MA:0001539 NCIT:C49243 UMLS:C1708547 bowel involuntary muscle bowel non-striated muscle bowel smooth muscle bowel smooth muscle tissue intestine involuntary muscle intestine non-striated muscle intestine smooth muscle tissue involuntary muscle of bowel involuntary muscle of intestine non-striated muscle of bowel non-striated muscle of intestine smooth muscle of bowel smooth muscle of intestine smooth muscle tissue of bowel smooth muscle tissue of intestine uberon intestinal muscularis intestinal smooth muscle UBERON:0004221 intestine smooth muscle consider merging A portion of smooth muscle tissue that is part of a intestine [Automatically generated definition]. OBOL:automatic MA class may specifically mean muscle layer, but we treat as the sum of smooth muscle in both muscle layer and muscularis mucosa MA UMLS:C1708547 ncithesaurus:Intestinal_Smooth_Muscle_Tissue bowel involuntary muscle OBOL:automatic bowel non-striated muscle OBOL:automatic bowel smooth muscle OBOL:automatic bowel smooth muscle tissue OBOL:automatic intestine involuntary muscle OBOL:automatic intestine non-striated muscle OBOL:automatic intestine smooth muscle tissue OBOL:automatic involuntary muscle of bowel OBOL:automatic involuntary muscle of intestine OBOL:automatic non-striated muscle of bowel OBOL:automatic non-striated muscle of intestine OBOL:automatic smooth muscle of bowel OBOL:automatic smooth muscle of intestine OBOL:automatic smooth muscle tissue of bowel OBOL:automatic smooth muscle tissue of intestine OBOL:automatic intestinal muscularis EMAPA:35441 intestinal smooth muscle BTO:0000643 A portion of smooth muscle tissue that is part of a stomach [Automatically generated definition]. BTO:0001818 EMAPA:35823 MA:0001627 involuntary muscle of stomach involuntary muscle of ventriculus non-striated muscle of stomach non-striated muscle of ventriculus smooth muscle of stomach smooth muscle of ventriculus smooth muscle tissue of stomach smooth muscle tissue of ventriculus stomach involuntary muscle stomach non-striated muscle stomach smooth muscle tissue ventriculus involuntary muscle ventriculus non-striated muscle ventriculus smooth muscle ventriculus smooth muscle tissue uberon gastric muscle gastric smooth muscle stomach muscle UBERON:0004222 stomach smooth muscle A portion of smooth muscle tissue that is part of a stomach [Automatically generated definition]. OBOL:automatic involuntary muscle of stomach OBOL:automatic involuntary muscle of ventriculus OBOL:automatic non-striated muscle of stomach OBOL:automatic non-striated muscle of ventriculus OBOL:automatic smooth muscle of stomach OBOL:automatic smooth muscle of ventriculus OBOL:automatic smooth muscle tissue of stomach OBOL:automatic smooth muscle tissue of ventriculus OBOL:automatic stomach involuntary muscle OBOL:automatic stomach non-striated muscle OBOL:automatic stomach smooth muscle tissue OBOL:automatic ventriculus involuntary muscle OBOL:automatic ventriculus non-striated muscle OBOL:automatic ventriculus smooth muscle OBOL:automatic ventriculus smooth muscle tissue OBOL:automatic gastric muscle BTO:0001818 gastric smooth muscle MA:0001627 stomach muscle BTO:0001818 A portion of smooth muscle tissue that is part of a respiratory system [Automatically generated definition]. BTO:0001660 EMAPA:35734 MA:0001830 respiratory smooth muscle smooth muscle of respiratory system uberon airway smooth muscle airway smooth muscle cell UBERON:0004225 respiratory system smooth muscle A portion of smooth muscle tissue that is part of a respiratory system [Automatically generated definition]. OBOL:automatic respiratory smooth muscle BTO:0001660 smooth muscle of respiratory system OBOL:automatic airway smooth muscle BTO:0001660 airway smooth muscle cell BTO:0001660 A portion of smooth muscle tissue that is part of a digestive system [Automatically generated definition]. EMAPA:35117 MA:0001523 smooth muscle tissue of gastrointestinal system uberon UBERON:0004226 gastrointestinal system smooth muscle A portion of smooth muscle tissue that is part of a digestive system [Automatically generated definition]. OBOL:automatic smooth muscle tissue of gastrointestinal system OBOL:automatic A portion of smooth muscle tissue that is part of an anal region [Automatically generated definition]. EMAPA:37394 MA:0001532 anal part of perineum involuntary muscle anal part of perineum non-striated muscle anal part of perineum smooth muscle anal part of perineum smooth muscle tissue anal region involuntary muscle anal region non-striated muscle anal region smooth muscle tissue anal triangle involuntary muscle anal triangle non-striated muscle anal triangle smooth muscle anal triangle smooth muscle tissue involuntary muscle of anal part of perineum involuntary muscle of anal region involuntary muscle of anal triangle non-striated muscle of anal part of perineum non-striated muscle of anal region non-striated muscle of anal triangle smooth muscle of anal part of perineum smooth muscle of anal region smooth muscle of anal triangle smooth muscle tissue of anal part of perineum smooth muscle tissue of anal region smooth muscle tissue of anal triangle uberon UBERON:0004231 anal region smooth muscle A portion of smooth muscle tissue that is part of an anal region [Automatically generated definition]. OBOL:automatic EMAPA:37394 MA:th anal part of perineum involuntary muscle OBOL:automatic anal part of perineum non-striated muscle OBOL:automatic anal part of perineum smooth muscle OBOL:automatic anal part of perineum smooth muscle tissue OBOL:automatic anal region involuntary muscle OBOL:automatic anal region non-striated muscle OBOL:automatic anal region smooth muscle tissue OBOL:automatic anal triangle involuntary muscle OBOL:automatic anal triangle non-striated muscle OBOL:automatic anal triangle smooth muscle OBOL:automatic anal triangle smooth muscle tissue OBOL:automatic involuntary muscle of anal part of perineum OBOL:automatic involuntary muscle of anal region OBOL:automatic involuntary muscle of anal triangle OBOL:automatic non-striated muscle of anal part of perineum OBOL:automatic non-striated muscle of anal region OBOL:automatic non-striated muscle of anal triangle OBOL:automatic smooth muscle of anal part of perineum OBOL:automatic smooth muscle of anal region OBOL:automatic smooth muscle of anal triangle OBOL:automatic smooth muscle tissue of anal part of perineum OBOL:automatic smooth muscle tissue of anal region OBOL:automatic smooth muscle tissue of anal triangle OBOL:automatic A portion of smooth muscle tissue that is part of a lower respiratory tract [Automatically generated definition]. EMAPA:35520 MA:0002410 involuntary muscle of lower respiratory tract lower respiratory tract involuntary muscle lower respiratory tract non-striated muscle lower respiratory tract smooth muscle tissue non-striated muscle of lower respiratory tract smooth muscle of lower respiratory tract smooth muscle tissue of lower respiratory tract uberon UBERON:0004233 lower respiratory tract smooth muscle A portion of smooth muscle tissue that is part of a lower respiratory tract [Automatically generated definition]. OBOL:automatic involuntary muscle of lower respiratory tract OBOL:automatic lower respiratory tract involuntary muscle OBOL:automatic lower respiratory tract non-striated muscle OBOL:automatic lower respiratory tract smooth muscle tissue OBOL:automatic non-striated muscle of lower respiratory tract OBOL:automatic smooth muscle of lower respiratory tract OBOL:automatic smooth muscle tissue of lower respiratory tract OBOL:automatic A portion of smooth muscle tissue that is part of a iris [Automatically generated definition]. see notes for muscle of iris. BTO:0000655 EMAPA:35448 FMA:312338 MA:0001270 involuntary muscle of iris iridial smooth muscle iris involuntary muscle iris non-striated muscle iris smooth muscle tissue non-striated muscle of iris smooth muscle of iris smooth muscle tissue of iris uberon UBERON:0004234 iris smooth muscle MA A portion of smooth muscle tissue that is part of a iris [Automatically generated definition]. OBOL:automatic involuntary muscle of iris OBOL:automatic iridial smooth muscle http://orcid.org/0000-0002-6601-2165 iris involuntary muscle OBOL:automatic iris non-striated muscle OBOL:automatic iris smooth muscle tissue OBOL:automatic non-striated muscle of iris OBOL:automatic smooth muscle of iris OBOL:automatic smooth muscle tissue of iris OBOL:automatic A portion of smooth muscle tissue that is part of an arteriole [Automatically generated definition]. EMAPA:36287 FMA:312251 MA:0000706 uberon UBERON:0004236 arteriole smooth muscle A portion of smooth muscle tissue that is part of an arteriole [Automatically generated definition]. OBOL:automatic smooth muscle found within, and composing the majority of the wall of blood vessels. Vascular smooth muscle contracts or relaxes to both change the volume of blood vessels and the local blood pressure, a mechanism that is responsible for the redistribution of the blood within the body to areas where it is needed (i.e. areas with temporarily enhanced oxygen consumption). Thus the main function of vascular smooth muscle tonus is to regulate the caliber of the blood vessels in the body. Excessive vasoconstriction leads to hypertension, while excessive vasodilation as in shock leads to hypotension. UBERON:0010508 BTO:0001431 CALOHA:TS-1107 EMAPA:35177 MA:0000710 MESH:D009131 NCIT:C33853 TAO:0005321 UMLS:C1519956 Wikipedia:Vascular_smooth_muscle ZFA:0005321 blood vessel involuntary muscle blood vessel non-striated muscle blood vessel smooth muscle tissue involuntary muscle of blood vessel non-striated muscle of blood vessel smooth muscle of blood vessel smooth muscle tissue of blood vessel vascular smooth muscle vascular smooth muscle tissue uberon UBERON:0004237 blood vessel smooth muscle smooth muscle found within, and composing the majority of the wall of blood vessels. Wikipedia:Vascular_smooth_muscle UMLS:C1519956 ncithesaurus:Vascular_Smooth_Muscle_Tissue blood vessel involuntary muscle OBOL:automatic blood vessel non-striated muscle OBOL:automatic blood vessel smooth muscle tissue OBOL:automatic involuntary muscle of blood vessel OBOL:automatic non-striated muscle of blood vessel OBOL:automatic smooth muscle of blood vessel OBOL:automatic smooth muscle tissue of blood vessel OBOL:automatic vascular smooth muscle ZFA:0005321 A portion of smooth muscle tissue that is part of a outflow tract [Automatically generated definition]. EMAPA:37708 MA:0000492 involuntary muscle of outflow tract non-striated muscle of outflow tract outflow tract involuntary muscle outflow tract non-striated muscle outflow tract smooth muscle tissue smooth muscle of outflow tract smooth muscle tissue of outflow tract uberon UBERON:0004246 outflow tract smooth muscle A portion of smooth muscle tissue that is part of a outflow tract [Automatically generated definition]. OBOL:automatic EMAPA:37708 MA:th involuntary muscle of outflow tract OBOL:automatic non-striated muscle of outflow tract OBOL:automatic outflow tract involuntary muscle OBOL:automatic outflow tract non-striated muscle OBOL:automatic outflow tract smooth muscle tissue OBOL:automatic smooth muscle of outflow tract OBOL:automatic smooth muscle tissue of outflow tract OBOL:automatic A bone that is part of the dorsal region of an animal. this class may be obsoleted. See: https://github.com/obophenotype/mouse-anatomy-ontology/issues/93 https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern EMAPA:37248 MA:0000494 uberon back bone bone of back dorsal region bone UBERON:0004247 bone of dorsum A bone that is part of the dorsal region of an animal. http://orcid.org/0000-0002-6601-2165 EMAPA:37248 MA:th back bone MA:0000494 bone of back OBOL:automatic dorsal region bone http://orcid.org/0000-0002-6601-2165 Any muscle organ that is part of a skin of body [Automatically generated definition]. review as part of general integumentary system review - part of skin, or more generally, integumental system in MA, the only skin muscle is arrector pili. The only integumental muscle is panniculus carnosus. In EMAPA, the arrector pili only UBERON:0015797 EMAPA:18187 EMAPA:35776 MA:0002710 MA:0003139 integumental system muscle muscle of integumental system muscle organ of skin skin muscle organ uberon UBERON:0004253 skin muscle Any muscle organ that is part of a skin of body [Automatically generated definition]. OBOL:automatic in MA, the only skin muscle is arrector pili. The only integumental muscle is panniculus carnosus. In EMAPA, the arrector pili only MA integumental system muscle MA:0003139 muscle of integumental system EMAPA:18187 muscle organ of skin OBOL:automatic skin muscle organ OBOL:automatic A blood vessel that is part of a back [Automatically generated definition]. EMAPA:37243 MA:0000493 blood vessel of back uberon UBERON:0004258 back blood vessel A blood vessel that is part of a back [Automatically generated definition]. OBOL:automatic EMAPA:37243 MA:th blood vessel of back OBOL:automatic A myocardium that is part of a outflow tract [Automatically generated definition]. (...) (theme) is how the vertebrate cardiovascular system differs from that of the presumptive evolutionary chordate ancestor. (...) At best we can tell there are two essential new ingredients: (1) vertebrates all have a continuous endothelial lining to the heart and vessels and (2) vertebrates have developed a second chamber in the heart, one designed for generating high systemic blood pressure.[uncertain][VHOG] EHDAA2:0001358 EMAPA:35623 MA:0000489 VHOG:0000603 cardiac muscle of outflow tract heart muscle of outflow tract heart myocardium of outflow tract muscle of heart of outflow tract myocardium of outflow tract outflow tract cardiac muscle outflow tract heart muscle outflow tract heart myocardium outflow tract muscle of heart uberon UBERON:0004265 outflow tract myocardium A myocardium that is part of a outflow tract [Automatically generated definition]. OBOL:automatic (...) (theme) is how the vertebrate cardiovascular system differs from that of the presumptive evolutionary chordate ancestor. (...) At best we can tell there are two essential new ingredients: (1) vertebrates all have a continuous endothelial lining to the heart and vessels and (2) vertebrates have developed a second chamber in the heart, one designed for generating high systemic blood pressure.[uncertain][VHOG] 2012-09-17 VHOG:0000603 VHOG PMID:9187138 Fishman MC, Chien KR, Fashioning the vertebrate heart: earliest embryonic decisions. Development (1997) http://bgee.unil.ch/ cardiac muscle of outflow tract OBOL:automatic heart muscle of outflow tract OBOL:automatic heart myocardium of outflow tract OBOL:automatic muscle of heart of outflow tract OBOL:automatic myocardium of outflow tract OBOL:automatic outflow tract cardiac muscle OBOL:automatic outflow tract heart muscle OBOL:automatic outflow tract heart myocardium OBOL:automatic outflow tract muscle of heart OBOL:automatic A portion of connective tissue that is part of a back [Automatically generated definition]. EMAPA:37256 MA:0000495 uberon mesenchyne of back UBERON:0004267 back connective tissue A portion of connective tissue that is part of a back [Automatically generated definition]. OBOL:automatic EMAPA:37256 MA:th mesenchyne of back OBOL:automatic A pericardium that is part of a outflow tract [Automatically generated definition]. EMAPA:37707 MA:0000491 pericardium of outflow tract uberon UBERON:0004271 outflow tract pericardium A pericardium that is part of a outflow tract [Automatically generated definition]. OBOL:automatic EMAPA:37707 MA:th pericardium of outflow tract OBOL:automatic A muscle that is part of the eye region. AAO:0000156 EMAPA:35335 MA:0000271 OpenCyc:Mx8Ngx4rwKSh9pwpEbGdrcN5Y29ycB4rvViTvpwpEbGdrcN5Y29ycB4rvYA8cJwpEbGdrcN5Y29ycA uberon UBERON:0004277 eye muscle MA A muscle that is part of the eye region. OBOL:automatic Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body. Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO] skeletal AEO:0000168 EHDAA2:0001843 EHDAA:5047 EMAPA:17213 FMA:23875 GAID:177 MA:0003006 MAT:0000032 MESH:D012863 MIAA:0000032 OpenCyc:Mx4rvVi1rpwpEbGdrcN5Y29ycA SCTID:361378004 VSAO:0000026 Wikipedia:Skeleton XAO:0004053 galen:Skeleton set of all bones set of bones of body uberon UBERON:0004288 skeleton https://github.com/obophenotype/uberon/wiki/The-skeletal-system Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body. VSAO:0000026 Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO] 2012-08-14 VSAO:0000026 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 The bilaminar epithelium formed from the myotome and dermatome. Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis. Within the dermomyotome there is also a medio-lateral difference. The central region makes dermis, the mesenchymal connective tissue of the back skin. The medial region (closest to neural tube) makes epaxial muscle, and the lateral region (furthest from neural tube) makes hypaxial muscle[http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768]. Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis.[TAO] Portion of somites that gives rise to dermis and muscles.[AAO] all but the sclerotome of a mesodermal somite; the primordium of skeletal muscle and, perhaps, of the dermis. Thus, representatives of the agnathan vertebrates, chondrichthyans, and sarcopterygians all have a layer of undifferentiated cells external to the embryonic myotome. In the amniotes, this external cell layer is the dermomyotome. The simplest interpretation of the similar position, morphology, and lack of myosin labeling is that a dermomyotome epithelium is a shared, ancestral vertebrate characteristic.[well established][VHOG] AAO:0010572 AEO:0000214 EHDAA2:0003259 EMAPA:31109 FMA:295654 NCIT:C34140 TAO:0001513 UMLS:C1511786 VHOG:0000676 ZFA:0001513 uberon dermamyotome dermomyotomes UBERON:0004290 dermomyotome AEO AEO EHDAA2 ZFA The bilaminar epithelium formed from the myotome and dermatome. AEO:0000214 Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis. Within the dermomyotome there is also a medio-lateral difference. The central region makes dermis, the mesenchymal connective tissue of the back skin. The medial region (closest to neural tube) makes epaxial muscle, and the lateral region (furthest from neural tube) makes hypaxial muscle[http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768]. http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768 Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis.[TAO] 2012-08-14 TAO:0001513 TAO ZFIN:curator Portion of somites that gives rise to dermis and muscles.[AAO] 2012-06-20 AAO:0010572 AAO AAO:EJS all but the sclerotome of a mesodermal somite; the primordium of skeletal muscle and, perhaps, of the dermis. http://medical-dictionary.thefreedictionary.com/dermomyotome Thus, representatives of the agnathan vertebrates, chondrichthyans, and sarcopterygians all have a layer of undifferentiated cells external to the embryonic myotome. In the amniotes, this external cell layer is the dermomyotome. The simplest interpretation of the similar position, morphology, and lack of myosin labeling is that a dermomyotome epithelium is a shared, ancestral vertebrate characteristic.[well established][VHOG] 2012-09-17 VHOG:0000676 VHOG DOI:10.1111/j.1525-142X.2006.05079.x Devoto SH, Stoiber W, Hammond CL, Steinbacher P, Haslett JR, Barresi MJF, Patterson SE, Adiarte EG and Hughes SM, Generality of vertebrate developmental patterns: evidence for a dermomyotome in fish. Evolution and Development (2006) http://bgee.unil.ch/ UMLS:C1511786 ncithesaurus:Dermomyotome dermamyotome VHOG:0000676 dermomyotomes VHOG:0000676 A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube. The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO] TAO:0000115 ZFA:0000115 heart cone rudimentary heart uberon UBERON:0004291 heart rudiment A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube. GO:0003313 The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO] 2012-08-14 TAO:0000115 TAO ZFIN:curator heart cone GO:0003313 rudimentary heart ZFA:0000115 Dense connective tissue that separates the atria from the ventricles and provides physical support for the heart. It is not a true skeleton, but it does provide structure and support for the heart, as well as isolating the atria from the ventricles. This allows the AV node and AV bundle to delay the wave of depolarisation such that the atria can contract and assist in ventricular filling before the ventricles themselves depolarise and contract (the AV bundle is the only part of the conduction system that passes from the atria to the ventricles in a normal heart). It also allows the valves (bicuspid, tricuspid, semilunar) to keep open by giving them structural support[WP] EMAPA:36645 FMA:9496 Wikipedia:Cardiac_skeleton cardiac fibrous skeleton fibrous skeleton of heart heart fibrous skeleton skeleton of heart uberon anulus fibrosus dexter cordis anulus fibrosus sinister cordis trigona fibrosa trigonum fibrosum dextrum cordis trigonum fibrosum sinistrum cordis UBERON:0004292 cardiac skeleton http://upload.wikimedia.org/wikipedia/commons/5/50/Gray495.png Dense connective tissue that separates the atria from the ventricles and provides physical support for the heart. GO:0003204 Wikipedia:Cardiac_skeleton cardiac fibrous skeleton EMAPA:36645 heart fibrous skeleton GO:0003204 skeleton of heart FMA:9496 anulus fibrosus dexter cordis Wikipedia:Cardiac_skeleton anulus fibrosus sinister cordis Wikipedia:Cardiac_skeleton trigona fibrosa Wikipedia:Cardiac_skeleton trigonum fibrosum dextrum cordis Wikipedia:Cardiac_skeleton trigonum fibrosum sinistrum cordis Wikipedia:Cardiac_skeleton A blood vessel smooth muscle that is part of a respiratory system [Automatically generated definition]. EMAPA:37573 MA:0001806 smooth muscle tissue of blood vessel of respiratory system uberon UBERON:0004297 respiratory system blood vessel smooth muscle A blood vessel smooth muscle that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37573 MA:th smooth muscle tissue of blood vessel of respiratory system OBOL:automatic The embryonic structure that gives rise to the corneal ectoderm EHDAA:938 EMAPA:16322 RETIRED_EHDAA2:0001308 VHOG:0001296 uberon UBERON:0004348 optic eminence The embryonic structure that gives rise to the corneal ectoderm MP:0006305 multilayered ectodermal region at the distal tip of a limb or fin bud necessary for the proper development of the underlying mesenchyme[MP,modified]. Along with the zone of polarizing activity, it is a crucial organizing region during limb development[WP]. note that media, dorsal fins etc have AERs. Distal ectodermal thickening which forms along the anterior-posterior limb axis. Signaling from this region influences proximal-distal patterning of the limb. Structure is missing in some lineages (salamanders, Eleutherodactylus coqui) however morphologically their indistinct distal ectoderm may still be involved in signaling.[AAO] Proliferative region that is part of the developing fin fold or fin.[TAO] relationship loss: subclass proliferative region (TAO:0000098)[TAO] The AER of tetrapods regresses after specification of skeletal progenitors, the AER of teleosts form an elongating fin fold maintaining mesenchyme in plastic proliferating state; maintaining expression of A-P axis genes; interacting with D-V proteins. Genes: AER induced by Fgf10 in mesenchyme. AER secretes Fgf8, which stimulates mitosis in the mesenchyme causing Fgf10 production - positive feedback loop AAO:0010760 EMAPA:32744 NCIT:C34109 TAO:0002146 UMLS:C1516037 Wikipedia:Apical_ectodermal_ridge XAO:0004121 ZFA:0001702 apical epidermal ridge uberon AER crista ectodermalis apicalis UBERON:0004356 apical ectodermal ridge http://upload.wikimedia.org/wikipedia/commons/5/56/Limbbuddiagram.jpg multilayered ectodermal region at the distal tip of a limb or fin bud necessary for the proper development of the underlying mesenchyme[MP,modified]. Along with the zone of polarizing activity, it is a crucial organizing region during limb development[WP]. MP:0001676 Wikipedia:Apical_ectodermal_ridge Distal ectodermal thickening which forms along the anterior-posterior limb axis. Signaling from this region influences proximal-distal patterning of the limb. Structure is missing in some lineages (salamanders, Eleutherodactylus coqui) however morphologically their indistinct distal ectoderm may still be involved in signaling.[AAO] 2012-06-20 AAO:0010760 AAO AAO:EJS Proliferative region that is part of the developing fin fold or fin.[TAO] 2012-08-14 TAO:0002146 TAO ZFIN:curator relationship loss: subclass proliferative region (TAO:0000098)[TAO] 2012-08-14 TAO:0002146 TAO The AER of tetrapods regresses after specification of skeletal progenitors, the AER of teleosts form an elongating fin fold PMID:20574421 UMLS:C1516037 ncithesaurus:Apical_Ectodermal_Ridge apical epidermal ridge XAO:0004121 AER MP:0001676 crista ectodermalis apicalis Wikipedia:Apical_ectodermal_ridge An outgrowth on the lateral trunk of the embryo that develops into a limb or paired fin. The limb/fin bud is divided into ectoderm and mesenchyme[cjm, modified from MP]. The tetrapod limb is derived from a posterior part of the fin endoskeleton of elasmobranchs and basal bony fish, the so-called metapterygium, a series of endoskeletal elements that is the first to form in the developing paired fins. (...) In addition, there is an independent endoskeletal element called the protopterygium that develops anterior to the metapterygium in many basal fishes (e.g., the bichir and sturgeon). Teleosts have lost the metapterygium whereas the sarcopterygians, on the other hand, have lost the protopterygium. Sarcopterygians thus develop all their endoskeletal structures from the metapterygium and consequently the tetrapod limb skeleton is derived from the metapterygium.[uncertain][VHOG] VHOG:0001258 limb - fin bud paired appendage bud paired limb/fin bud uberon UBERON:0004357 Genes: In limb buds of chick and mouse, Shh expression is activated as soon as there is a morphological bud, whereas in S. canicula fin buds, consistent with reported data in other cartilaginous fishes, Shh is transcribed late in fin development[PMID:17187056] paired limb/fin bud An outgrowth on the lateral trunk of the embryo that develops into a limb or paired fin. The limb/fin bud is divided into ectoderm and mesenchyme[cjm, modified from MP]. ISBN:9780878932504 MP:0005650 https://orcid.org/0000-0002-6601-2165 The tetrapod limb is derived from a posterior part of the fin endoskeleton of elasmobranchs and basal bony fish, the so-called metapterygium, a series of endoskeletal elements that is the first to form in the developing paired fins. (...) In addition, there is an independent endoskeletal element called the protopterygium that develops anterior to the metapterygium in many basal fishes (e.g., the bichir and sturgeon). Teleosts have lost the metapterygium whereas the sarcopterygians, on the other hand, have lost the protopterygium. Sarcopterygians thus develop all their endoskeletal structures from the metapterygium and consequently the tetrapod limb skeleton is derived from the metapterygium.[uncertain][VHOG] 2012-09-17 VHOG:0001258 VHOG DOI:10.1002/jez.1100 Wagner GP, Chiu C, The tetrapod limb: A hypothesis on its origin. J Exp Zool (Mol Dev Evol) (2001) http://bgee.unil.ch/ limb - fin bud VHOG:0001258 paired limb/fin bud VHOG:0001258 The first of the series of pharyngeal arches that develop into jaw bones or their homologs, and their associated nerves and arteries The first of the series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO] the first arch which contributes to development of mastication muscles, maxilla, mandible, incus, malleus, Meckel's cartilage, trigeminal nerve, and maxillary artery A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] 1 AAO:0010364 CALOHA:TS-2089 EHDAA2:0000006 EHDAA:573 EMAPA:16118 FMA:293019 MFMO:0000095 NCIT:C34175 SCTID:308767008 TAO:0001595 UMLS:C1517197 VHOG:0000296 Wikipedia:First_pharyngeal_arch XAO:0000097 ZFA:0001612 1st pharyngeal arch branchial arch 1 first branchial arch first pharyngeal arch first visceral arch mandibular arch visceral arch 1 uberon 1st arch 1st visceral arch arcus pharyngeus primus UBERON:0004362 pharyngeal arch 1 http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray48.png The first of the series of pharyngeal arches that develop into jaw bones or their homologs, and their associated nerves and arteries http://orcid.org/0000-0002-6601-2165 The first of the series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO] 2012-06-20 AAO:0010364 AAO XAO:EJS the first arch which contributes to development of mastication muscles, maxilla, mandible, incus, malleus, Meckel's cartilage, trigeminal nerve, and maxillary artery MP:0006337,MGI:smb A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] 2012-09-17 VHOG:0000296 VHOG DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005) http://bgee.unil.ch/ UMLS:C1517197 ncithesaurus:First_Pharyngeal_Arch branchial arch 1 first branchial arch first visceral arch visceral arch 1 1st arch EHDAA2:0000006 1st visceral arch VHOG:0000296 arcus pharyngeus primus Wikipedia:First_pharyngeal_arch One of a series of paired embryological vascular structures formed within a pharyngeal arch; in the adult, some of these vessels give rise to the great vessels[MP] add specific artery derivatives Do not confuse with arch of aorta. Paired vessels arching from the ventral to the dorsal aorta through the pharyngeal arches. [TFD][VHOG] When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG] Number varies - Lampreys have 8, hagfishes 15; only up to 6 appear in embryonic development in most gnathostome fishes and all tetrapods The third, fourth, and sixth arches, along with the seventh intersegmental arteries and the left dorsal aorta, are the primary contributors to the normal aortic arch and its major thoracic branches UBERON:0004342 AAO:0010414 EFO:0003695 EHDAA2:0000186 EHDAA:398 EHDAA:7327 EMAPA:16684 NCIT:C32123 TAO:0005004 UMLS:C0003489 VHOG:0000122 Wikipedia:Aortic_arches XAO:0000341 ZFA:0005004 PAA aortic arch aortic arches branchial aortic arches branchial arch artery embryonic aortic arch artery pharyngeal arch artery uberon a. arcuum pharyngeorum aortic arch artery arteriae arcuum pharyngeorum branchial aortic arches pharyngeal arch arteries pharyngeal arch artery UBERON:0004363 pharyngeal arch artery http://upload.wikimedia.org/wikipedia/commons/8/84/Gray473.png ZFA One of a series of paired embryological vascular structures formed within a pharyngeal arch; in the adult, some of these vessels give rise to the great vessels[MP] MP:0002672 Paired vessels arching from the ventral to the dorsal aorta through the pharyngeal arches. [TFD][VHOG] 2012-09-17 VHOG:0000122 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/aortic+arches When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG] 2012-09-17 VHOG:0000122 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620 http://bgee.unil.ch/ UMLS:C0003489 ncithesaurus:Aortic_Arch PAA MP:0002672 aortic arch ZFA:0005004 aortic arches ZFA:0005004 branchial aortic arches ZFIN:ZDB-PUB-080512-6 branchial arch artery EMAPA:16684 embryonic aortic arch artery EMAPA:16684 MP:0002672 pharyngeal arch artery MP:0002672 a. arcuum pharyngeorum Wikipedia:Aortic_arches aortic arch artery EMAPA:16684 arteriae arcuum pharyngeorum Wikipedia:Aortic_arches branchial aortic arches ZFA:0005004 ZFIN:ZDB-PUB-080512-6 pharyngeal arch arteries pharyngeal arch artery VHOG:0000122 A transparent homogeneous acellular layer found between the substantia propria and the endothelial layer of the cornea[MP]. Acellular anatomical structure composed of collagen, Descemet's membrane is secreted as a basement membrane of the corneal endothelium. Located between the stroma and the corneal endothelium, it is approximately 0.15 micrometer thick at 6 months post-fertilization.[ZFIN] EMAPA:18804 FMA:58309 GAID:894 MA:0001246 MESH:D003886 NCIT:C32454 SCTID:281076002 TAO:0002157 UMLS:C0011665 Wikipedia:Descemet%27s_membrane ZFA:0001686 Descemet membrane Descemet's posterior elastic lamina lamina limitans posterior lamina limitans posterior corneae posterior limiting lamina posterior limiting lamina of cornea posterior limiting membrane uberon UBERON:0004367 The strong, resistant, thin, noncellular fourth layer of the cornea, located between the endothelium (from which it is secreted) and the stroma. (Cline et al., Dictionary of Visual Science, 4th ed) Descemet's membrane https://github.com/obophenotype/uberon/issues/15 Cline et al lexical A transparent homogeneous acellular layer found between the substantia propria and the endothelial layer of the cornea[MP]. MP:0004285 https://github.com/obophenotype/uberon/issues/15 Acellular anatomical structure composed of collagen, Descemet's membrane is secreted as a basement membrane of the corneal endothelium. Located between the stroma and the corneal endothelium, it is approximately 0.15 micrometer thick at 6 months post-fertilization.[ZFIN] 2016-05-01 TAO:0002157 ZFIN ORCiD:0000-0001-9114-8737 ZFIN:ZDB-PUB-061010-3 UMLS:C0011665 ncithesaurus:Descemet_s_Membrane Descemet's posterior elastic lamina FMA:58309 lamina limitans posterior FMA:58309 lamina limitans posterior corneae FMA:58309 FMA:TA posterior limiting lamina MA:0001246 posterior limiting lamina of cornea FMA:58309 posterior limiting membrane ZFA:0001686 A transparent homogeneous acellular layer, 6 to 9 um thick, lying between the basal lamina of the outer layer of stratified epithelium and the substantia propria of the cornea; it is considered to be a basement membrane. Acellular anatomical structure that is the zone of collagen fibers adjacent the basement membrane of the corneal epithelium.[TAO] Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals FMA:58273 MA:0001240 NCIT:C32226 SCTID:281075003 TAO:0002155 UMLS:C0229127 Wikipedia:Bowman%27s_membrane ZFA:0001684 Bowman's anterior elastic lamina Bowman's layer Bowman's membrane anterior elastic lamina anterior limiting lamina anterior limiting lamina of cornea lamina limitans anterior (cornea) lamina limitans anterior corneae uberon Reichert's membrane anterior limiting membrane UBERON:0004370 anterior limiting lamina of cornea lexical A transparent homogeneous acellular layer, 6 to 9 um thick, lying between the basal lamina of the outer layer of stratified epithelium and the substantia propria of the cornea; it is considered to be a basement membrane. ncithesaurus:Bowman_s_Membrane Acellular anatomical structure that is the zone of collagen fibers adjacent the basement membrane of the corneal epithelium.[TAO] 2012-08-14 TAO:0002155 TAO ZFIN:ZDB-PUB-061010-3 UMLS:C0229127 ncithesaurus:Bowman_s_Membrane Bowman's anterior elastic lamina FMA:58273 Bowman's layer FMA:58273 Bowman's membrane FMA:58273 anterior elastic lamina ZFA:0001684 anterior limiting lamina MA:0001240 anterior limiting lamina of cornea FMA:58273 lamina limitans anterior (cornea) FMA:58273 lamina limitans anterior corneae FMA:58273 FMA:TA Reichert's membrane http://sourceforge.net/tracker/?func=detail&aid=2956371&group_id=76834&atid=974957 anterior limiting membrane ZFA:0001684 A bone that is part of an appendage [Automatically generated definition]. appendage bone bone of appendage bone of free segment of appendicular skeleton uberon UBERON:0004375 bone of free limb or fin A bone that is part of an appendage [Automatically generated definition]. OBOL:automatic One of three main pairs of arteries and their branches, which irrigate the cerebrum of the brain. Part of the internal carotid containing many branches supplying blood to the chorioid plexuses of the brain.[AAO] relationship loss: part_of internal carotid (AAO:0010219)[AAO] in AAO this is part_of the internal carotid, but in humans the PCA intervenes for some cerebral arteries. Proper comparative review required AAO:0010493 BTO:0005205 CALOHA:TS-0126 EHDAA2:0000233 EHDAA:5294 EMAPA:18613 GAID:484 MA:0002562 MESH:D002536 NCIT:C12691 SCTID:181308008 UMLS:C0007770 Wikipedia:Cerebral_artery XAO:0000367 uberon UBERON:0004449 cerebral artery One of three main pairs of arteries and their branches, which irrigate the cerebrum of the brain. Wikipedia:Cerebral_artery Part of the internal carotid containing many branches supplying blood to the chorioid plexuses of the brain.[AAO] 2012-06-20 AAO:0010493 AAO AAO:BJB relationship loss: part_of internal carotid (AAO:0010219)[AAO] 2012-06-20 AAO:0010493 AAO in AAO this is part_of the internal carotid, but in humans the PCA intervenes for some cerebral arteries. Proper comparative review required AAO UMLS:C0007770 ncithesaurus:Cerebral_Artery A vertebra in the trunk or cervical region. Includes all cervical, thoracic and lumbar vertebrae, but excludes caudal vertebra. In humans, there are 24 presacral vertebrae (7 cervical, 12 thoracic, and 5 lumbar) it's not clear if the XAO class belongs here or below EMAPA:37722 MA:0002869 XAO:0003077 uberon presacral vertebra UBERON:0004451 trunk or cervical vertebra A vertebra in the trunk or cervical region. Includes all cervical, thoracic and lumbar vertebrae, but excludes caudal vertebra. UBERONREF:0000006 it's not clear if the XAO class belongs here or below XAO EMAPA:37722 MA:th presacral vertebra MA:0002869 An embryo at the neurula stage. UBERON:0007013 BILA:0000061 BTO:0001766 NCIT:C34229 UMLS:C1518306 neurula uberon UBERON:0004455 neurula embryo An embryo at the neurula stage. http://orcid.org/0000-0002-6601-2165 UMLS:C1518306 ncithesaurus:Neurula neurula BTO:0001766 Sum of all sensory systems in an organism. note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs FMA:78499 sense organ system uberon UBERON:0004456 entire sense organ system Sum of all sensory systems in an organism. http://orcid.org/0000-0002-6601-2165 sense organ system FMA:78499 Any collection of skeletal muscles that is part of a head [Automatically generated definition]. EMAPA:18171 FMA:71287 head musculature muscle group of head muscles of head musculi capitis set of muscles of head uberon UBERON:0004461 This class is restricted to skeletal muscles that attach to the cranial skeleton. This seems to be consistent with FMA and EMAPA usage. Note that by definition this excludes invertebrate head musculature. It corresponds to the individual muscle organ term UBERON:0002376 skeletal musculature of head https://github.com/obophenotype/mouse-anatomy-ontology/issues/4 https://github.com/obophenotype/uberon/issues/1405 Any collection of skeletal muscles that is part of a head [Automatically generated definition]. OBOL:automatic head musculature FMA:71287 muscle group of head FMA:71287 muscles of head FMA:71287 musculi capitis FMA:71287 FMA:TA set of muscles of head FMA:71287 Any collection of muscles that is part of a thorax [Automatically generated definition]. BTO and FMA do not mean precisely the same thing here. BTO thorax muscle is a pectoral muscle or diaphragm BTO:0000508 EMAPA:37260 FMA:71293 muscle group of thorax muscles of thorax musculi thoracis set of muscles of thorax thoracic musculature uberon UBERON:0004464 musculature of thorax Any collection of muscles that is part of a thorax [Automatically generated definition]. OBOL:automatic BTO and FMA do not mean precisely the same thing here. BTO thorax muscle is a pectoral muscle or diaphragm BTO EMAPA:37260 MA:th muscle group of thorax FMA:71293 muscles of thorax FMA:71293 musculi thoracis FMA:71293 FMA:TA set of muscles of thorax FMA:71293 thoracic musculature FMA:71293 Any collection of muscles that is part of a neck [Automatically generated definition]. AAO:0000091 EMAPA:36050 FMA:71290 MESH:D009334 cervical muscles muscle group of neck muscles of neck musculi cervicis musculi colli neck musculature set of muscles of neck uberon UBERON:0004465 musculature of neck Any collection of muscles that is part of a neck [Automatically generated definition]. OBOL:automatic cervical muscles AAO:0000091 muscle group of neck FMA:71290 muscles of neck FMA:71290 musculi cervicis FMA:71290 FMA:TA musculi colli FMA:71290 FMA:TA neck musculature FMA:71290 set of muscles of neck FMA:71290 FMA:33061 muscle group of vertebral column uberon UBERON:0004468 set of muscles of vertebral column muscle group of vertebral column FMA:33061 Any collection of muscles that is part of a back [Automatically generated definition]. FMA:71291 muscle group of back muscles of back musculi dorsi set of muscles of back uberon UBERON:0004469 musculature of back Any collection of muscles that is part of a back [Automatically generated definition]. OBOL:automatic muscle group of back FMA:71291 muscles of back FMA:71291 musculi dorsi FMA:71291 FMA:TA set of muscles of back FMA:71291 Any collection of muscles that is part of a pelvic girdle [Automatically generated definition]. we merge two FMA classes here UBERON:0004485 UBERON:0005633 AAO:0000427 EHDAA2:0001429 EMAPA:18184 FMA:50205 FMA:50248 muscle group of pelvic girdle muscle group of pelvis pelvic girdle muscle system pelvic girdle muscles pelvic girdle musculature set of muscles of pelvic girdle uberon muscular system of pelvis set of muscles of pelvis UBERON:0004470 musculature of pelvic girdle Any collection of muscles that is part of a pelvic girdle [Automatically generated definition]. OBOL:automatic we merge two FMA classes here FMA muscle group of pelvic girdle FMA:50205 muscle group of pelvis FMA:50248 pelvic girdle muscle system EHDAA2:0001429 pelvic girdle muscles AAO:0000427 pelvic girdle musculature FMA:50205 set of muscles of pelvic girdle FMA:50205 muscular system of pelvis FMA:50248 set of muscles of pelvis FMA:50248 Any collection of muscles that is part of a face. originally created to reflect the distinction drawn in FMA between a facial muscle and the entire musculature of the face. However, naming both does not serve any particular purpose FMA:71288 entire facial musculature facial muscles muscle group of face musculi faciei uberon set of facial muscles set of muscles of face UBERON:0004473 musculature of face Any collection of muscles that is part of a face. OBOL:automatic entire facial musculature https://orcid.org/0000-0002-6601-2165 facial muscles FMA:71288 muscle group of face FMA:71288 musculi faciei FMA:71288 FMA:TA set of facial muscles FMA:71288 set of muscles of face FMA:71288 The collection of muscles that are part of the larynx. currently defined by location rather than attachment FMA:264611 FMA:46616 MESH:D007821 Wikipedia:Muscles_of_larynx laryngeal muscles laryngeal muscles set muscle group of larynx set of laryngeal muscles set of muscles of larynx uberon UBERON:0004478 musculature of larynx The collection of muscles that are part of the larynx. http://orcid.org/0000-0002-6601-2165 laryngeal muscles FMA:46616 laryngeal muscles set FMA:46616 muscle group of larynx FMA:46616 set of laryngeal muscles FMA:46616 set of muscles of larynx FMA:264611 Any collection of muscles that is part of a trunk [Automatically generated definition]. currently defined by location rather than attachment AAO:0011572 EFO:0003531 FMA:50187 muscle group of trunk set of muscles of trunk uberon muscular system of trunk UBERON:0004479 musculature of trunk Any collection of muscles that is part of a trunk [Automatically generated definition]. OBOL:automatic muscle group of trunk FMA:50187 set of muscles of trunk FMA:50187 muscular system of trunk FMA:50187 A portion of cardiac muscle tissue that is part of an atrium [Automatically generated definition]. in GO, this is equivalent to the atrial myocardium, but FMA distinguishes these two. Consider merging. FMA:7283 atrial cardiac muscle tissue atrial heart muscle cardiac atrium muscle uberon atrial myocardium UBERON:0004490 cardiac muscle tissue of atrium A portion of cardiac muscle tissue that is part of an atrium [Automatically generated definition]. OBOL:automatic in GO, this is equivalent to the atrial myocardium, but FMA distinguishes these two. Consider merging. GO atrial cardiac muscle tissue GO:0055009 atrial heart muscle GO:0055009 cardiac atrium muscle GO:0055009 atrial myocardium GO:0055009 GOC:mtg_heart A portion of cardiac muscle tissue that is part of a interatrial septum [Automatically generated definition]. FMA:84083 interatrial septum cardiac muscle tissue interatrial septum heart muscle interatrial septum muscle interatrial septum myocardium uberon UBERON:0004491 cardiac muscle tissue of interatrial septum A portion of cardiac muscle tissue that is part of a interatrial septum [Automatically generated definition]. OBOL:automatic interatrial septum cardiac muscle tissue http://orcid.org/0000-0002-6601-2165 interatrial septum heart muscle http://orcid.org/0000-0002-6601-2165 interatrial septum muscle http://orcid.org/0000-0002-6601-2165 interatrial septum myocardium http://orcid.org/0000-0002-6601-2165 A portion of cardiac muscle tissue that is part of a cardiac septum [Automatically generated definition]. FMA:226279 cardiac septum cardiac muscle tissue cardiac septum heart muscle cardiac septum muscle cardiac septum myocardium uberon UBERON:0004492 cardiac muscle tissue of cardiac septum A portion of cardiac muscle tissue that is part of a cardiac septum [Automatically generated definition]. OBOL:automatic cardiac septum cardiac muscle tissue http://orcid.org/0000-0002-6601-2165 cardiac septum heart muscle http://orcid.org/0000-0002-6601-2165 cardiac septum muscle http://orcid.org/0000-0002-6601-2165 cardiac septum myocardium http://orcid.org/0000-0002-6601-2165 A portion of cardiac muscle tissue that is part of a myocardium [Automatically generated definition]. Note placement of MA class based on parthood relationship EMAPA:32688 FMA:261726 MA:0002441 uberon UBERON:0004493 cardiac muscle tissue of myocardium MA A portion of cardiac muscle tissue that is part of a myocardium [Automatically generated definition]. OBOL:automatic A portion of skeletal muscle tissue that is part of a diaphragm [Automatically generated definition]. FMA:261898 uberon UBERON:0004495 skeletal muscle tissue of diaphragm A portion of skeletal muscle tissue that is part of a diaphragm [Automatically generated definition]. OBOL:automatic A muscle that is attached to a vertebra of the vertebral column. FMA:22594 vertebral column muscle uberon UBERON:0004518 muscle of vertebral column A muscle that is attached to a vertebra of the vertebral column. https://orcid.org/0000-0002-6601-2165 vertebral column muscle FMA:22594 A vasculature that is part of a muscle organ [Automatically generated definition]. FMA:87123 muscular organ vasculature uberon UBERON:0004521 vasculature of muscle organ A vasculature that is part of a muscle organ [Automatically generated definition]. OBOL:automatic muscular organ vasculature FMA:87123 A vasculature that is part of a musculoskeletal system [Automatically generated definition]. FMA:239607 uberon UBERON:0004522 vasculature of musculoskeletal system A vasculature that is part of a musculoskeletal system [Automatically generated definition]. OBOL:automatic Anatomical system that has as its parts the heart and blood vessels. we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph. The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG] AAO:0011001 BILA:0000016 BTO:0000088 CALOHA:TS-1297 EFO:0000791 EHDAA2:0000216 EHDAA:394 EMAPA:16104 EMAPA:16370 EV:0100017 FMA:7161 GAID:467 MA:0000010 MAT:0000016 MESH:D002319 MIAA:0000016 NCIT:C12686 OpenCyc:Mx4rvVjzG5wpEbGdrcN5Y29ycA SCTID:278198007 TAO:0000010 UMLS:C0007226 VHOG:0000302 WikipediaCategory:Cardiovascular_system XAO:0000100 XAO:0001010 ZFA:0000010 uberon CV system Herz und Gefaesssystem UBERON:0004535 cardiovascular system Anatomical system that has as its parts the heart and blood vessels. BTO:0000088 The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG] 2012-09-17 VHOG:0000302 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.451 http://bgee.unil.ch/ UMLS:C0007226 ncithesaurus:Cardiovascular_System CV system BTO:0000088 Herz und Gefaesssystem BTO:0000088 A vascular network consisting of blood vessels. TAO:0001079 ZFA:0001079 blood vascular network set of blood vessels uberon blood system blood vessel system blood vessels UBERON:0004537 blood vasculature A vascular network consisting of blood vessels. https://orcid.org/0000-0002-6601-2165 blood vessels TAO:0001079 An eye that is part of a left side of organism [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EMAPA:37362 FMA:12515 MA:0002949 NCIT:C119334 SCTID:362503005 left eyeball left orbital part of face left orbital region uberon UBERON:0004548 left eye An eye that is part of a left side of organism [Automatically generated definition]. OBOL:automatic EMAPA:37362 MA:th left eyeball FMA:12515 left orbital part of face FMA:54450 left orbital region FMA:54450 An eye that is part of a right side of organism [Automatically generated definition]. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EMAPA:37363 FMA:12514 MA:0002950 NCIT:C119333 SCTID:362502000 right eyeball right orbital part of face right orbital region uberon UBERON:0004549 right eye An eye that is part of a right side of organism [Automatically generated definition]. OBOL:automatic EMAPA:37363 MA:th right eyeball FMA:12514 right orbital part of face FMA:54449 right orbital region FMA:54449 The part of the arterial system which carries oxygenated blood away from the heart to the body, and returns deoxygenated blood back to the heart. FMA:45623 Wikipedia:Systemic_circulation#Arteries systemic arterial circulatory system uberon UBERON:0004571 systemic arterial system MA-inferred The part of the arterial system which carries oxygenated blood away from the heart to the body, and returns deoxygenated blood back to the heart. Wikipedia:Systemic_circulation#Arteries http://orcid.org/0000-0002-6601-2165 systemic arterial circulatory system FMA:45623 The part of the cardiovascular system consisting of all arteries. The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] BTO:0004690 EHDAA2:0000143 EHDAA:396 EMAPA:16201 EMAPA:16371 MA:0002719 SCTID:362030008 VHOG:0000273 uberon UBERON:0004572 arterial system MA The part of the cardiovascular system consisting of all arteries. https://orcid.org/0000-0002-6601-2165 The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] 2012-09-17 VHOG:0000273 VHOG DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005) http://bgee.unil.ch/ An artery of the systemic circulation, which is the part of the cardiovascular system which carries oxygenated blood away from the heart, to the body, and returns deoxygenated blood back to the heart. EMAPA:37126 FMA:66464 Wikipedia:Artery#Systemic_arteries systemic arterial subtree uberon UBERON:0004573 systemic artery An artery of the systemic circulation, which is the part of the cardiovascular system which carries oxygenated blood away from the heart, to the body, and returns deoxygenated blood back to the heart. Wikipedia:Artery#Systemic_arteries http://orcid.org/0000-0002-6601-2165 EMAPA:37126 MA:th systemic arterial subtree FMA:66464 The part of the venous system that drains the general body tissues[Kardong] In human anatomy, the systemic venous system refers to veins that drain into the right atrium without passing through two vascular beds (i.e. they originate from a set of capillaries and do not pass through a second set of capillaries before reaching the right side of the heart). The term systemic venous system is often used to differentiate veins from veins that drain the pulmonary system (the pulmonary venous system) and veins that drain the digestive tract (the portal venous system). Large veins that are considered part of the systemic venous system are the: Superior vena cava; Inferior vena cava[WP] Subdivision of cardiovascular system which has as its parts the right side of heart, the superior vena cava and the inferior vena cava[FMA] The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] FMA:45626 Wikipedia:Systemic_venous_system systemic venous circulatory system uberon UBERON:0004581 systemic venous system The part of the venous system that drains the general body tissues[Kardong] ISBN:0073040584 Wikipedia:Systemic_venous_system In human anatomy, the systemic venous system refers to veins that drain into the right atrium without passing through two vascular beds (i.e. they originate from a set of capillaries and do not pass through a second set of capillaries before reaching the right side of the heart). The term systemic venous system is often used to differentiate veins from veins that drain the pulmonary system (the pulmonary venous system) and veins that drain the digestive tract (the portal venous system). Large veins that are considered part of the systemic venous system are the: Superior vena cava; Inferior vena cava[WP] Wikipedia:Systemic_venous_system Subdivision of cardiovascular system which has as its parts the right side of heart, the superior vena cava and the inferior vena cava[FMA] FMA FMA:45626 The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] 2012-09-17 VHOG:0000277 VHOG DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005) http://bgee.unil.ch/ systemic venous circulatory system FMA:45626 The part of the cardiovascular system consisting of all venous vessels. In vertebrates with a double circulation, this can be divided into systemic and pulmonary portions. The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] BTO:0004692 EHDAA2:0002171 EHDAA:486 EMAPA:16240 MA:0002720 NCIT:C33858 SCTID:362060003 UMLS:C1267406 VHOG:0000277 vein system uberon UBERON:0004582 venous system MA The part of the cardiovascular system consisting of all venous vessels. In vertebrates with a double circulation, this can be divided into systemic and pulmonary portions. https://orcid.org/0000-0002-6601-2165 The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] 2012-09-17 VHOG:0000277 VHOG DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005) http://bgee.unil.ch/ UMLS:C1267406 ncithesaurus:Venous_System An endothelium that lines the blood vasculature. Other endothelia may line lymph vessels, the heart BTO:0000766 CALOHA:TS-2155 EMAPA:35176 MA:0000709 NCIT:C53395 TAO:0005257 UMLS:C1706972 ZFA:0005257 uberon UBERON:0004638 blood vessel endothelium An endothelium that lines the blood vasculature. Other endothelia may line lymph vessels, the heart https://orcid.org/0000-0002-6601-2165 UMLS:C1706972 ncithesaurus:Blood_Vessel_Endothelium An anatomical wall that is part of an aorta, enclosing the luminal space. EMAPA:35139 FMA:14156 MA:0002901 aortic wall wall of aorta uberon UBERON:0004663 aorta wall An anatomical wall that is part of an aorta, enclosing the luminal space. http://orcid.org/0000-0002-6601-2165 aortic wall FMA:14156 wall of aorta FMA:14156 the outermost layer of the aorta wall, containing connective tissue and collagen and elastic fibers EMAPA:35136 FMA:14283 MA:0002902 SCTID:24996002 tunica adventitia of aorta uberon UBERON:0004664 aorta tunica adventitia the outermost layer of the aorta wall, containing connective tissue and collagen and elastic fibers ISBN:0-683-40008-8 MP:0009871 tunica adventitia of aorta FMA:14283 The muscular portion of the wall between the two lower chambers of the heart The muscular septum is the lower part of the ventricular septum[GO] UBERON:0004144 muscular septum EHDAA2:0000885 EHDAA:2607 EMAPA:18247 FMA:7134 MA:0002940 RETIRED_EHDAA2:0000888 cardiac ventricular muscular septum muscular interventricular septum muscular part interventricular septum muscular part of interventricular septum pars muscularis (septi interventricularis) pars muscularis septi interventricularis septum membranaceum ventricular muscular septum uberon muscular interventricular septum UBERON:0004667 interventricular septum muscular part The muscular portion of the wall between the two lower chambers of the heart Wikipedia:Interventricular_septum#Portions http://orcid.org/0000-0002-6601-2165 The muscular septum is the lower part of the ventricular septum[GO] GO:0003150 muscular septum GO:0003150 cardiac ventricular muscular septum http://orcid.org/0000-0002-6601-2165 muscular interventricular septum FMA:7134 muscular part of interventricular septum FMA:7134 pars muscularis (septi interventricularis) FMA:7134 pars muscularis septi interventricularis FMA:7134 FMA:TA septum membranaceum muscular interventricular septum MA:0002940 The raphe nuclei are thin plates of cells in and immediately adjacent to the sagittal plane. BAMS:RA EMAPA:35721 FMA:84017 MA:0003147 MESH:A08.186.211.132.659.632 NCIT:C97335 NLXANAT:20090205 TAO:0001429 UMLS:C0034671 Wikipedia:Raphe_nuclei ZFA:0001429 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=2495 nuclei raphes raphe nuclei raphe nuclei set uberon nuclei raphes raphe cluster raphe nucleus raphe of mesenchephalon set of raphe nuclei UBERON:0004684 we treat NR obscurus, NR magnus etc as parts of the raphe nuclei. This is consistent with treatment in FMA, where the class is 'set of raphe nuclei' raphe nuclei http://upload.wikimedia.org/wikipedia/commons/9/94/Gray694.png GO Wikipedia Wikipedia The raphe nuclei are thin plates of cells in and immediately adjacent to the sagittal plane. NLXANAT:20090205 https://sourceforge.net/tracker/?func=detail&aid=3248146&group_id=36855&atid=440764 UMLS:C0034671 ncithesaurus:Raphe_Nuclei nuclei raphes FMA:84017 FMA:TA raphe nuclei FMA:84017 raphe nuclei NLXANAT:20090205 raphe nuclei set FMA:84017 nuclei raphes Wikipedia:Raphe_nuclei raphe cluster Wikipedia:Raphe_nuclei raphe nucleus ZFA:0001429 raphe of mesenchephalon BAMS:RA set of raphe nuclei FMA:84017 The costocervical trunk arises from the upper and back part of the subclavian artery, behind the scalenus anterior on the right side, and medial to that muscle on the left side. Passing backward, it splits into the deep cervical artery and the supreme intercostal artery (or the Highest intercostal artery), which descends behind the pleura in front of the necks of the first and second ribs, and anastomoses with the first aortic intercostal (3rd posterior intercostal artery). As it crosses the neck of the first rib it lies medial to the anterior division of the first thoracic nerve, and lateral to the first thoracic ganglion of the sympathetic trunk. In the first intercostal space, it gives off a branch which is distributed in a manner similar to the distribution of the aortic intercostals. The branch for the second intercostal space usually joins with one from the highest aortic intercostal artery. This branch is not constant, but is more commonly found on the right side; when absent, its place is supplied by an intercostal branch from the aorta. Each intercostal gives off a posterior branch which goes to the posterior vertebral muscles, and sends a small spinal branch through the corresponding intervertebral foramen to the medulla spinalis and its membranes. [WP,unvetted]. EMAPA:37496 FMA:10636 MA:0001939 SCTID:244225009 Wikipedia:Costocervical_trunk costocervical trunk trunk of costocervical artery uberon truncus costocervicalis UBERON:0004688 costo-cervical trunk http://upload.wikimedia.org/wikipedia/commons/b/b3/Costocervical_trunk_with_branches.png The costocervical trunk arises from the upper and back part of the subclavian artery, behind the scalenus anterior on the right side, and medial to that muscle on the left side. Passing backward, it splits into the deep cervical artery and the supreme intercostal artery (or the Highest intercostal artery), which descends behind the pleura in front of the necks of the first and second ribs, and anastomoses with the first aortic intercostal (3rd posterior intercostal artery). As it crosses the neck of the first rib it lies medial to the anterior division of the first thoracic nerve, and lateral to the first thoracic ganglion of the sympathetic trunk. In the first intercostal space, it gives off a branch which is distributed in a manner similar to the distribution of the aortic intercostals. The branch for the second intercostal space usually joins with one from the highest aortic intercostal artery. This branch is not constant, but is more commonly found on the right side; when absent, its place is supplied by an intercostal branch from the aorta. Each intercostal gives off a posterior branch which goes to the posterior vertebral muscles, and sends a small spinal branch through the corresponding intervertebral foramen to the medulla spinalis and its membranes. [WP,unvetted]. Wikipedia:Costocervical_trunk EMAPA:37496 MA:th costocervical trunk FMA:10636 trunk of costocervical artery FMA:10636 truncus costocervicalis Wikipedia:Costocervical_trunk A portion of smooth muscle tissue that is part of an arterial system [Automatically generated definition]. EMAPA:36503 MA:0000704 uberon UBERON:0004695 arterial system smooth muscle A portion of smooth muscle tissue that is part of an arterial system [Automatically generated definition]. OBOL:automatic A portion of smooth muscle tissue that is part of a venous system [Automatically generated definition]. EMAPA:36613 MA:0000715 uberon UBERON:0004696 venous system smooth muscle A portion of smooth muscle tissue that is part of a venous system [Automatically generated definition]. OBOL:automatic An endothelium that is part of a outflow tract [Automatically generated definition]. It is assumed that during evolution, a circulatory system composed of the heart and endothelial tubular system first formed in vertebrates, medial smooth muscle then appeared for regulation of the system, and innervation of the muscle tissue took place. This sequence of development assumed for phylogenesis is actually realized in the ontogenetic processes.[well established][VHOG] MA:0000490 VHOG:0001524 uberon UBERON:0004699 outflow tract endothelium An endothelium that is part of a outflow tract [Automatically generated definition]. OBOL:automatic It is assumed that during evolution, a circulatory system composed of the heart and endothelial tubular system first formed in vertebrates, medial smooth muscle then appeared for regulation of the system, and innervation of the muscle tissue took place. This sequence of development assumed for phylogenesis is actually realized in the ontogenetic processes.[well established][VHOG] 2012-09-17 VHOG:0001524 VHOG DOI:10.1254/jjp.87.253 Shigei T, Tsuru H, Ishikawa N, Yoshioka K, Absence of endothelium in invertebrate blood vessels: significance of endothelium and sympathetic nerve/medial smooth muscle in the vertebrate vascular system. Japanese Journal of Pharmacology (2001) http://bgee.unil.ch/ An endothelium that is part of an arterial system [Automatically generated definition]. EMAPA:35145 MA:0000703 NCIT:C49329 UMLS:C1706849 uberon UBERON:0004700 arterial system endothelium An endothelium that is part of an arterial system [Automatically generated definition]. OBOL:automatic UMLS:C1706849 ncithesaurus:Arterial_System_Endothelium An endothelium that is part of a venous system [Automatically generated definition]. EMAPA:35907 MA:0000714 NCIT:C49320 UMLS:C1710626 uberon UBERON:0004701 venous system endothelium An endothelium that is part of a venous system [Automatically generated definition]. OBOL:automatic UMLS:C1710626 ncithesaurus:Venous_System_Endothelium A blood vessel endothelium that is part of a respiratory system [Automatically generated definition]. EMAPA:35732 MA:0001805 uberon UBERON:0004702 respiratory system blood vessel endothelium A blood vessel endothelium that is part of a respiratory system [Automatically generated definition]. OBOL:automatic a transient fetal dilation of the distal (or cranial) heart tube located where the arterial trunk joins the ventral roots of the aortic arches TODO - check relationship to bulbus arteriosus A pear shaped chamber that functions as a capacitor, maintaining continuous blood flow into the gill arches. The bulbus arteriosus has three distinct layers. Hu et al. 2000.[TAO] EHDAA2:0000197 EHDAA:438 EHDAA:768 EMAPA:16333 FMA:70300 NCIT:C34114 SCTID:361525002 UMLS:C1284055 Wikipedia:Bulbus_cordis primitive right ventricle endocardium uberon UBERON:0004706 bulbus cordis http://upload.wikimedia.org/wikipedia/commons/c/c9/Gray466.png a transient fetal dilation of the distal (or cranial) heart tube located where the arterial trunk joins the ventral roots of the aortic arches ISBN:0-683-40008-8 MP:0010568 A pear shaped chamber that functions as a capacitor, maintaining continuous blood flow into the gill arches. The bulbus arteriosus has three distinct layers. Hu et al. 2000.[TAO] 2012-08-14 TAO:0000173 TAO ZFIN:curator UMLS:C1284055 ncithesaurus:Bulbus_Cordis primitive right ventricle endocardium EHDAA2:0000197 JB:def An appendage that is part of an appendage girdle complex. this class is the union of the classes limb, pectoral fin and pelvic fin. UBERON:0009872 VSAO:0000067 girdle-associated appendage limb or fin limb/fin pectoral or pelvic appendage pelvic/pectoral appendage jointed paired lateral appendage paired appendage uberon UBERON:0004708 paired limb/fin VSAO VSAO definitional An appendage that is part of an appendage girdle complex. UBERON:cjm https://github.com/geneontology/go-ontology/issues/9029 girdle-associated appendage https://orcid.org/0000-0002-6601-2165 limb or fin https://orcid.org/0000-0002-6601-2165 limb/fin https://orcid.org/0000-0002-6601-2165 pectoral or pelvic appendage https://orcid.org/0000-0002-6601-2165 pelvic/pectoral appendage https://orcid.org/0000-0002-6601-2165 jointed paired lateral appendage https://orcid.org/0000-0002-6601-2165 paired appendage VSAO:0000067 Paired appendage that consists of the posterior appendicular skeleton and associated soft and hard tissues, but excludes the pelvic girdle and its associated soft and hard tissues. UBERON:0009876 posterior appendage VSAO:0000126 hindlimb/pelvic fin pelvic appendage pelvic limb/fin posterior limb/fin posterior paired appendage uberon UBERON:0004709 pelvic appendage definitional Paired appendage that consists of the posterior appendicular skeleton and associated soft and hard tissues, but excludes the pelvic girdle and its associated soft and hard tissues. VSAO:0000150 hindlimb/pelvic fin https://orcid.org/0000-0002-6601-2165 pelvic appendage VSAO:0000126 pelvic limb/fin https://orcid.org/0000-0002-6601-2165 posterior paired appendage VSAO:0000126 The jugular veins are veins that bring deoxygenated blood from the head back to the heart via the superior vena cava. BTO:0001744 CALOHA:TS-0497 EMAPA:18638 GAID:536 MA:0002154 MESH:D007601 NCIT:C12738 SCTID:244403000 UMLS:C0022427 Wikipedia:Jugular_vein uberon jugular vena jugularis UBERON:0004711 jugular vein http://upload.wikimedia.org/wikipedia/commons/f/f8/Gray558.png The jugular veins are veins that bring deoxygenated blood from the head back to the heart via the superior vena cava. Wikipedia:Jugular_vein UMLS:C0022427 ncithesaurus:Jugular_Vein vena jugularis BTO:0001744 The embryo and its adnexa (appendages or adjunct parts) or associated membranes (i.e. the products of conception) The conceptus includes all structures that develop from the zygote, both embryonic and extraembryonic. It includes the embryo as well as the embryonic part of the placenta and its associated membranes - amnion, chorion (gestational sac), and yolk sac[WP]. EHDAA2 places this as a subtype of organism. This leads to the inference that a conceptus is an embryo (if an embryo is defined as an organism at embryo stage), which eliminates the embryonic + extra-embryonic = conceptus AEO:0000194 BTO:0003834 EHDAA2:0000001 EHDAA2:0003235 EMAPA:36040 NCIT:C34131 UMLS:C1516779 Wikipedia:Conceptus embryo plus adnexa uberon UBERON:0004716 conceptus The embryo and its adnexa (appendages or adjunct parts) or associated membranes (i.e. the products of conception) The conceptus includes all structures that develop from the zygote, both embryonic and extraembryonic. It includes the embryo as well as the embryonic part of the placenta and its associated membranes - amnion, chorion (gestational sac), and yolk sac[WP]. BTO:0003834 Wikipedia:Conceptus UMLS:C1516779 ncithesaurus:Conceptus A transverse unitary subdivision of the neural tube that shares a common dorsoventral structure (floor, basal, alar, and roof plates), but each having differential molecular identities and fates; they comprise the secondary prosencephalon, diencephalon (prosomeres), the midbrain (mesomeres), and the hindbrain (rhombomeres). We take the definition of neuromere from Puelles et al, although the existence of mesomeres and prosomeres may not be widely accepted A metameric segment of the central nervous system.[ZFA] Melissa Haendel 2009-06-18T09:00:04Z NLX:147842 TAO:0001328 Wikipedia:Neuromere ZFA:0001328 neural tube metameric segment neural tube segment neuromere neuromeres uberon neural metamere neural segment UBERON:0004731 neuromere A transverse unitary subdivision of the neural tube that shares a common dorsoventral structure (floor, basal, alar, and roof plates), but each having differential molecular identities and fates; they comprise the secondary prosencephalon, diencephalon (prosomeres), the midbrain (mesomeres), and the hindbrain (rhombomeres). DOI:10.1016/j.tins.2013.06.004 https://github.com/obophenotype/uberon/issues/318 A metameric segment of the central nervous system.[ZFA] 2012-08-14 TAO:0001328 TAO ZFIN:curator neural tube metameric segment http://orcid.org/0000-0002-6601-2165 neuromeres TAO:0001328 Any segmental subdivision of a nervous system. Includes metameric developmental segments, such as vertebrates neuromeres. revisit this after CARO is revised and/or we have defined metameric segment; note that with the additional of an A/P axis constraint this corresponds to what Richter at al call a neuromere (PMID:21062451) FBbt:00005140 uberon neuromere UBERON:0004732 segmental subdivision of nervous system Any segmental subdivision of a nervous system. Includes metameric developmental segments, such as vertebrates neuromeres. FBbt:00005140 http://orcid.org/0000-0002-6601-2165 neuromere FBbt:00005140 An organ subunit that is part of a hindbrain [Automatically generated definition]. FMA:61998 hindbrain segment segment of hindbrain uberon UBERON:0004733 segmental subdivision of hindbrain An organ subunit that is part of a hindbrain [Automatically generated definition]. OBOL:automatic hindbrain segment FMA:61998 segment of hindbrain FMA:61998 Organism at the gastrula stage. We explicitly merge the NCITA terms here UBERON:0007012 BILA:0000060 BTO:0001403 FBbt:00005317 FMA:293108 GAID:1302 MESH:A16.254.412 MIAA:0000179 NCIT:C34057 NCIT:C34058 UMLS:C0017199 UMLS:C1284022 Wikipedia:Gastrula Wikipedia:Trilaminar_blastocyst gastrula embryo uberon blastocystis trilaminaris tri-laminar disc tri-laminar disk trilaminar blastocyst trilaminar blastoderm trilaminar disc trilaminar disk trilaminar germ UBERON:0004734 gastrula Organism at the gastrula stage. Wikipedia:Gastrula Wikipedia:Trilaminar_blastocyst We explicitly merge the NCITA terms here NCIT UMLS:C0017199 ncithesaurus:Gastrula UMLS:C1284022 ncithesaurus:Trilaminar_Embryonic_Disc gastrula embryo BILA:0000060 blastocystis trilaminaris https://orcid.org/0000-0002-6601-2165 tri-laminar disc https://orcid.org/0000-0002-6601-2165 tri-laminar disk https://orcid.org/0000-0002-6601-2165 trilaminar blastocyst https://orcid.org/0000-0002-6601-2165 trilaminar blastoderm https://orcid.org/0000-0002-6601-2165 trilaminar disc https://orcid.org/0000-0002-6601-2165 trilaminar disk https://orcid.org/0000-0002-6601-2165 trilaminar germ https://orcid.org/0000-0002-6601-2165 A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO] A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO] EMAPA:37744 MA:0003047 SCTID:309311006 VSAO:0000015 XAO:0004038 ZFA:0005619 uberon UBERON:0004755 Four classes of mineralized tissues are found in vertebrates: bone, cartilage, dentine, and enamel. We think of cartilage and bone as skeletal tissues and of enamel and dentine as dental tissues, but enamel and dentine arose evolutionarily together with bone as skeletal tissues in the dermal skeleton (exoskeleton) of early vertebrates. Scales and teeth of sharks are examples of dermal skeletal elements that are still composed of the three ancient components-enamel, dentine, and bone. Cartilage, on the other hand, provided the basis for the second vertebrate skeletal system, the endoskeleton (Smith and Hall, 1990; Hall, 1998a,b). some invertebrate skeletal tissues have surprisingly bone-like features. Examples include chondrocytes interconnected by cell processes in cephalopod cartilages (Cole and Hall, 2004a,b), and the calcium phosphate layer in the shells of brachiopods (Rodland et al., 2003). However, neither bone nor mineralized cartilage have been found in invertebrates. Editors notes: TODO - develops_from skeletal tissue VSAO 2012-08-14 VSAO:0000015 VSAO A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO] GO_REF:0000034 PSPUB:0000170 VSAO:0000015 http://dx.plos.org/10.1371/journal.pone.0051070 https://github.com/obophenotype/uberon/issues/134 A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO] 2012-08-14 VSAO:0000015 taken from version of VSAO used in TAO and used directly in Uberon VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 PSPUB:0000170 EMAPA:37744 MA:th dermis-derived entity that is made of skeletal tissue. dermal element uberon UBERON:0004756 dermal skeletal element dermis-derived entity that is made of skeletal tissue. http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/206 dermal element VSAO:curator A gland that is part of an anal canal [Automatically generated definition]. EMAPA:27221 EMAPA:27233 EMAPA:27543 FMA:15720 FMA:15724 NCIT:C32068 SCTID:245448005 UMLS:C0162322 Wikipedia:Anal_gland gland of anal canal uberon anal gland anal sac gland of anus rectal gland UBERON:0004760 gland of anal canal A gland that is part of an anal canal [Automatically generated definition]. OBOL:automatic Wikipedia:Anal_gland UMLS:C0162322 ncithesaurus:Anal_Gland gland of anal canal OBOL:automatic anal sac Wikipedia:Anal_gland The primitive cartilagionous skeletal structure of the fetal skull that grows to envelop the rapidly growing embyonic brain. In humans, the chondrocranium begins forming at 28 days from mesenchymal condensations and is fully formed between week 7 and 9 of fetal development. While the majority of the chondrocranium is succeeded by the bony skull in most higher vertebrates, some components do persist into adulthood.[1] In Cartilagious fishes and Agnathans, the chondrocranium persist throughout life.[2] Embryologically, the chondrocranium represent the basal cranial structure, and lay the base for the formation of the endocranium in higher vertebrates[WP]. in contrast to chondrocranium, this structure is entirely cartiliginous. In Chondricthyes this is the same as the neurocranium. FMA:76621 is an undefined fetal structure, so we assume the correct placement is here. Note that this is distinct from MA:0000317 which is the uberon:neurocranium (the part of the cranium that encloses the brain) AAO:0000094 AAO:0010153 EHDAA:6031 FMA:76621 NCIT:C34121 SCTID:155540009 UMLS:C1516496 Wikipedia:Chondrocranium XAO:0003059 cartilaginous chondocranium cartiligionous skeletal structure of skull uberon cartilaginous skull chondocranium embryonic chondocranium neurocranium UBERON:0004761 cartilaginous neurocranium FMA PMC1571569 The primitive cartilagionous skeletal structure of the fetal skull that grows to envelop the rapidly growing embyonic brain. In humans, the chondrocranium begins forming at 28 days from mesenchymal condensations and is fully formed between week 7 and 9 of fetal development. While the majority of the chondrocranium is succeeded by the bony skull in most higher vertebrates, some components do persist into adulthood.[1] In Cartilagious fishes and Agnathans, the chondrocranium persist throughout life.[2] Embryologically, the chondrocranium represent the basal cranial structure, and lay the base for the formation of the endocranium in higher vertebrates[WP]. Wikipedia:Chondrocranium in contrast to chondrocranium, this structure is entirely cartiliginous. In Chondricthyes this is the same as the neurocranium. FMA:76621 is an undefined fetal structure, so we assume the correct placement is here. Note that this is distinct from MA:0000317 which is the uberon:neurocranium (the part of the cranium that encloses the brain) FMA UMLS:C1516496 ncithesaurus:Chondrocranium chondocranium Wikipedia:Chondrocranium neurocranium Bone tissue that forms directly within mesenchyme, and does not replace other tissues[TAO]. Intramembranous ossification is the formation of bone in which osteoblasts secrete a collagen-proteoglycan matrix that binds calcium salts and becomes calcified[GO]. Intramembranous ossification is the way flat bones and the shell of a turtle are formed[GO]. Unlike endochondral ossification, cartilage is not present during intramembranous ossification[WP]. note the distinction between intramembranous bone and intramembranous bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type (it is under bone tissue and connective tissue; there are no child classes) MA:0002837 Wikipedia:Intramembranous_ossification uberon UBERON:0004764 intramembranous bone tissue Bone tissue that forms directly within mesenchyme, and does not replace other tissues[TAO]. Intramembranous ossification is the formation of bone in which osteoblasts secrete a collagen-proteoglycan matrix that binds calcium salts and becomes calcified[GO]. Intramembranous ossification is the way flat bones and the shell of a turtle are formed[GO]. Unlike endochondral ossification, cartilage is not present during intramembranous ossification[WP]. GO:0001957 Wikipedia:Intramembranous_ossification note the distinction between intramembranous bone and intramembranous bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type (it is under bone tissue and connective tissue; there are no child classes) MA Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO] Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO] AAO:0011129 TAO:0001890 VSAO:0000128 XAO:0004012 ZFA:0005494 galen:SkeletalStructure uberon UBERON:0004765 skeletal element VSAO Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. https://orcid.org/0000-0002-6601-2165 Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO] 2012-08-14 VSAO:0000128 VSAO PSPUB:0000170 Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO] 2012-08-14 TAO:0001890 TAO TAO:VSAO_workshop A bone that is part of a cranium. here cranium = skull - mandible SCTID:181792001 cranium bone uberon UBERON:0004766 cranial bone A bone that is part of a cranium. UBERON:automatic cranium bone UBERON:automatic Any bone that is part of the lower jaw skeleton. This includes (when present): the dentary/mandible, the articular, the splenial, the suprangular Do not manually classify under here - bones are automatically classified lower jaw bone uberon UBERON:0004768 bone of lower jaw Any bone that is part of the lower jaw skeleton. This includes (when present): the dentary/mandible, the articular, the splenial, the suprangular https://orcid.org/0000-0002-6601-2165 Anatomical system that consists of all the joints of the body. EMAPA:35150 FMA:23878 MA:0003007 SCTID:361827000 VSAO:0000181 joint system set of all joints of body uberon set of all joints set of joints of body UBERON:0004770 articular system FMA Anatomical system that consists of all the joints of the body. VSAO:0000181 joint system FMA:23878 set of all joints of body FMA:23878 set of joints of body FMA:23878 A submucosa that is part of a respiratory system [Automatically generated definition]. EMAPA:37578 MA:0001822 apparatus respiratorius submucosa submucosa of apparatus respiratorius submucosa of respiratory system uberon UBERON:0004777 respiratory system submucosa A submucosa that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37578 MA:th apparatus respiratorius submucosa OBOL:automatic submucosa of apparatus respiratorius OBOL:automatic submucosa of respiratory system OBOL:automatic A submucosa that is part of a larynx [Automatically generated definition]. EMAPA:35474 FMA:321584 MA:0002728 SCTID:361941005 submucosa of larynx uberon laryngeal submucosa UBERON:0004778 larynx submucosa A submucosa that is part of a larynx [Automatically generated definition]. OBOL:automatic submucosa of larynx OBOL:automatic laryngeal submucosa EMAPA:35474 A lamina propria that is part of a respiratory system [Automatically generated definition]. EMAPA:37576 MA:0001821 apparatus respiratorius lamina propria apparatus respiratorius lamina propria mucosa lamina propria mucosa of apparatus respiratorius lamina propria mucosa of respiratory system lamina propria of apparatus respiratorius lamina propria of respiratory system respiratory system lamina propria mucosa uberon UBERON:0004779 respiratory system lamina propria true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships A lamina propria that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37576 MA:th apparatus respiratorius lamina propria OBOL:automatic apparatus respiratorius lamina propria mucosa OBOL:automatic lamina propria mucosa of apparatus respiratorius OBOL:automatic lamina propria mucosa of respiratory system OBOL:automatic lamina propria of apparatus respiratorius OBOL:automatic lamina propria of respiratory system OBOL:automatic respiratory system lamina propria mucosa OBOL:automatic A lamina propria that is part of a gastrointestinal system. MA:0001899 NCIT:C49299 UMLS:C1708197 uberon UBERON:0004780 gastrointestinal system lamina propria true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships A lamina propria that is part of a gastrointestinal system. OBOL:automatic UMLS:C1708197 ncithesaurus:Gastrointestinal_Tract_Lamina_Propria A serous membrane that is part of a digestive system [Automatically generated definition]. EMAPA:37592 MA:0001522 digestive system serosa digestive system serous membrane gastrointestinal system serous membrane serosa of digestive system serosa of gastrointestinal system serous membrane of digestive system serous membrane of gastrointestinal system uberon UBERON:0004782 gastrointestinal system serosa A serous membrane that is part of a digestive system [Automatically generated definition]. OBOL:automatic EMAPA:37592 MA:th digestive system serosa OBOL:automatic digestive system serous membrane OBOL:automatic gastrointestinal system serous membrane OBOL:automatic serosa of digestive system OBOL:automatic serosa of gastrointestinal system OBOL:automatic serous membrane of digestive system OBOL:automatic serous membrane of gastrointestinal system OBOL:automatic An anatomical wall that is part of a cardiac ventricle [Automatically generated definition]. FMA:13884 MA:0002791 NCIT:C119295 anatomical wall of cardiac ventricle anatomical wall of heart ventricle anatomical wall of lower chamber of heart anatomical wall of ventricle of heart cardiac ventricle anatomical wall cardiac ventricle wall heart ventricle anatomical wall lower chamber of heart anatomical wall lower chamber of heart wall ventricle of heart anatomical wall ventricle of heart wall ventricular wall wall of cardiac ventricle wall of heart ventricle wall of lower chamber of heart wall of ventricle of heart uberon wall of ventricle UBERON:0004784 heart ventricle wall An anatomical wall that is part of a cardiac ventricle [Automatically generated definition]. OBOL:automatic anatomical wall of cardiac ventricle OBOL:automatic anatomical wall of heart ventricle OBOL:automatic anatomical wall of lower chamber of heart OBOL:automatic anatomical wall of ventricle of heart OBOL:automatic cardiac ventricle anatomical wall OBOL:automatic cardiac ventricle wall OBOL:automatic heart ventricle anatomical wall OBOL:automatic lower chamber of heart anatomical wall OBOL:automatic lower chamber of heart wall OBOL:automatic ventricle of heart anatomical wall OBOL:automatic ventricle of heart wall OBOL:automatic ventricular wall FMA:13884 wall of cardiac ventricle OBOL:automatic wall of heart ventricle OBOL:automatic wall of lower chamber of heart OBOL:automatic wall of ventricle of heart OBOL:automatic wall of ventricle MA:0002791 the mucous membrane lining the respiratory tract TODO - split respiratory tract mucosa from respiratory system mucosa BTO:0000973 EMAPA:18334 EMAPA:37577 FMA:302092 GAID:304 MA:0001827 MESH:D020545 apparatus respiratorius mucosa apparatus respiratorius mucosa of organ apparatus respiratorius mucous membrane mucosa of apparatus respiratorius mucosa of organ of apparatus respiratorius mucosa of organ of respiratory system mucosa of respiratory system mucous membrane of apparatus respiratorius mucous membrane of respiratory system respiratory system mucosa of organ respiratory system mucous membrane uberon laryngeal mucous membrane respiratory mucosa respiratory tract mucosa UBERON:0004785 respiratory system mucosa the mucous membrane lining the respiratory tract MESH:A04.760 MGI:cwg MP:0002277 EMAPA:37577 MA:th apparatus respiratorius mucosa OBOL:automatic apparatus respiratorius mucosa of organ OBOL:automatic apparatus respiratorius mucous membrane OBOL:automatic mucosa of apparatus respiratorius OBOL:automatic mucosa of organ of apparatus respiratorius OBOL:automatic mucosa of organ of respiratory system OBOL:automatic mucosa of respiratory system OBOL:automatic mucous membrane of apparatus respiratorius OBOL:automatic mucous membrane of respiratory system OBOL:automatic respiratory system mucosa of organ OBOL:automatic respiratory system mucous membrane OBOL:automatic laryngeal mucous membrane EMAPA:18334 respiratory mucosa BTO:0000973 A mucosa that is part of a gastrointestinal system. BTO:0000546 BTO:0005568 EMAPA:36591 MA:0001521 SCTID:410433007 digestive tract mucosa gut mucosa gut mucuous membrane mucosa of gut uberon UBERON:0004786 The gut mucosa of amphioxus has insulin-secreting cells. http://www.ncbi.nlm.nih.gov/pubmed/16417468 gastrointestinal system mucosa PMID:16417468 PMID:16417468 PMID:16417468 BTO-modified A mucosa that is part of a gastrointestinal system. OBOL:automatic digestive tract mucosa https://orcid.org/0000-0002-6601-2165 gut mucosa BTO:0000546 gut mucuous membrane https://orcid.org/0000-0002-6601-2165 mucosa of gut https://orcid.org/0000-0002-6601-2165 A secretion that is part of a esophagus [Automatically generated definition]. FMA:79662 MA:0002514 NCIT:C52555 UMLS:C0227179 esophageal secretion gullet secretion oesophagus secretion secretion of esophagus secretion of gullet secretion of oesophagus uberon UBERON:0004794 esophagus secretion A secretion that is part of a esophagus [Automatically generated definition]. OBOL:automatic UMLS:C0227179 ncithesaurus:Esophagus_Secretion esophageal secretion FMA:79662 gullet secretion OBOL:automatic oesophagus secretion OBOL:automatic secretion of esophagus OBOL:automatic secretion of gullet OBOL:automatic secretion of oesophagus OBOL:automatic Any of the tissue layers that comprise a blood vessel. Examples: tunica media, tunica adventitia. EMAPA:36296 MA:0002854 uberon UBERON:0004797 blood vessel layer Blood:vessels.svg Any of the tissue layers that comprise a blood vessel. Examples: tunica media, tunica adventitia. http://orcid.org/0000-0002-6601-2165 the pseudostratified ciliated epithelium that lines much of the conducting portion of the airway, including part of the nasal cavity and larynx, the trachea, and bronchi BTO:0000419 CALOHA:TS-0023 EMAPA:32827 MA:0001480 SCTID:321764001 VHOG:0000981 epithelial tissue of respiratory tract epithelium of respiratory tract respiratory tract epithelial tissue uberon airway epithelium respiratory epithelium UBERON:0004802 respiratory tract epithelium the pseudostratified ciliated epithelium that lines much of the conducting portion of the airway, including part of the nasal cavity and larynx, the trachea, and bronchi ISBN:0-683-40008-8 MGI:anna MP:0010942 epithelial tissue of respiratory tract OBOL:automatic epithelium of respiratory tract OBOL:automatic respiratory tract epithelial tissue OBOL:automatic airway epithelium BTO:0000419 respiratory epithelium BTO:0000419 An epithelium that is part of a respiratory system [Automatically generated definition]. CALOHA:TS-0023 EMAPA:32826 MA:0001823 VHOG:0000981 apparatus respiratorius epithelial tissue apparatus respiratorius epithelium epithelial tissue of apparatus respiratorius epithelial tissue of respiratory system epithelium of apparatus respiratorius epithelium of respiratory system respiratory system epithelial tissue uberon UBERON:0004807 respiratory system epithelium An epithelium that is part of a respiratory system [Automatically generated definition]. OBOL:automatic apparatus respiratorius epithelial tissue OBOL:automatic apparatus respiratorius epithelium OBOL:automatic epithelial tissue of apparatus respiratorius OBOL:automatic epithelial tissue of respiratory system OBOL:automatic epithelium of apparatus respiratorius OBOL:automatic epithelium of respiratory system OBOL:automatic respiratory system epithelial tissue OBOL:automatic An epithelium that is part of a digestive system [Automatically generated definition]. EMAPA:32683 MA:0001520 digestive system epithelial tissue digestive system epithelium epithelial tissue of digestive system epithelial tissue of gastrointestinal system epithelium of digestive system epithelium of gastrointestinal system gastrointestinal system epithelial tissue uberon UBERON:0004808 gastrointestinal system epithelium An epithelium that is part of a digestive system [Automatically generated definition]. OBOL:automatic digestive system epithelial tissue OBOL:automatic digestive system epithelium OBOL:automatic epithelial tissue of digestive system OBOL:automatic epithelial tissue of gastrointestinal system OBOL:automatic epithelium of digestive system OBOL:automatic epithelium of gastrointestinal system OBOL:automatic gastrointestinal system epithelial tissue OBOL:automatic An epithelium that is part of a lower respiratory tract [Automatically generated definition]. EMAPA:37549 MA:0001481 epithelial tissue of lower respiratory tract epithelium of lower respiratory tract lower respiratory tract epithelial tissue uberon UBERON:0004815 lower respiratory tract epithelium An epithelium that is part of a lower respiratory tract [Automatically generated definition]. OBOL:automatic EMAPA:37549 MA:th epithelial tissue of lower respiratory tract OBOL:automatic epithelium of lower respiratory tract OBOL:automatic lower respiratory tract epithelial tissue OBOL:automatic An epithelium that is part of a larynx [Automatically generated definition]. composed of squamous epithelium in the upper larynx and ciliated columnar epithelium in the lower larynx [ISBN:0-397-51047-0] EHDAA2:0004065 EMAPA:35472 MA:0001765 NCIT:C49247 UMLS:C0751258 epithelial tissue of larynx epithelium of larynx laryngeal epithelium larynx epithelial tissue uberon UBERON:0004816 larynx epithelium An epithelium that is part of a larynx [Automatically generated definition]. OBOL:automatic UMLS:C0751258 ncithesaurus:Laryngeal_Epithelium epithelial tissue of larynx OBOL:automatic epithelium of larynx OBOL:automatic laryngeal epithelium OBOL:automatic larynx epithelial tissue OBOL:automatic A portion of skeletal muscle tissue that is part of a respiratory system [Automatically generated definition]. EMAPA:37583 MA:0001829 respiratory system skeletal muscle tissue skeletal muscle of apparatus respiratorius skeletal muscle of respiratory system skeletal muscle tissue of apparatus respiratorius skeletal muscle tissue of respiratory system uberon UBERON:0004830 respiratory system skeletal muscle A portion of skeletal muscle tissue that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37583 MA:th respiratory system skeletal muscle tissue OBOL:automatic skeletal muscle of apparatus respiratorius OBOL:automatic skeletal muscle of respiratory system OBOL:automatic skeletal muscle tissue of apparatus respiratorius OBOL:automatic skeletal muscle tissue of respiratory system OBOL:automatic A portion of skeletal muscle tissue that is part of a esophagus [Automatically generated definition]. EMAPA:36523 MA:0001572 esophagus skeletal muscle tissue skeletal muscle of esophagus uberon UBERON:0004831 Most muscle tissue lining the digestive tract is smooth, but part of the externa of the esophagus is skeletal esophagus skeletal muscle A portion of skeletal muscle tissue that is part of a esophagus [Automatically generated definition]. OBOL:automatic esophagus skeletal muscle tissue OBOL:automatic skeletal muscle of esophagus OBOL:automatic A portion of skeletal muscle tissue that is part of an anal region [Automatically generated definition]. EMAPA:37393 MA:0001530 anal part of perineum skeletal muscle anal part of perineum skeletal muscle tissue anal region skeletal muscle tissue anal triangle skeletal muscle anal triangle skeletal muscle tissue skeletal muscle of anal part of perineum skeletal muscle of anal region skeletal muscle of anal triangle skeletal muscle tissue of anal part of perineum skeletal muscle tissue of anal region skeletal muscle tissue of anal triangle uberon UBERON:0004832 anal region skeletal muscle A portion of skeletal muscle tissue that is part of an anal region [Automatically generated definition]. OBOL:automatic EMAPA:37393 MA:th anal part of perineum skeletal muscle OBOL:automatic anal part of perineum skeletal muscle tissue OBOL:automatic anal region skeletal muscle tissue OBOL:automatic anal triangle skeletal muscle OBOL:automatic anal triangle skeletal muscle tissue OBOL:automatic skeletal muscle of anal part of perineum OBOL:automatic skeletal muscle of anal region OBOL:automatic skeletal muscle of anal triangle OBOL:automatic skeletal muscle tissue of anal part of perineum OBOL:automatic skeletal muscle tissue of anal region OBOL:automatic skeletal muscle tissue of anal triangle OBOL:automatic A portion of skeletal muscle tissue that is part of a lip [Automatically generated definition]. this class is derived from MA. Consider re-modeling this as being a muscle that acts on the lips. See: Wikipedia:Lip#Muscles_acting_on_the_lips EMAPA:37642 MA:0001578 lip skeletal muscle tissue skeletal muscle of lip skeletal muscle tissue of lip uberon UBERON:0004833 lip skeletal muscle A portion of skeletal muscle tissue that is part of a lip [Automatically generated definition]. OBOL:automatic EMAPA:37642 MA:th lip skeletal muscle tissue OBOL:automatic skeletal muscle of lip OBOL:automatic skeletal muscle tissue of lip OBOL:automatic An endothelium of artery that is part of a respiratory system [Automatically generated definition]. EMAPA:37566 MA:0001801 apparatus respiratorius arterial endothelium apparatus respiratorius artery endothelium apparatus respiratorius endothelium of artery arterial endothelium of apparatus respiratorius arterial endothelium of respiratory system artery endothelium of apparatus respiratorius artery endothelium of respiratory system endothelium of artery of apparatus respiratorius endothelium of artery of respiratory system respiratory system artery endothelium respiratory system endothelium of artery uberon UBERON:0004848 respiratory system arterial endothelium true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships An endothelium of artery that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37566 MA:th apparatus respiratorius arterial endothelium OBOL:automatic apparatus respiratorius artery endothelium OBOL:automatic apparatus respiratorius endothelium of artery OBOL:automatic arterial endothelium of apparatus respiratorius OBOL:automatic arterial endothelium of respiratory system OBOL:automatic artery endothelium of apparatus respiratorius OBOL:automatic artery endothelium of respiratory system OBOL:automatic endothelium of artery of apparatus respiratorius OBOL:automatic endothelium of artery of respiratory system OBOL:automatic respiratory system artery endothelium OBOL:automatic respiratory system endothelium of artery OBOL:automatic An endothelium of vein that is part of a respiratory system [Automatically generated definition]. EMAPA:37585 MA:0001811 apparatus respiratorius endothelium of vein apparatus respiratorius vein endothelium apparatus respiratorius venous endothelium endothelium of vein of apparatus respiratorius endothelium of vein of respiratory system respiratory system endothelium of vein respiratory system vein endothelium vein endothelium of apparatus respiratorius vein endothelium of respiratory system venous endothelium of apparatus respiratorius venous endothelium of respiratory system uberon UBERON:0004849 respiratory system venous endothelium An endothelium of vein that is part of a respiratory system [Automatically generated definition]. OBOL:automatic EMAPA:37585 MA:th apparatus respiratorius endothelium of vein OBOL:automatic apparatus respiratorius vein endothelium OBOL:automatic apparatus respiratorius venous endothelium OBOL:automatic endothelium of vein of apparatus respiratorius OBOL:automatic endothelium of vein of respiratory system OBOL:automatic respiratory system endothelium of vein OBOL:automatic respiratory system vein endothelium OBOL:automatic vein endothelium of apparatus respiratorius OBOL:automatic vein endothelium of respiratory system OBOL:automatic venous endothelium of apparatus respiratorius OBOL:automatic venous endothelium of respiratory system OBOL:automatic the thin layer of flat cells that line the aorta and form a barrier between circulating blood in the lumen and the rest of the vessel wall BTO:0000394 CALOHA:TS-0047 EFO:0002597 EMAPA:35134 MA:0000701 NCIT:C49190 UMLS:C1706824 adult aorta endothelium endothelium of adult aorta endothelium of aorta endothelium of trunk of aortic tree endothelium of trunk of systemic arterial tree trunk of aortic tree endothelium trunk of systemic arterial tree endothelium uberon aortic endothelium UBERON:0004851 aorta endothelium the thin layer of flat cells that line the aorta and form a barrier between circulating blood in the lumen and the rest of the vessel wall MGI:csmith MP:0009864 UMLS:C1706824 ncithesaurus:Aorta_Endothelium adult aorta endothelium OBOL:automatic endothelium of adult aorta OBOL:automatic endothelium of aorta OBOL:automatic endothelium of trunk of aortic tree OBOL:automatic endothelium of trunk of systemic arterial tree OBOL:automatic trunk of aortic tree endothelium OBOL:automatic trunk of systemic arterial tree endothelium OBOL:automatic aortic endothelium BTO:0000394 An endothelium that is part of the cardiovascular system. consider merging with 'endothelium' Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] BTO:0001853 EMAPA:35201 GAID:519 MA:0000717 MESH:D004730 NCIT:C13053 TAO:0002171 UMLS:C0014261 VHOG:0001217 XAO:0000356 ZFA:0001639 uberon endothelia vascular endothelia UBERON:0004852 cardiovascular system endothelium An endothelium that is part of the cardiovascular system. https://orcid.org/0000-0002-6601-2165 Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] 2012-09-17 VHOG:0001217 VHOG ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207 http://bgee.unil.ch/ UMLS:C0014261 ncithesaurus:Vascular_Endothelium endothelia ZFA:0001639 vascular endothelia XAO:0000356 A connective tissue that surrounds a skeletal muscle tissue. EMAPA:37743 MA:0002868 connective tissue of skeletal muscle connective tissue of skeletal muscle tissue portion of connective tissue of skeletal muscle portion of connective tissue of skeletal muscle tissue skeletal muscle portion of connective tissue skeletal muscle textus connectivus skeletal muscle tissue connective tissue skeletal muscle tissue portion of connective tissue skeletal muscle tissue textus connectivus textus connectivus of skeletal muscle textus connectivus of skeletal muscle tissue uberon skeletal muscle interstitial tissue skeletal muscle interstitum UBERON:0004857 skeletal muscle connective tissue A connective tissue that surrounds a skeletal muscle tissue. OBOL:automatic EMAPA:37743 MA:th connective tissue of skeletal muscle OBOL:automatic connective tissue of skeletal muscle tissue OBOL:automatic portion of connective tissue of skeletal muscle OBOL:automatic portion of connective tissue of skeletal muscle tissue OBOL:automatic skeletal muscle portion of connective tissue OBOL:automatic skeletal muscle textus connectivus OBOL:automatic skeletal muscle tissue connective tissue OBOL:automatic skeletal muscle tissue portion of connective tissue OBOL:automatic skeletal muscle tissue textus connectivus OBOL:automatic textus connectivus of skeletal muscle OBOL:automatic textus connectivus of skeletal muscle tissue OBOL:automatic skeletal muscle interstitial tissue MA:0002868 skeletal muscle interstitum MA:0002868 A gland that is part of a eye. The eye is a compound unit which depending on the species may consist of an eyeballs plus associated ducts and integumentary structures. Eye glands therefore include the various types of lacrimal gland, the various types of apocrine and sebaceous glands associated with the eyelid. EMAPA:35334 MA:0000267 eye-associated gland gland of eye uberon UBERON:0004859 Examples: harderian gland, accessory lacrimal gland, gland of Moll, gland of Zeis, nictitating membrane glands eye gland A gland that is part of a eye. The eye is a compound unit which depending on the species may consist of an eyeballs plus associated ducts and integumentary structures. Eye glands therefore include the various types of lacrimal gland, the various types of apocrine and sebaceous glands associated with the eyelid. http://orcid.org/0000-0002-6601-2165 eye-associated gland http://orcid.org/0000-0002-6601-2165 gland of eye OBOL:automatic A vasculature that is part of a retina [Automatically generated definition]. FMA:76552 MESH:D012171 XAO:0004153 retina vasculature retina vasculature of camera-type eye retinal blood vessels retinal blood vessels set retinal vasculature set of blood vessels of retina set of retinal blood vessels vasa sanguinea retinae uberon UBERON:0004864 vasculature of retina A vasculature that is part of a retina [Automatically generated definition]. OBOL:automatic PMID:21622558 PMID:2772405 michaelerice retina vasculature GO:0061298 retina vasculature of camera-type eye GO:0061298 retinal blood vessels FMA:76552 retinal blood vessels set FMA:76552 retinal vasculature OBOL:automatic set of blood vessels of retina OBOL:automatic set of retinal blood vessels FMA:76552 vasa sanguinea retinae FMA:76552 FMA:TA Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP]. We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors visceral mesoderm AAO:0011102 BILA:0000044 FMA:295568 Wikipedia:Lateral_plate_mesoderm#Division_into_layers XAO:0000276 inner layer of lateral plate mesoderm uberon splanchnic mesoderm UBERON:0004872 splanchnic layer of lateral plate mesoderm Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP]. Wikipedia:Lateral_plate_mesoderm#Division_into_layers We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors BILA visceral mesoderm BILA:0000044 http://www.drugs.com/dict/visceral-mesoderm.html http://www.stedmans.com/ splanchnic mesoderm ISBN:9780878932504 A structure created during embryogenesis when the lateral mesoderm splits into two layers - the inner (or splanchnic) layer adheres to the endoderm, and with it forms the splanchnopleure[WP]. TODO - check relationship to LPM EHDAA2:0001903 EHDAA:383 EMAPA:16181 FMA:295564 NCIT:C34303 UMLS:C1519472 VHOG:0000558 Wikipedia:Splanchnopleure uberon ventral splanchnic mesoderm UBERON:0004873 splanchnopleure http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png EHDAA2 A structure created during embryogenesis when the lateral mesoderm splits into two layers - the inner (or splanchnic) layer adheres to the endoderm, and with it forms the splanchnopleure[WP]. Wikipedia:Splanchnopleure UMLS:C1519472 ncithesaurus:Splanchnopleure ventral splanchnic mesoderm Wikipedia:Intraembryonic_coelom A structure created during embryogenesis when the lateral mesoderm splits into two layers - the outer (or somatic) layer becomes applied to the inner surface of the ectoderm, and with it forms the somatopleure.[WP]. Gives rise to the paired appendages in jawed vertebrates. a persistent somatopleure through the redistribution and expansion of the lateral plate mesoderm is a synapomorphy for gnathostomes and a critical step in generating a novel developmental module with dramatic evolutionary potentia (Tulenko et al. 2012) http://burkelab.research.wesleyan.edu/current-projects/lamprey/ sources differ as to whether this is part-of or develops-from the LPM EHDAA2:0001847 EHDAA:381 EMAPA:16180 FMA:295566 NCIT:C34301 UMLS:C1519423 VHOG:0000557 Wikipedia:Somatopleure uberon UBERON:0004874 somatopleure http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png EHDAA2 A structure created during embryogenesis when the lateral mesoderm splits into two layers - the outer (or somatic) layer becomes applied to the inner surface of the ectoderm, and with it forms the somatopleure.[WP]. Wikipedia:Somatopleure UMLS:C1519423 ncithesaurus:Somatopleure The central region of trunk mesoderm. This tissue forms the notochord Notochord rudiment[ZFIN:ZDB-PUB-961014-576]. WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord. AAO:0000478 EFO:0003426 TAO:0000091 ZFA:0000091 axial chorda mesoderm chorda mesoderm dorsal mesoderm presumptive notochord uberon UBERON:0004880 chordamesoderm The central region of trunk mesoderm. This tissue forms the notochord https://orcid.org/0000-0002-6601-2165 Notochord rudiment[ZFIN:ZDB-PUB-961014-576]. ZFIN:ZDB-PUB-961014-576 axial chorda mesoderm ZFA:0000091 dorsal mesoderm https://github.com/obophenotype/uberon/wiki/The-neural-crest presumptive notochord ZFA:0000091 The mass of tissue made up of mesenchymal cells in the lung. EMAPA:32866 lung-associated mesenchyme mesenchyme of lung pulmonary mesenchyme uberon UBERON:0004883 lung mesenchyme The mass of tissue made up of mesenchymal cells in the lung. GO:0060484 lung-associated mesenchyme GO:0060484 mesenchyme of lung OBOL:automatic pulmonary mesenchyme GO:0060484 A neuron projection bundle that connects the retina or its analog in the eye with the brain. This includes the vertebrate optic nerve (not truly a nerve) as well as analogous structures such as the Bolwig nerve in Drosophila optic nerve BTO:0000966 EV:0100351 FBbt:00001956 TADS:0000232 optic nerve (generic) uberon UBERON:0004904 for the vertebrate-specific structure, see UBERON:0000941 (cranial nerve II) neuron projection bundle connecting eye with brain A neuron projection bundle that connects the retina or its analog in the eye with the brain. This includes the vertebrate optic nerve (not truly a nerve) as well as analogous structures such as the Bolwig nerve in Drosophila http://orcid.org/0000-0002-6601-2165 optic nerve BTO:0000966 Anatomical cluster that connects two or more adjacent skeletal elements or hardened body parts. FBbt:00005811 joint uberon UBERON:0004905 articulation Anatomical cluster that connects two or more adjacent skeletal elements or hardened body parts. http://orcid.org/0000-0002-6601-2165 A portion of the gut that is derived from ectoderm. ectodermal gut gut ectoderm uberon UBERON:0004906 ectodermal part of digestive tract A portion of the gut that is derived from ectoderm. GO:0007439 gut ectoderm EMAPA:32930 The region of the digestive tract extending from the beginning of the intestines to the anus[GO - gut definition]. MA class was moved from here. See https://github.com/obophenotype/uberon/issues/509 WP: small intestine, large intestine, anus. Anal canal not part of LGIT according to FMA, but anus is considered part of LGIT according to WP. Duodenum overlaps both U/L gut FMA:49179 NCIT:C33010 SCTID:279973004 UMLS:C0226875 Wikipedia:Alimentary_canal#Upper_gastrointestinal_tract galen:LowerGastrointestinalTract lower GI tract lower gastrointestinal tract uberon UBERON:0004907 lower digestive tract The region of the digestive tract extending from the beginning of the intestines to the anus[GO - gut definition]. Wikipedia:Alimentary_canal#Upper_gastrointestinal_tract MA class was moved from here. See https://github.com/obophenotype/uberon/issues/509 MA WP: small intestine, large intestine, anus. Anal canal not part of LGIT according to FMA, but anus is considered part of LGIT according to WP. Duodenum overlaps both U/L FMA gut GO:0048565 UMLS:C0226875 ncithesaurus:Lower_Gastrointestinal_Tract The region of the digestive tract extending from the mouth cavity through pharynx esophagus stomach and duodenum. WP: small intestine, large intestine, anus. Anal canal not part of LGIT according to FMA, but anus is considered part of LGIT according to WP. Duodenum overlaps both U/L. In Galen, entire GI tract excludes esophagus FMA:49177 NCIT:C33837 SCTID:181244000 UMLS:C0226874 Wikipedia:Alimentary_canal#Upper_gastrointestinal_tract galen:UpperGastrointestinalTract upper GI tract upper gastrointestinal tract uberon UBERON:0004908 upper digestive tract The region of the digestive tract extending from the mouth cavity through pharynx esophagus stomach and duodenum. Wikipedia:Alimentary_canal#Upper_gastrointestinal_tract WP: small intestine, large intestine, anus. Anal canal not part of LGIT according to FMA, but anus is considered part of LGIT according to WP. Duodenum overlaps both U/L. In Galen, entire GI tract excludes esophagus FMA UMLS:C0226874 ncithesaurus:Upper_Gastrointestinal_Tract An epithelium surrounding a gonad. after reasoning this should subsume the more specific germinal epithelium classes. We include the fly structure here although it is not clear if the sheath is an epithelium or a multi-tissue structure that includes epithelium as parts EHDAA:4032 EHDAA:5931 FBbt:00004859 NCIT:C32676 UMLS:C1517534 gonad epithelium gonadal epithelium uberon gonadal sheath UBERON:0004909 epithelium of gonad An epithelium surrounding a gonad. OBOL:automatic UMLS:C1517534 ncithesaurus:Germinal_Epithelium gonad epithelium OBOL:automatic gonadal epithelium OBOL:automatic gonadal sheath FBbt:00004859 An epithelium surrounding an ovary. after reasoning this should subsume the more specific germinal epithelium classes. We include the fly structure here although it is not clear if the sheath is an epithelium or a multi-tissue structure that includes epithelium as parts BTO:0003661 FBbt:00004896 ovarian epithelium ovary epithelium ovarian sheath uberon UBERON:0004911 epithelium of female gonad An epithelium surrounding an ovary. OBOL:automatic ovarian epithelium OBOL:automatic ovary epithelium OBOL:automatic ovarian sheath FBbt:00004896 A proximal-distal subdivision of the digestive tract. intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct. FBbt:00100315 FMA:71131 uberon alimentary system subdivision intestinal tract segment of intestinal tract subdivision of alimentary system UBERON:0004921 subdivision of digestive tract A proximal-distal subdivision of the digestive tract. http://orcid.org/0000-0002-6601-2165 alimentary system subdivision FMA:71131 subdivision of alimentary system FMA:71131 A part of a wall of an organ that forms a layer. FMA:82485 uberon UBERON:0004923 organ component layer A part of a wall of an organ that forms a layer. http://orcid.org/0000-0002-6601-2165 The tissue underlying the tunica mucosa of the pharynx. BTO:0002113 FMA:75144 SCTID:19594009 pharyngeal submucosa pharynx submucosa tela submucosa pharyngea tela submucosa pharyngis uberon pharyngobasilar fascia submucous coat of pharynx submucous layer of pharynx UBERON:0004924 submucosa of pharynx The tissue underlying the tunica mucosa of the pharynx. BTO:0002113 pharyngeal submucosa FMA:75144 pharynx submucosa OBOL:automatic tela submucosa pharyngea FMA:75144 FMA:TA tela submucosa pharyngis BTO:0002113 submucous coat of pharynx BTO:0002113 submucous layer of pharynx BTO:0002113 A submucosa that is part of a sigmoid colon [Automatically generated definition]. FMA:15027 sigmoid colon submucosa uberon UBERON:0004932 submucosa of sigmoid colon A submucosa that is part of a sigmoid colon [Automatically generated definition]. OBOL:automatic sigmoid colon submucosa OBOL:automatic A mucosa that is part of a sigmoid colon [Automatically generated definition]. FMA:15026 mucosa of organ of sigmoid colon mucous membrane of sigmoid colon organ mucosa of sigmoid colon sigmoid colon mucosa sigmoid colon mucosa of organ sigmoid colon mucous membrane sigmoid colon organ mucosa uberon UBERON:0004993 mucosa of sigmoid colon A mucosa that is part of a sigmoid colon [Automatically generated definition]. OBOL:automatic mucosa of organ of sigmoid colon OBOL:automatic mucous membrane of sigmoid colon OBOL:automatic organ mucosa of sigmoid colon OBOL:automatic sigmoid colon mucosa OBOL:automatic sigmoid colon mucosa of organ OBOL:automatic sigmoid colon mucous membrane OBOL:automatic sigmoid colon organ mucosa OBOL:automatic A mucosa that is part of a lower lip [Automatically generated definition]. FMA:59833 NCIT:C12225 SCTID:362089001 UMLS:C0226939 lower labial mucosa lower lip mucosa lower lip mucosa of organ lower lip mucous membrane lower lip organ mucosa mucosa of organ of lower lip mucous membrane of lower lip organ mucosa of lower lip uberon UBERON:0005032 mucosa of lower lip A mucosa that is part of a lower lip [Automatically generated definition]. OBOL:automatic UMLS:C0226939 ncithesaurus:Mucosa_of_the_Lower_Lip lower labial mucosa UBERON:cjm lower lip mucosa OBOL:automatic lower lip mucosa of organ OBOL:automatic lower lip mucous membrane OBOL:automatic lower lip organ mucosa OBOL:automatic mucosa of organ of lower lip OBOL:automatic mucous membrane of lower lip OBOL:automatic organ mucosa of lower lip OBOL:automatic An external genitalia that is part of a female reproductive system [Automatically generated definition]. in eutherians, this is known as the vulva in and composed of the mons pubis, the labia majora and minora, the clitoris, the vestibule of the vagina and its glands, and the opening of the urethra and of the vagina [MP:0003126] BTO:0003100 EMAPA:30984 FMA:45649 SCTID:362234008 galen:FemaleExternalGenitalia external female genital organ external genitalia of female reproductive system female external genitalia uberon organa genitalia feminina externa UBERON:0005056 TODO: Relabel. Make distinct organ class. See https://github.com/obophenotype/uberon/issues/547 external female genitalia An external genitalia that is part of a female reproductive system [Automatically generated definition]. OBOL:automatic external female genital organ BTO:0003100 external genitalia of female reproductive system OBOL:automatic female external genitalia FMA:45649 organa genitalia feminina externa BTO:0003100 An organ that is part of a immune system [Automatically generated definition]. immune system organ uberon UBERON:0005057 immune organ An organ that is part of a immune system [Automatically generated definition]. OBOL:automatic A gland that is part of a hemolymphoid system [Automatically generated definition]. hemopoietic or lymphoid organ EMAPA:18766 MA:0002962 hemopoietic or lymphoid gland uberon haemolymphoid system gland UBERON:0005058 hemolymphoid system gland A gland that is part of a hemolymphoid system [Automatically generated definition]. OBOL:automatic hemopoietic or lymphoid organ GO:0048534 hemopoietic or lymphoid gland http://orcid.org/0000-0002-6601-2165 haemolymphoid system gland EMAPA:18766 The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds. The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]. AAO:0011071 EMAPA:35594 FMA:295624 NCIT:C34224 SCTID:361463007 UMLS:C0814992 Wikipedia:Neural_groove XAO:0000248 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1363 uberon UBERON:0005061 neural groove The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds. GO:0001842 Wikipedia:Neural_groove http://orcid.org/0000-0002-6601-2165 The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]. Wikipedia:Neural_groove UMLS:C0814992 ncithesaurus:Neural_Groove One of the two elevated edges of the neural groove[GO,MP]. In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]. EHDAA2:0001249 FMA:295618 NCIT:C34223 SCTID:361461009 UMLS:C0814993 Wikipedia:Neural_fold XAO:0004087 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1364 medullary fold uberon UBERON:0005062 neural fold One of the two elevated edges of the neural groove[GO,MP]. GO:0001842 MP:0011256 Wikipedia:Neural_fold In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]. Wikipedia:Neural_fold UMLS:C0814993 ncithesaurus:Neural_Fold medullary fold MP:0011256 A solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts[GO]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube[ZFIN]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO] EFO:0003498 TAO:0000133 ZFA:0000133 uberon neural tube rod UBERON:0005068 neural rod A solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts[GO]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube[ZFIN]. GO:0014024 ZFA:0000133 An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000133 TAO ZFIN:curator neural tube rod GO:0014027 An anatomical boundary that adjacent_to a forebrain and adjacent_to a midbrain. The boundary between the diencephalon and the mesencephalon.[TAO] relationship loss: develops_from forebrain midbrain boundary neural tube (TAO:0007040)[TAO] EMAPA:36449 TAO:0001367 ZFA:0001367 diencephalic-mesencephalic boundary forebrain midbrain boundary forebrain-midbrain boundary region uberon UBERON:0005075 forebrain-midbrain boundary definitional An anatomical boundary that adjacent_to a forebrain and adjacent_to a midbrain. OBOL:automatic The boundary between the diencephalon and the mesencephalon.[TAO] 2012-08-14 TAO:0001367 TAO ZFIN:curator relationship loss: develops_from forebrain midbrain boundary neural tube (TAO:0007040)[TAO] 2012-08-14 TAO:0001367 TAO diencephalic-mesencephalic boundary ZFA:0001367 forebrain midbrain boundary ZFA:0001367 forebrain-midbrain boundary region EMAPA:36449 An anatomical boundary that adjacent_to a hindbrain and adjacent_to a spinal cord. hindbrain-spinal cord boundary region uberon UBERON:0005076 hindbrain-spinal cord boundary An anatomical boundary that adjacent_to a hindbrain and adjacent_to a spinal cord. OBOL:automatic A hole in a tube[GO]. AEO:0000078 EHDAA2:0004618 RETIRED_EHDAA2:0003078 uberon UBERON:0005082 tube lumen A hole in a tube[GO]. GO:0060609 An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm[GO] consder adding placodal ectoderm as a distinct class? Also place placodal ectoderm as develops_from ectoderm; need to check taxon-appropriateness With the exception of the adenohypophysis, homologues of the nonneurogenic placodes (e.g. placodes giving rise to the teeth, hair follicles and lens), appear to be lacking in invertebrate chordates. in GO, covers optic, otic, olfactory, mammary, hair, tooth, sebaceous - and also insect structures AEO:0000218 uberon epithelial placode UBERON:0005085 ectodermal placode An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm[GO] GO:0060788 in GO, covers optic, otic, olfactory, mammary, hair, tooth, sebaceous - and also insect structures GO https://github.com/geneontology/go-ontology/issues/12223#issuecomment-215692347 epithelial placode AEO:0000112 Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO]. in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila EMAPA:32715 FBbt:00005073 FMA:30316 musculus uberon muscle muscle element UBERON:0005090 muscle structure Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO]. GO:0061061 musculus FMA:30316 Three major adaptations, or 'novel cardiac components', that were not present in the ancestor chordate heart tube can be distinguished in the lower vertebrate heart: the atrium, ventricle, and possibly the muscular sinus venosus.[uncertain][VHOG] EHDAA2:0001841 EHDAA:484 EMAPA:16239 FMA:70318 VHOG:0000489 sinus venosus right horn uberon UBERON:0005092 right horn of sinus venosus FMA Three major adaptations, or 'novel cardiac components', that were not present in the ancestor chordate heart tube can be distinguished in the lower vertebrate heart: the atrium, ventricle, and possibly the muscular sinus venosus.[uncertain][VHOG] 2012-09-17 VHOG:0000489 VHOG DOI:10.1152/physrev.00006.2003 Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003 http://bgee.unil.ch/ sinus venosus right horn VHOG:0000489 A bud is a protrusion that forms from an epithelial sheet by localized folding. BTO:0001639 uberon UBERON:0005153 epithelial bud A bud is a protrusion that forms from an epithelial sheet by localized folding. GO:0060572 Any anatomical structure that is part of the reproductive system. reproductive system element reproductive system structure uberon UBERON:0005156 reproductive structure Any anatomical structure that is part of the reproductive system. http://orcid.org/0000-0002-6601-2165 An epithelial sheet bent on a linear axis. uberon UBERON:0005157 epithelial fold An epithelial sheet bent on a linear axis. GO:0060571 The functional tissue of the central nervous system consisting of neurons and glial cells. CNS parenchyma central nervous system parenchyma parenchyma of CNS parenchyma of central nervous system uberon UBERON:0005158 parenchyma of central nervous system The functional tissue of the central nervous system consisting of neurons and glial cells. CL:tm https://github.com/obophenotype/uberon/issues/8 CNS parenchyma OBOL:automatic central nervous system parenchyma OBOL:automatic parenchyma of CNS OBOL:automatic A remnant structure from earlier development or evolution. Wikipedia:Vestigiality uberon UBERON:0005160 vestigial structure A remnant structure from earlier development or evolution. PATOC:MAH A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part. we go with the FMA classification rather than the CARO one. FMA def: 'Anatomical cluster which has as direct parts cell parts from two or more cells.' AAO:0011000 CARO:0001000 FBbt:00007060 FMA:83115 multi-cell-component structure multi-cell-part structure uberon cell part cluster UBERON:0005162 multi cell part structure FMA A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part. CARO:0001000 we go with the FMA classification rather than the CARO one. FMA def: 'Anatomical cluster which has as direct parts cell parts from two or more cells.' CARO FMA multi-cell-component structure CARO:0001000 multi-cell-part structure CARO:0001000 cell part cluster FMA:83115 An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland. MA:0000522 SCTID:272631008 abdomen organ uberon UBERON:0005172 abdomen element An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland. http://orcid.org/0000-0002-6601-2165 abdomen organ MA:0000522 An organ or element that is part of the adbominal segment of the organism. This region can be further subdivided into the abdominal cavity and the pelvic region. EMAPA:37062 MA:0000529 abdominal segment organ uberon UBERON:0005173 abdominal segment element An organ or element that is part of the adbominal segment of the organism. This region can be further subdivided into the abdominal cavity and the pelvic region. http://orcid.org/0000-0002-6601-2165 EMAPA:37062 MA:th abdominal segment organ MA:0000529 An organ or element that part of the dorsum of the organism. Examples: spinal cord, vertebrae, muscles of back. EMAPA:37274 MA:0001901 back organ dorsal region organ uberon UBERON:0005174 dorsal region element An organ or element that part of the dorsum of the organism. Examples: spinal cord, vertebrae, muscles of back. http://orcid.org/0000-0002-6601-2165 EMAPA:37274 MA:th back organ MA:0001901 An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions. EMAPA:37270 MA:0000516 trunk organ uberon UBERON:0005177 trunk region element An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions. http://orcid.org/0000-0002-6601-2165 EMAPA:37270 MA:th trunk organ MA:0000516 An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli. EMAPA:37273 MA:0000557 thoracic cavity organ uberon UBERON:0005178 thoracic cavity element An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli. http://orcid.org/0000-0002-6601-2165 EMAPA:37273 MA:th thoracic cavity organ MA:0000557 An organ or element that is part of the pelvic region. Examples: reproductive organs (in some organisms), urinary bladder, bones of the pelvis. EMAPA:37275 MA:0000543 pelvic element pelvis organ pelvis region organ uberon UBERON:0005179 pelvic region element An organ or element that is part of the pelvic region. Examples: reproductive organs (in some organisms), urinary bladder, bones of the pelvis. http://orcid.org/0000-0002-6601-2165 EMAPA:37275 MA:th pelvis organ MA:0000543 An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions. EMAPA:37271 MA:0000563 uberon upper body organ UBERON:0005181 thoracic segment organ An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions. http://orcid.org/0000-0002-6601-2165 EMAPA:37271 MA:th upper body organ MA:0000563 A vein that is part of a thorax [Automatically generated definition]. EMAPA:37197 MA:0002235 NCIT:C53142 SCTID:281472008 UMLS:C0226629 uberon UBERON:0005194 thoracic vein A vein that is part of a thorax [Automatically generated definition]. OBOL:automatic EMAPA:37197 MA:th UMLS:C0226629 ncithesaurus:Thoracic_Vein A gland that is part of a larynx submucosa [Automatically generated definition]. EMAPA:35475 MA:0002729 uberon laryngeal submucosa gland UBERON:0005204 larynx submucosa gland A gland that is part of a larynx submucosa [Automatically generated definition]. OBOL:automatic laryngeal submucosa gland EMAPA:35475 An external ectoderm that is part of a optic eminence [Automatically generated definition]. EMAPA:16539 RETIRED_EHDAA2:0001311 VHOG:0000520 uberon UBERON:0005216 optic eminence surface ectoderm true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships An external ectoderm that is part of a optic eminence [Automatically generated definition]. OBOL:automatic An ectoderm that is part of a optic eminence [Automatically generated definition]. EHDAA:940 EMAPA:16539 RETIRED_EHDAA2:0001309 VHOG:0001105 uberon UBERON:0005234 optic eminence ectoderm An ectoderm that is part of a optic eminence [Automatically generated definition]. OBOL:automatic The ventral half of the developing neural tube that is the metencephalon. [Chordate_evolution_and_the_origin_of_craniates:_An_old_brain_in_a_new_head._AnaT_Rec_(New_Anat)_(2000)_261(3):_111-125, See_Butler_AB][VHOG] EHDAA2:0001154 EMAPA:17078 VHOG:0000320 metencephalon basal plate uberon UBERON:0005239 basal plate metencephalon The ventral half of the developing neural tube that is the metencephalon. [Chordate_evolution_and_the_origin_of_craniates:_An_old_brain_in_a_new_head._AnaT_Rec_(New_Anat)_(2000)_261(3):_111-125, See_Butler_AB][VHOG] 2012-09-17 VHOG:0000320 VHOG http://bgee.unil.ch/ metencephalon basal plate EHDAA2:0001154 An endocardium that is part of a interventricular septum [Automatically generated definition]. TODO - split? EHDAA2:0000886 EHDAA2:0000887 FMA:83584 VHOG:0000615 endocardium of interventricular septum uberon interventricular septum endocardial tissue UBERON:0005243 interventricular septum endocardium An endocardium that is part of a interventricular septum [Automatically generated definition]. OBOL:automatic endocardium of interventricular septum FMA:83584 interventricular septum endocardial tissue VHOG:0000615 A myocardium that is part of a bulbus cordis [Automatically generated definition]. EMAPA:36488 VHOG:0000609 uberon bulbus cordis cardiac muscle UBERON:0005248 bulbus cordis myocardium A myocardium that is part of a bulbus cordis [Automatically generated definition]. OBOL:automatic bulbus cordis cardiac muscle VHOG:0000609 A gland that is part of a stomodeum. check this VHOG:0000658 stomatodaeum gland uberon UBERON:0005250 stomatodeum gland A gland that is part of a stomodeum. OBOL:automatic stomatodaeum gland VHOG:0000658 Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells. Mesoderm that will give rise, along with cranial neural crest cells, to connective tissue, bone and musculature in the head. (Source: BioGlossary, www.Biology-Text.com)[TAO] EFO:0003492 EHDAA2:0000732 EHDAA:179 EMAPA:16098 EMAPA_RETIRED:16269 FMA:76622 TAO:0000113 VHOG:0000332 ZFA:0000113 cephalic mesenchyme uberon cranial mesenchyme desmocranium UBERON:0005253 head mesenchyme EHDAA2 Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells. ISBN:0683400088 MP:0011260 Mesoderm that will give rise, along with cranial neural crest cells, to connective tissue, bone and musculature in the head. (Source: BioGlossary, www.Biology-Text.com)[TAO] 2012-08-14 TAO:0000113 TAO ZFIN:curator cephalic mesenchyme MP:0011260 cranial mesenchyme MGI:anna desmocranium FMA:76622 Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 EHDAA:377 EMAPA:16177 TAO:0000081 VHOG:0000281 ZFA:0000081 uberon trunk and cervical mesenchyme UBERON:0005256 trunk mesenchyme EHDAA2 Mesenchyme that is part of a developing trunk. OBOL:automatic trunk and cervical mesenchyme EHDAA2:0002092 The posterior part of the developing vertebrate hindbrain or the corresponding part of the adult brain composed of the medulla oblongata and a portion of the fourth ventricle; as well as the glossopharyngeal nerve (CN IX), vagus nerve (CN X), accessory nerve (CN XI), hypoglossal nerve (CN XII), and a portion of the vestibulocochlear nerve (CN VIII).[BTO,WP]. The posterior of the two brain vesicles formed by specialization of the rhombencephalon in the developing embryo, it comprises the medulla oblongata. [TFD][VHOG] The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG] the terms metencephalon and myelencephalon are only meaningful in mammals and birds - Neuroanatomy of the Zebrafish Brain. Note that its not clear if this refers to the developing medulla oblongata - MA (adult) has two distinct classes BTO:0000758 CALOHA:TS-0607 CALOHA:TS-2365 DHBA:10662 EHDAA2:0001207 EHDAA:5526 EMAPA:17082 HBA:9512 MA:0000205 VHOG:0000456 Wikipedia:Myelencephalon uberon myelencephalon (medulla oblongata) UBERON:0005290 myelencephalon http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg definitional The posterior part of the developing vertebrate hindbrain or the corresponding part of the adult brain composed of the medulla oblongata and a portion of the fourth ventricle; as well as the glossopharyngeal nerve (CN IX), vagus nerve (CN X), accessory nerve (CN XI), hypoglossal nerve (CN XII), and a portion of the vestibulocochlear nerve (CN VIII).[BTO,WP]. BTO:0000758 Wikipedia:Myelencephalon The posterior of the two brain vesicles formed by specialization of the rhombencephalon in the developing embryo, it comprises the medulla oblongata. [TFD][VHOG] 2012-09-17 VHOG:0000456 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/myelencephalon The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000456 VHOG ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500 http://bgee.unil.ch/ myelencephalon (medulla oblongata) DHBA:10662 A portion of tissue that is part of an embryo. CALOHA:TS-2100 portion of embryonic tissue uberon developing tissue UBERON:0005291 embryonic tissue A portion of tissue that is part of an embryo. OBOL:automatic portion of embryonic tissue OBOL:automatic Portion of tissue that is contiguous with the embryo and is comprised of portions of tissue or cells that will not contribute to the embryo. BTO:0003360 CALOHA:TS-2119 EFO:0001406 MAT:0000061 MIAA:0000061 extra-embryonic tissue uberon UBERON:0005292 extraembryonic tissue Portion of tissue that is contiguous with the embryo and is comprised of portions of tissue or cells that will not contribute to the embryo. https://orcid.org/0000-0002-6601-2165 The endothelial lining of the endocardium. FMA:83596 endocardium endothelium endothelium of endocardium uberon UBERON:0005316 endocardial endothelium The endothelial lining of the endocardium. UBERON:cjm endocardium endothelium FMA:83596 endothelium of endocardium FMA:83596 An pulmonary artery endothelium is an epithelium that lines the pulmonary artery[GO]. BTO:0000137 pulmonary artery endothelial tube uberon UBERON:0005317 pulmonary artery endothelium An pulmonary artery endothelium is an epithelium that lines the pulmonary artery[GO]. GO:0061155 pulmonary artery endothelial tube GO:0061155 A lamina propria that is part of a mucosa of oral region. EMAPA:26947 lamina propria of oral mucosa uberon UBERON:0005334 oral lamina propria A lamina propria that is part of a mucosa of oral region. OBOL:automatic A ventricular outflow tract is a portion of either the left ventricle or right ventricle of the heart through which blood passes in order to enter the great arteries. The right ventricular outflow tract (RVOT) is an infundibular extension of the ventricular cavity which connects to the pulmonary artery. The left ventricular outflow tract (LVOT), which connects to the aorta, is nearly indistinguishable from the rest of the ventricle[WP]. FMA:13225 Wikipedia:Ventricular_outflow_tract XAO:0004140 heart ventricle outflow tract outflow part of ventricle ventricular outflow tract uberon UBERON:0005337 outflow tract of ventricle A ventricular outflow tract is a portion of either the left ventricle or right ventricle of the heart through which blood passes in order to enter the great arteries. The right ventricular outflow tract (RVOT) is an infundibular extension of the ventricular cavity which connects to the pulmonary artery. The left ventricular outflow tract (LVOT), which connects to the aorta, is nearly indistinguishable from the rest of the ventricle[WP]. Wikipedia:Ventricular_outflow_tract heart ventricle outflow tract MP:0010224 ventricular outflow tract Wikipedia:Ventricular_outflow_tract An outflow tract that is part of a aorta. merge with LVOT? EHDAA2:0001353 EMAPA:17329 MA:0000101 VHOG:0001394 uberon UBERON:0005338 outflow tract aortic component An outflow tract that is part of a aorta. OBOL:automatic merge with RVOT? EHDAA2:0001359 EHDAA:4401 EMAPA:17330 MA:0000102 VHOG:0001395 uberon UBERON:0005339 outflow tract pulmonary component The outer neural tube region in which post-mitotic neuroblasts migrate along radial glia to form the adult cortical layers[MP]. A single stem cell in the ventricular layer can give rise to neurons (and glial cells) in any of the cortical layers (Walsh and Cepko 1988)[NCBIBook:NBK10047] in humans develops into cortical layers II-VI CP CxP BAMS:CTXpl DHBA:10515 EMAPA:32711 MBA:695 PBA:294021914 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=2702 cerebral cortex cortical plate future cortical layers II-VI neocortex cortical plate uberon future neocortex UBERON:0005343 cortical plate NCBIBook:NBK10047 The outer neural tube region in which post-mitotic neuroblasts migrate along radial glia to form the adult cortical layers[MP]. MP:0008439 http://www.ncbi.nlm.nih.gov/books/NBK10047 CP BRAINSPAN:BRAINSPAN CxP PMID:23375746 future cortical layers II-VI http://orcid.org/0000-0002-6601-2165 future neocortex http://orcid.org/0000-0002-6601-2165 the group of sensory neuron cell bodies associated with the vagus nerve gX EMAPA:16798 FMA:53472 MA:0001081 SCTID:244452001 TAO:0007067 VHOG:0000684 Wikipedia:Vagus_ganglion ZFA:0007067 ganglion of vagus nerve right glossopharyngeal ganglion vagal ganglion vagus ganglion vagus neural ganglion uberon vagus X UBERON:0005362 vagus X ganglion ZFA the group of sensory neuron cell bodies associated with the vagus nerve ISBN:0-683-40008-8 MP:0001100 gX ZFA:0007067 ganglion of vagus nerve FMA:53472 right glossopharyngeal ganglion FMA:53472 vagal ganglion ZFA:0007067 vagus neural ganglion FMA:53472 vagus X EMAPA:16798 An array of photoreceptors and any supporting cells found in an eye. FBbt:00004200 light-sensitive tissue uberon UBERON:0005388 photoreceptor array An array of photoreceptors and any supporting cells found in an eye. https://orcid.org/0000-0002-6601-2165 A transparent structure that is part of a visual sense organ, the function of which is to direct or focus light onto a photoreceptor array. directing or focusing light onto light receptors lens uberon UBERON:0005389 transparent eye structure A transparent structure that is part of a visual sense organ, the function of which is to direct or focus light onto a photoreceptor array. http://orcid.org/0000-0002-6601-2165 One of: the common carotid artery, or its branches, the external and internal carotid arteries. This is a generic grouping class that is the superclass of the trunks/branches of the common carotid artery. Note that AOs vary widely in how they divide up and generalize arteries Artery originating at the junction of the first two aortic arches and supplying the anterior brain. Kimmel et al, 1995.[TAO] AAO:0010217 BTO:0000168 CALOHA:TS-0116 EFO:0000818 EHDAA:6385 EMAPA:18609 EV:0100379 FMA:70504 GAID:478 MA:0001925 MAT:0000501 MESH:D002339 NCIT:C12687 OpenCyc:Mx4rvg7rcJwpEbGdrcN5Y29ycA SCTID:362040006 SCTID:69105007 TAO:0000097 UMLS:C0007272 VHOG:0000266 Wikipedia:Carotid_artery ZFA:0000097 galen:CarotidArtery carotid carotid artery subdivision of common carotid artery uberon common carotid arterial subdivision UBERON:0005396 carotid artery segment FMA One of: the common carotid artery, or its branches, the external and internal carotid arteries. Wikipedia:Carotid_artery https://sourceforge.net/tracker/?func=detail&aid=3486870&group_id=76834&atid=994764 Artery originating at the junction of the first two aortic arches and supplying the anterior brain. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000097 TAO ZFIN:curator UMLS:C0007272 ncithesaurus:Carotid_Artery carotid AAO:0010217 carotid artery MA:0001925 subdivision of common carotid artery FMA:70504 common carotid arterial subdivision FMA:70504 A sex gland that is part of a female reproductive system. BTO:0000254 MA:0000383 uberon UBERON:0005398 female reproductive gland A sex gland that is part of a female reproductive system. OBOL:automatic A gray matter that is part of a cerebral hemisphere. BTO may actually be a more generic structure; FMA may represent a more specific structure. Consider merging with gray matter of telencephalon BTO:0000823 CALOHA:TS-2361 EMAPA:37477 FMA:61821 MA:0000944 cerebral gray matter cerebral grey matter cerebral hemisphere grey matter uberon UBERON:0005401 cerebral hemisphere gray matter A gray matter that is part of a cerebral hemisphere. OBOL:automatic BTO may actually be a more generic structure; FMA may represent a more specific structure. Consider merging with gray matter of telencephalon BTO EMAPA:37477 MA:th cerebral gray matter BTO:0000823 cerebral grey matter MA:0000944 The part of the digestive system that excludes the hepatobiliary system. the decision to split digestive and gastrointestinal in this way may be revisited. As it currently stands, this class more closely aligns what MA calls the alimentary system The system that includes the esophagus, stomach, small and large intestine, anus, liver, biliary tract, and pancreas[ncithesaurus:Gastrointestinal_System]. All metazoans (with degenerate exceptions) have some sort of digestive cavity with a means of entrance to and exit from it.[well established][VHOG] that many anatomy ontologies consider this synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class. We have one entity that is part of both gastrointestinal and hepatobiliary systems: hepatopancreatic ampulla. BTO:0000058 CALOHA:TS-0407 EHDAA2:0000110 EHDAA:514 EMAPA:16246 EV:0100056 FMA:71132 GAID:294 MA:0000323 MESH:A03.492 NCIT:C12378 SCTID:373871007 UMLS:C0012240 VHOG:0000412 galen:GastrointestinalTract uberon GI tract alimentary system alimentary tract gastro-intestinal system gastroenterological system gastrointestinal (GI) tract gastrointestinal system gastrointestinal tract UBERON:0005409 alimentary part of gastrointestinal system The part of the digestive system that excludes the hepatobiliary system. http://orcid.org/0000-0002-6601-2165 The system that includes the esophagus, stomach, small and large intestine, anus, liver, biliary tract, and pancreas[ncithesaurus:Gastrointestinal_System]. ncithesaurus:Gastrointestinal_System All metazoans (with degenerate exceptions) have some sort of digestive cavity with a means of entrance to and exit from it.[well established][VHOG] 2012-09-17 VHOG:0000412 VHOG ISBN:978-0721676685 Sherwood Romer A and Parsons T, Vertebrate body (1977) p.3 http://bgee.unil.ch/ that many anatomy ontologies consider this synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class. We have one entity that is part of both gastrointestinal and hepatobiliary systems: hepatopancreatic ampulla. MA UMLS:C0012240 ncithesaurus:Gastrointestinal_System GI tract GAID:294 alimentary system MA:0000323 alimentary tract MA:0000323 gastro-intestinal system FMA:71132 gastroenterological system UBERON:cjm gastrointestinal (GI) tract GAID:294 gastrointestinal system FMA:71132 gastrointestinal tract FMA:71132 A limb bud that develops into a hindlimb or pelvic fin. Fin bud that develops into the pelvic fin.[TAO] Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] EFO:0003469 TAO:0001384 VHOG:0001260 ZFA:0001384 hindlimb/pelvic fin bud uberon pelvic fin bud pelvic fin buds UBERON:0005420 at this time we have no need to name a more specific 'pelvic fin bud' class, but we may in future pelvic appendage bud A limb bud that develops into a hindlimb or pelvic fin. OBOL:automatic PMID:15893975 Fin bud that develops into the pelvic fin.[TAO] 2012-08-14 TAO:0001384 TAO ZFIN:curator Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] 2012-09-17 VHOG:0001260 VHOG ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268 http://bgee.unil.ch/ hindlimb/pelvic fin bud VHOG:0001260 pelvic fin bud TAO:0001384 pelvic fin buds ZFA:0001384 An apical ectodermal ridge that is part of a pelvic appendage bud. An ectodermal thickening at the end of the hindlimb bud in the developing embryo. [TFD][VHOG] Apical ectodermal ridge that is part of the pelvic fin bud.[TAO] Pectoral and pelvic fins are homologous to the tetrapod fore and hindlimb, respectively. (...) The zebrafish AER [apical ectodermal ridge] is an apical ectodermal thickening at the distal tip of the fin bud and consists of wedge-shaped cells of the basal stratum. The AER is observed only transiently, and from 36 hpf onwards the cells of this region form the apical fold (AF), which consists of a dorsal and a ventral layer of cylindrically-shaped ectodermal cells extending from the anterior to the posterior fin margin. Despite the change in shape, the AF still carries out the same functions as the AER. Indeed, although the AER receives its name from its characteristic shape, being composed of a pseudostratified ectoderm in the chicken and a polystratified ectoderm in the mouse, this independence of AER morphology from its function is also observed in tetrapods. The AF also expresses similar molecular markers to the tetrapod AER, suggesting that it fulfills similar functions in the fin as the AER does in tetrapod limbs.[well established][VHOG] EFO:0003681 EHDAA2:0003194 EMAPA:16892 TAO:0001385 VHOG:0001066 ZFA:0001385 apical ectodermal ridge hind limb apical ectodermal ridge hindlimb lower lmb bud apical ectodermal ridge uberon AER hindlimb apical ectodermal ridge pelvic fin bud leg AER UBERON:0005422 pelvic appendage apical ectodermal ridge EHDAA2 An apical ectodermal ridge that is part of a pelvic appendage bud. OBOL:automatic An ectodermal thickening at the end of the hindlimb bud in the developing embryo. [TFD][VHOG] 2012-09-17 VHOG:0001066 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/apical+ectodermal+ridge Apical ectodermal ridge that is part of the pelvic fin bud.[TAO] 2012-08-14 TAO:0001385 TAO ZIFIN:curator Pectoral and pelvic fins are homologous to the tetrapod fore and hindlimb, respectively. (...) The zebrafish AER [apical ectodermal ridge] is an apical ectodermal thickening at the distal tip of the fin bud and consists of wedge-shaped cells of the basal stratum. The AER is observed only transiently, and from 36 hpf onwards the cells of this region form the apical fold (AF), which consists of a dorsal and a ventral layer of cylindrically-shaped ectodermal cells extending from the anterior to the posterior fin margin. Despite the change in shape, the AF still carries out the same functions as the AER. Indeed, although the AER receives its name from its characteristic shape, being composed of a pseudostratified ectoderm in the chicken and a polystratified ectoderm in the mouse, this independence of AER morphology from its function is also observed in tetrapods. The AF also expresses similar molecular markers to the tetrapod AER, suggesting that it fulfills similar functions in the fin as the AER does in tetrapod limbs.[well established][VHOG] 2012-09-17 VHOG:0001066 VHOG DOI:10.1111/j.1440-169X.2007.00942.x http://bgee.unil.ch/ apical ectodermal ridge hind limb VHOG:0001066 apical ectodermal ridge hindlimb VHOG:0001066 lower lmb bud apical ectodermal ridge EHDAA2:0003194 AER hindlimb VHOG:0001066 apical ectodermal ridge pelvic fin bud TAO:0001385 AEO:0000125 CALOHA:TS-2122 EHDAA2:0003125 FBbt:00007006 FMA:292313 MIAA:0000019 uberon developing structure developmental structure developmental tissue UBERON:0005423 developing anatomical structure developmental tissue MIAA:0000019 Portion of tissue that is the inner layer of the optic cup and will become the neural retina. (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] EHDAA2:0001304 EMAPA:16675 TAO:0001071 VHOG:0000490 ZFA:0001071 future neural retina future retinal neural layer inner layer optic cup optic cup inner layer presumptive retinas uberon future NR future neural epithelium future neural layer presumptive retina UBERON:0005425 presumptive neural retina Portion of tissue that is the inner layer of the optic cup and will become the neural retina. ZFIN:curator (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] 2012-09-17 VHOG:0000490 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 http://bgee.unil.ch/ inner layer optic cup ZFA:0001071 optic cup inner layer EHDAA2:0001304 presumptive retinas ZFA:0001071 future neural epithelium EMAPA:16675 future neural layer EMAPA:16675 presumptive retina TAO:0001071 Portion of tissue that gives rise to the lens. A vesicle formed from the lens pit of the embryo, developing into the crystalline lens. [TFD][VHOG] (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG] the lens of zebrafish (and other teleosts) forms from delamination of cells from the lens placode; thus, there is no formation of a hollow lens vesicle, in contrast to the situation in mammals and birds (Glass and Dahm, 2004) [PMID:16496288] The lens of the zebrafish forms by delamination of lens placodal cells and not through invagination. This results in a solid spherical mass as opposed to a hollow lens vesicle. Detachment of the solid lens vesicle of zebrafish at 24b26 hpf is accomplished in part by apoptosis, similar to mammals EHDAA2:0000983 EHDAA:4737 EMAPA:17163 SCTID:361510002 TAO:0002205 VHOG:0001163 ZFA:0001679 hollow lens vesicle solid lens vesicle uberon immature lens lens mass presumptive lens UBERON:0005426 lens vesicle Portion of tissue that gives rise to the lens. ZFIN:curator https://sourceforge.net/tracker/?func=detail&atid=994726&aid=3514998&group_id=76834 A vesicle formed from the lens pit of the embryo, developing into the crystalline lens. [TFD][VHOG] 2012-09-17 VHOG:0001163 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/lens+vesicle (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG] 2012-09-17 VHOG:0001163 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 http://bgee.unil.ch/ the lens of zebrafish (and other teleosts) forms from delamination of cells from the lens placode; thus, there is no formation of a hollow lens vesicle, in contrast to the situation in mammals and birds (Glass and Dahm, 2004) [PMID:16496288] The lens of the zebrafish forms by delamination of lens placodal cells and not through invagination. This results in a solid spherical mass as opposed to a hollow lens vesicle. Detachment of the solid lens vesicle of zebrafish at 24b26 hpf is accomplished in part by apoptosis, similar to mammals ZFA hollow lens vesicle solid lens vesicle ZFA:0001679 immature lens ZFA:0001679 lens mass ZFA:0001679 ZFIN:ZDB-PUB-091023-49 presumptive lens ZFA:0001679 Portion of tissue that is part of the eye and gives rise to the mature, fully layered cornea. TAO:0002188 ZFA:0001688 uberon UBERON:0005427 corneal primordium ZFA Obol ZFA Portion of tissue that is part of the eye and gives rise to the mature, fully layered cornea. ZFIN:ZDB-PUB-061010-3 Vagal neural crest is adjacent to the first seven somites gives rise to both ganglionic and ectomesenchymal derivatives[ZFA]. Vagal neural crest is adjacent to the first seven somites gives rise to both ganglionic and ectomesenchymal derivatives.[TAO] We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] In chicken fate mapping studies it was found to originate from neural crest residing between Somite 1-7 (S1-7); In mouse it is considered to be derived from rhombencephalic (post otic) neural crest cells and trunk neural crest cells (anterior to S5) EHDAA2:0002156 EHDAA:669 TAO:0000818 VHOG:0001208 XAO:0004191 ZFA:0000818 VNC uberon enteric neural crest post-otic neural crest UBERON:0005428 vagal neural crest Vagal neural crest is adjacent to the first seven somites gives rise to both ganglionic and ectomesenchymal derivatives[ZFA]. ZFIN:curator Vagal neural crest is adjacent to the first seven somites gives rise to both ganglionic and ectomesenchymal derivatives.[TAO] 2012-08-14 TAO:0000818 TAO ZFIN:curator We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] 2012-09-17 VHOG:0001208 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 http://bgee.unil.ch/ In chicken fate mapping studies it was found to originate from neural crest residing between Somite 1-7 (S1-7); In mouse it is considered to be derived from rhombencephalic (post otic) neural crest cells and trunk neural crest cells (anterior to S5) filemaps.com VNC XAO:0004191 post-otic neural crest ZFA:0000818 The dilated structure that is lined by endothelial cells and located at the arterial pole of the heart just above (distal to) the truncus arteriosus in mammalian embryos; it is the primordial vascular channel from which the aortic arches (and eventually the dorsal aortae) arise; the aortic sac is homologous to the ventral aorta of gill-bearing vertebrates the merged ventral aortae of the embryo which supplies blood to the aortic arches[TMD][http://medical-dictionary.thefreedictionary.com/aortic+sac]. EHDAA2:0004145 EHDAA:9826 EMAPA:36461 FMA:71008 RETIRED_EHDAA2:0000133 SCTID:361527005 saccus aorticus uberon UBERON:0005432 aortic sac EHDAA2 EHDAA2 The dilated structure that is lined by endothelial cells and located at the arterial pole of the heart just above (distal to) the truncus arteriosus in mammalian embryos; it is the primordial vascular channel from which the aortic arches (and eventually the dorsal aortae) arise; the aortic sac is homologous to the ventral aorta of gill-bearing vertebrates MP:0012510 the merged ventral aortae of the embryo which supplies blood to the aortic arches[TMD][http://medical-dictionary.thefreedictionary.com/aortic+sac]. http://medical-dictionary.thefreedictionary.com/aortic+sac saccus aorticus FMA:24219 SCTID:123958008 cervical region neck subdivision region of neck subdivision of neck uberon UBERON:0005434 cervical region cervical region FMA:24219 neck subdivision FMA:24219 region of neck FMA:24219 subdivision of neck FMA:24219 The jugular foramen is a large aperture in the base of the skull. It is located behind the carotid canal and is formed in front by the petrous portion of the temporal, and behind by the occipital; it is generally larger on the right than on the left side Large foramen that houses the glossopharyngeal and vagus nerves and is located inside the condyloid fossa.[AAO] One of a pair of openings between the lateral part of the occipital bone and the petrous part of the temporal bones in the skull. The foramen contains the inferior petrosal sinus; the transverse sinus; some meningeal branches of the occipital and ascending pharyngeal arteries; and the glossopharyngeal, vagus, and accessory nerves. [Free_Online_Medical_Dictionary] relationship loss: subclass braincase and otic capsule opening (AAO:0000051)[AAO] AAO:0000249 EHDAA2:0000893 EHDAA:10631 EMAPA:18713 FMA:56432 NCIT:C12496 SCTID:361735006 UMLS:C0222712 VHOG:0001113 Wikipedia:Jugular_foramen Posterior lacerate foramen uberon foramen jugulare UBERON:0005456 jugular foramen http://upload.wikimedia.org/wikipedia/commons/f/fa/Foramenjugulare.PNG The jugular foramen is a large aperture in the base of the skull. It is located behind the carotid canal and is formed in front by the petrous portion of the temporal, and behind by the occipital; it is generally larger on the right than on the left side Wikipedia:Jugular_foramen Large foramen that houses the glossopharyngeal and vagus nerves and is located inside the condyloid fossa.[AAO] 2012-06-20 AAO:0000249 AAO AAO:LAP One of a pair of openings between the lateral part of the occipital bone and the petrous part of the temporal bones in the skull. The foramen contains the inferior petrosal sinus; the transverse sinus; some meningeal branches of the occipital and ascending pharyngeal arteries; and the glossopharyngeal, vagus, and accessory nerves. [Free_Online_Medical_Dictionary] 2012-09-17 VHOG:0001113 VHOG http://bgee.unil.ch/ http://medical-dictionary.thefreedictionary.com/jugular+foramen relationship loss: subclass braincase and otic capsule opening (AAO:0000051)[AAO] 2012-06-20 AAO:0000249 AAO UMLS:C0222712 ncithesaurus:Jugular_Foramen Posterior lacerate foramen FMA:56432 foramen jugulare Wikipedia:Jugular_foramen A longitudinal groove in the neural tube wall that divides the neural tube into dorsal (alar) and ventral (basal) halves (dorsal receives input from sensory neurons, ventral effects motor functions); stretches from the mesencephalon caudad[TMD]. sulcus limitans BAMS:slim BAMS:slm http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=629 neural tube lateral wall sulcus limitans uberon UBERON:0005478 sulcus limitans of neural tube EHDAA2 A longitudinal groove in the neural tube wall that divides the neural tube into dorsal (alar) and ventral (basal) halves (dorsal receives input from sensory neurons, ventral effects motor functions); stretches from the mesencephalon caudad[TMD]. http://medical-dictionary.thefreedictionary.com/Sulcus+limitans http://www.ncbi.nlm.nih.gov/books/NBK10047 neural tube lateral wall sulcus limitans EHDAA2:0001265 Cranial neural crest which gives rise to the glossopharyngeal ganglion. EHDAA2:0000714 EHDAA:660 TAO:0007066 ZFA:0007066 uberon UBERON:0005491 glossopharyngeal neural crest Cranial neural crest which gives rise to the glossopharyngeal ganglion. ZFA:0007066 Portion of tissue on the side of the lumen of the neural tube. EHDAA2:0001257 EHDAA:2873 EHDAA:912 EMAPA:16166 TAO:0001435 VHOG:0000513 ZFA:0001435 lateral wall neural tube uberon UBERON:0005496 neural tube lateral wall Portion of tissue on the side of the lumen of the neural tube. ZFA:0001435 lateral wall neural tube ZFA:0001435 todo - epidermis? todo - track down EHDAA2 class in new release In the early gastrula of vertebrates, factors from the organizer (e.g. noggin, chordin, and follistatin in Xenopus) antagonize the epidermalizing factor bone morphogenetic protein 4 (BMP4), thus dividing the epiblast into neuroectoderm. In Drosophila, decapentaplegic, the homologue of BMP4, interacts similarly with the protein short gastrulation, the homologue of chordin. Thus, a comparable molecular mechanism for distinguishing non-neural ectoderm from neural ectoderm was probably present in the common ancestor of all bilaterally symmetrical animals.[well established][VHOG] After gastrulation, neural crest cells are specified at the border of the neural plate and the non-neural ectoderm. EFO:0003643 EHDAA:257 EMAPA:16074 RETIRED_EHDAA2:0001273 TAO:0001178 VHOG:0001372 XAO:0004091 ZFA:0001178 non neural ectoderm epidermal ectoderm epithelial ectoderm uberon surface ectoderm ventral ectoderm UBERON:0005497 Gene notes: One of the first genes to be expressed in nonneural ectoderm in amphioxus is BMP2/4 (Panopoulou et al. 1998). BMP2/4 homologues appear to have a very ancient role in distinguishing neural from nonneural ectoderm; in Drosophila as well as in amphioxus and vertebrates, BMP2/4 homologues are expressed in nonneural ectoderm and function in distinguishing neural from nonneural ectoderm (Francois & Bier, 1995 ; Sasai et al. 1995 ; Wilson & Hemmati-Brivanlou, 1995; Panopoulou et al. 1998). A change in level of BMP2/4 from very high in nonneural ectoderm to low in neural ectoderm appears to be a key factor in development of neural crest (Baker & Bronner-Fraser,1997a,1997b;Erickson&Reedy,1998;Marchantet al.1998 ;Selleck et al. 1998). non-neural ectoderm ZFA In the early gastrula of vertebrates, factors from the organizer (e.g. noggin, chordin, and follistatin in Xenopus) antagonize the epidermalizing factor bone morphogenetic protein 4 (BMP4), thus dividing the epiblast into neuroectoderm. In Drosophila, decapentaplegic, the homologue of BMP4, interacts similarly with the protein short gastrulation, the homologue of chordin. Thus, a comparable molecular mechanism for distinguishing non-neural ectoderm from neural ectoderm was probably present in the common ancestor of all bilaterally symmetrical animals.[well established][VHOG] 2012-09-17 VHOG:0001372 VHOG DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999) http://bgee.unil.ch/ non neural ectoderm ZFA:0001178 epidermal ectoderm https://github.com/obophenotype/uberon/wiki/The-neural-crest epithelial ectoderm https://github.com/obophenotype/uberon/wiki/The-neural-crest surface ectoderm https://github.com/obophenotype/uberon/wiki/The-neural-crest ventral ectoderm ZFA:0001178 Multi-tissue structure that arises from the heart rudiment and will become the heart tube. EHDAA2:0001512 EHDAA:424 EHDAA:436 EMAPA:16215 FMA:321916 SCTID:361522004 TAO:0000149 Wikipedia:Primitive_heart_tube ZFA:0000149 primitive heart tube early primitive heart tube uberon UBERON:0005498 primitive heart tube ZFA Multi-tissue structure that arises from the heart rudiment and will become the heart tube. ZFA:0000149 primitive heart tube EMAPA:16215 early primitive heart tube EMAPA:16208 A neural tube lateral wall that is part of a rhombomere. EMAPA:32819 EMAPA:35364 uberon future hindbrain lateral wall UBERON:0005501 rhombomere lateral wall A neural tube lateral wall that is part of a rhombomere. OBOL:automatic future hindbrain lateral wall EMAPA:35364 Cranial neural crest which gives rise to the trigeminal ganglion. todo - compare ZFA and EHDAA2 representation We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] EFO:0003484 EHDAA2:0002083 EHDAA:667 EMAPA:16170 TAO:0000080 VHOG:0000269 ZFA:0000080 uberon UBERON:0005563 trigeminal neural crest ZFA EHDAA2 EHDAA2 Cranial neural crest which gives rise to the trigeminal ganglion. ZFA:0000080 We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] 2012-09-17 VHOG:0000269 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 http://bgee.unil.ch/ Portion of tissue that gives rise to the immature gonad. Immature reproductive tissue that has not undergone final maturation into either testis or ovary.[TAO] this is a very broad grouping class EFO:0003651 EHDAA:5927 EMAPA:17204 RETIRED_EHDAA2:0002148 TAO:0001262 WBbt:0008366 ZFA:0001262 future gonad gonadal primordium primitive gonad undifferentiated gonad uberon immature gonad UBERON:0005564 gonad primordium Obol ZFA Portion of tissue that gives rise to the immature gonad. ZFA:0001262 Immature reproductive tissue that has not undergone final maturation into either testis or ovary.[TAO] 2012-08-14 TAO:0001262 TAO ZFIN:curator future gonad http://orcid.org/0000-0002-6601-2165 gonadal primordium ZFA:0001262 primitive gonad http://orcid.org/0000-0002-6601-2165 undifferentiated gonad ZFA:0001262 immature gonad http://orcid.org/0000-0002-6601-2165 Somite located in the head region, caudal to the otic vesicle in humans this includes somites 1-4 They provide the epaxial and hypaxial muscles of the neck, the pharyngeal and laryngeal muscles that develop in the caudal branchial arches and the musculature of the tongue. Despite their localisation in the head, myogenic precursors from occipital somites essentially follow the trunk programmes (E. H. Walters and S. D., unpublished). during evolution, have been secondarily incorporated into the head (Gans and Northcutt, 1983) EHDAA2 has both 'head somite' and 'head somite group', with part_of and develops_from for latter EHDAA2:0003437 EMAPA:16172 XAO:0000313 occipital somite uberon cranial somite UBERON:0005594 head somite EHDAA2 EHDAA2 Somite located in the head region, caudal to the otic vesicle PMID:11830559 They provide the epaxial and hypaxial muscles of the neck, the pharyngeal and laryngeal muscles that develop in the caudal branchial arches and the musculature of the tongue. Despite their localisation in the head, myogenic precursors from occipital somites essentially follow the trunk programmes (E. H. Walters and S. D., unpublished). during evolution, have been secondarily incorporated into the head (Gans and Northcutt, 1983) PMID:11830559 EHDAA2 has both 'head somite' and 'head somite group', with part_of and develops_from for latter EHDAA2 occipital somite PMID:11830559 XAO:0000313 cranial somite XAO:0000313 A pair of lateral diverticula just over the liver rudiment representing the primordia of the lungs, formed by the floor of the foregut just anterior to the liver diverticulum. UBERON:3010717 AAO:0011059 EFO:0002578 EMAPA:36007 XAO:0001002 uberon lateral diverticula lung diverticulum lung endoderm UBERON:0005597 lung primordium XAO XAO A pair of lateral diverticula just over the liver rudiment representing the primordia of the lungs, formed by the floor of the foregut just anterior to the liver diverticulum. XAO:0001002 lateral diverticula XAO:0001002 lung diverticulum AAO:3010717 lung endoderm EFO:0002578 A somite that is part of a trunk. AAO:0010385 EHDAA2:0003438 EMAPA:16184 XAO:0000314 uberon UBERON:0005598 trunk somite A somite that is part of a trunk. OBOL:automatic A study of embryos shows that in all vertebrates six arterial arches link the ventral aorta with a pair of lateral dorsal aortae on each side of the body. The latter unite posteriorly to form a single median dorsal aorta wich takes blood to the body.[well established][VHOG] Contributes to the arch of aorta in humans EHDAA2:0000936 EHDAA:404 EMAPA:16205 MA:0000478 SCTID:361403005 VHOG:0000484 uberon UBERON:0005613 left dorsal aorta A study of embryos shows that in all vertebrates six arterial arches link the ventral aorta with a pair of lateral dorsal aortae on each side of the body. The latter unite posteriorly to form a single median dorsal aorta wich takes blood to the body.[well established][VHOG] 2012-09-17 VHOG:0000484 VHOG ISBN:978-0174480198 Roberts MBV, Biology: a functional approach (1986) p.572 http://bgee.unil.ch/ Contributes to the arch of aorta in humans http://emedicine.medscape.com/article/899609-overview A layer of cuboidal epithelial cells bounded anteriorly by the capsule of the lens and posteriorly by the lens cortex. Cells of the subcapsular epithelium (or anterior lens cells) are mitotically active. In adult individuals they only cover the anterior 'hemisphere' of the lens. As they divide, cells gradually move towards the equator of the lens where they tranform into lens fibres. The apical part of the gradually elongating cell extends between the subcapsular epithelium and adjacent lens fibres towards the anterior pole of the lens. The basal part extends towards the posterior pole. The nucleus remains close to the equatorial plane of the lens - http://www.lab.anhb.uwa.edu.au/mb140/corepages/eye/eye.htm lens epithelium EHDAA2:0000984 EHDAA:9059 EMAPA:17304 EMAPA:17839 FMA:70612 MA:0001302 NCIT:C33641 RETIRED_EHDAA2:0000976 SCTID:362521008 UMLS:C1182652 VHOG:0001425 lens subcapsular epithelium subcapsular lens epithelium uberon anterior epithelium of lens vesicle anterior surface of lens UBERON:0005614 lens anterior epithelium A layer of cuboidal epithelial cells bounded anteriorly by the capsule of the lens and posteriorly by the lens cortex. http://orcid.org/0000-0002-6601-2165 UMLS:C1182652 ncithesaurus:Subcapsular_Epithelium_of_the_Lens lens subcapsular epithelium http://www.lab.anhb.uwa.edu.au/mb140/corepages/eye/eye.htm subcapsular lens epithelium FMA:70612 anterior epithelium of lens vesicle EMAPA:17304 anterior surface of lens FMA:58889 Arteries which arise from the abdominal aorta and distribute to most of the intestines. includes posterior and anterior mesenteric arteries, which branch from the dorsal aorta (see Kardong), and superior and inferior mesenteric arteries BTO:0000779 EHDAA2:0001123 EHDAA:4343 EMAPA:17312 MA:0002003 MESH:D008638 NCIT:C52975 SCTID:281084003 UMLS:C0025465 VHOG:0001117 Wikipedia:Mesenteric_artery XAO:0000370 uberon UBERON:0005616 mesenteric artery Arteries which arise from the abdominal aorta and distribute to most of the intestines. MESH:A07.231.114.565 Wikipedia:Mesenteric_artery UMLS:C0025465 ncithesaurus:Mesenteric_Artery A vein that returns blood from the intestines. In humans the inferior mesenteric vein empties into the splenic vein, the superior mesenteric vein joins the splenic vein to form the portal vein BTO:0002781 EHDAA:4442 EMAPA:17348 MA:0002177 MESH:D008642 NCIT:C53055 RETIRED_EHDAA2:0001125 SCTID:304045008 UMLS:C0025473 Wikipedia:Mesenteric_vein uberon intestinal vein UBERON:0005617 mesenteric vein A vein that returns blood from the intestines. MESH:A07.231.908.670.385 Wikipedia:Mesenteric_vein UMLS:C0025473 ncithesaurus:Mesenteric_Vein intestinal vein http://orcid.org/0000-0002-6601-2165 A study of embryos shows that in all vertebrates six arterial arches link the ventral aorta with a pair of lateral dorsal aortae on each side of the body. The latter unite posteriorly to form a single median dorsal aorta wich takes blood to the body.[well established][VHOG] Normally regresses in humans EHDAA2:0001720 EHDAA:406 EMAPA:16206 MA:0000479 SCTID:361404004 VHOG:0000485 uberon UBERON:0005622 right dorsal aorta A study of embryos shows that in all vertebrates six arterial arches link the ventral aorta with a pair of lateral dorsal aortae on each side of the body. The latter unite posteriorly to form a single median dorsal aorta wich takes blood to the body.[well established][VHOG] 2012-09-17 VHOG:0000485 VHOG ISBN:978-0174480198 Roberts MBV, Biology: a functional approach (1986) p.572 http://bgee.unil.ch/ Normally regresses in humans http://emedicine.medscape.com/article/899609-overview An epithelium that is part of a anterior chamber of eyeball. EHDAA2:0000130 uberon UBERON:0005638 anterior chamber epithelium An epithelium that is part of a anterior chamber of eyeball. OBOL:automatic An epithelium that is part of a lens vesicle. EHDAA2:0000987 EMAPA:17165 VHOG:0000532 uberon UBERON:0005656 lens vesicle epithelium An epithelium that is part of a lens vesicle. OBOL:automatic An ectoderm that is part of a pharyngeal arch 3. In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] EHDAA2:0000072 EMAPA:16400 EMAPA:16582 EMAPA:16584 RETIRED_EHDAA2:0000079 VHOG:0000946 3rd pharyngeal arch ectoderm uberon UBERON:0005661 3rd arch ectoderm An ectoderm that is part of a pharyngeal arch 3. OBOL:automatic In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] 2012-09-17 VHOG:0000946 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) http://bgee.unil.ch/ 3rd pharyngeal arch ectoderm VHOG:0000946 An ectoderm that is part of a pharyngeal arch 4. In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] EHDAA2:0004032 EMAPA:16762 EMAPA:16764 EMAPA:16768 RETIRED_EHDAA2:0000094 VHOG:0001095 4th pharyngeal arch ectoderm uberon UBERON:0005662 4th arch ectoderm An ectoderm that is part of a pharyngeal arch 4. OBOL:automatic In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] 2012-09-17 VHOG:0001095 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) http://bgee.unil.ch/ 4th pharyngeal arch ectoderm VHOG:0001095 An endoderm that is part of a pharyngeal arch 3. In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] EHDAA2:0000075 EMAPA:16401 EMAPA:16585 EMAPA:16587 RETIRED_EHDAA2:0000080 VHOG:0001081 3rd pharyngeal arch endoderm uberon UBERON:0005665 3rd arch endoderm An endoderm that is part of a pharyngeal arch 3. OBOL:automatic In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] 2012-09-17 VHOG:0001081 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) http://bgee.unil.ch/ 3rd pharyngeal arch endoderm VHOG:0001081 An endoderm that is part of a pharyngeal arch 4. In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] EHDAA2:0004033 EMAPA:16765 EMAPA:16767 EMAPA:16769 RETIRED_EHDAA2:0000095 VHOG:0001092 4th pharyngeal arch endoderm uberon UBERON:0005666 4th arch endoderm An endoderm that is part of a pharyngeal arch 4. OBOL:automatic In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] 2012-09-17 VHOG:0001092 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) http://bgee.unil.ch/ 4th pharyngeal arch endoderm VHOG:0001092 A mesothelium that is part of a peritoneal cavity. we believe that this corresponds to EMAPA:16139 based on synonyms and parenthood peritoneum BTO:0003156 EHDAA2:0001447 EMAPA:16139 FMA:18147 SCTID:34073007 mesothelium of peritoneal component mesothelium of peritoneum peritoneal mesothelium peritoneum mesothelium uberon UBERON:0005669 peritoneal cavity mesothelium A mesothelium that is part of a peritoneal cavity. OBOL:automatic we believe that this corresponds to EMAPA:16139 based on synonyms and parenthood EMAPA peritoneum EMAPA:16139 mesothelium of peritoneal component EMAPA:16139 mesothelium of peritoneum FMA:18147 peritoneal mesothelium BTO:0003156 peritoneal mesothelium EMAPA:16139 peritoneum mesothelium FMA:18147 An endothelium that is part of a right lung. EHDAA2:0001755 uberon UBERON:0005672 right lung endothelium An endothelium that is part of a right lung. OBOL:automatic An endothelium that is part of a left lung. EHDAA2:0000961 uberon UBERON:0005673 left lung endothelium An endothelium that is part of a left lung. OBOL:automatic An anatomical cavity that is part of a lens vesicle. (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG] cavity of lens lens cavity EHDAA2:0000986 EMAPA:17164 VHOG:0000531 cavity of lens vesicle uberon UBERON:0005688 lens vesicle cavity An anatomical cavity that is part of a lens vesicle. OBOL:automatic (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG] 2012-09-17 VHOG:0000531 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 http://bgee.unil.ch/ lens cavity EHDAA2:0000986 cavity of lens vesicle EMAPA:17164 Mesenchyme that is part of a pharyngeal arch 3. In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] EHDAA2:0000081 EHDAA:1094 EMAPA:16402 FMA:295700 VHOG:0001083 3rd pharyngeal arch mesenchyme uberon 3rd branchial arch mesenchyme pharyngeal arch 3 mesenchyme UBERON:0005690 3rd arch mesenchyme Mesenchyme that is part of a pharyngeal arch 3. OBOL:automatic In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] 2012-09-17 VHOG:0001083 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) http://bgee.unil.ch/ 3rd pharyngeal arch mesenchyme VHOG:0001083 Mesenchyme that is part of a pharyngeal arch 4. In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] EHDAA2:0000096 EHDAA:1677 EMAPA:16770 FMA:295702 VHOG:0001052 4th pharyngeal arch mesenchyme uberon 4th branchial arch mesenchyme pharyngeal arch 4 mesenchyme UBERON:0005691 4th arch mesenchyme Mesenchyme that is part of a pharyngeal arch 4. OBOL:automatic In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] 2012-09-17 VHOG:0001052 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) http://bgee.unil.ch/ 4th pharyngeal arch mesenchyme VHOG:0001052 Mesenchyme that is part of a optic eminence. EHDAA:942 EMAPA:16324 RETIRED_EHDAA2:0001310 VHOG:0001073 uberon UBERON:0005702 optic eminence mesenchyme Mesenchyme that is part of a optic eminence. OBOL:automatic A venous system that is part of a hindbrain. EHDAA2:0000776 EMAPA:18632 VHOG:0001322 uberon rhombencephalon venous system UBERON:0005720 hindbrain venous system A venous system that is part of a hindbrain. OBOL:automatic rhombencephalon venous system VHOG:0001322 BILA:0000139 uberon UBERON:0005726 chemosensory system A limb/fin field that has the potential to develop into a pelvic appendage bud mesenchyme. Embryonic region that develops into the pelvic fin bud.[TAO] TAO:0001454 ZFA:0001454 pelvic appendage field of lateral plate mesoderm pelvic fin field uberon UBERON:0005730 pelvic appendage field A limb/fin field that has the potential to develop into a pelvic appendage bud mesenchyme. OBOL:automatic Embryonic region that develops into the pelvic fin bud.[TAO] 2012-08-14 TAO:0001454 TAO ZFIN:curator pelvic fin field ZFA:0001454 A ring of cells capable of forming a limb or paired fin[Gilbert,modified]. we represent the field as being a part of the LPM (consistent with ZFA, Gilbert). As a consequence, the relationship between limb bud (with is ectoderm+mesenchyme) stands in a weaker has_developmental_contribution_from relation to the field - TODO implement this. limb/fin field of lateral plate mesoderm paired limb/fin field uberon UBERON:0005732 paired limb/fin field ISBN:9780878932504 ZFA-inferred A ring of cells capable of forming a limb or paired fin[Gilbert,modified]. ISBN:9780878932504 The outermost layer of a blood vessel, composed mainly of fibrous tissue. TODO - note terminological problems. WP says tunica external layer of blood vessel. FMA says tunica externa = adventitia, and is FMA adventitia covers other kinds of vessels. Here we opt for a lengthier name that attempts to disambiguate. There is no precise FMA equivalent, as FMA has tunica externa of arteries, veins, genital ducts etc as siblings The outermost layer of a blood vessel, surrounding the tunica media. It is mainly composed of collagen. The collagen serves to anchor the blood vessel to nearby organs, giving it stability[Wikipedia:Tunica_externa_(vessels)]. BTO:0002010 EMAPA:36299 NCIT:C33818 SCTID:61066005 UMLS:C0225342 Wikipedia:Tunica_externa_(vessels) adventitia externa tunica adventitia tunica adventitia of vessel uberon external coat tunica adventitia vasorum tunica externa vasorum UBERON:0005734 tunica adventitia of blood vessel Illu:artery.jpg cjm The outermost layer of a blood vessel, composed mainly of fibrous tissue. ISBN:0073040584 Wikipedia:Tunica_externa_(vessels) The outermost layer of a blood vessel, surrounding the tunica media. It is mainly composed of collagen. The collagen serves to anchor the blood vessel to nearby organs, giving it stability[Wikipedia:Tunica_externa_(vessels)]. Wikipedia:Tunica_externa_(vessels) UMLS:C0225342 ncithesaurus:Tunica_Adventitia adventitia externa Wikipedia:Tunica_externa_(vessels) tunica adventitia Wikipedia:Tunica_externa_(vessels) tunica adventitia of vessel Wikipedia:Tunica_externa_(vessels) external coat Wikipedia:Tunica_externa_(vessels) tunica adventitia vasorum Wikipedia:Tunica_externa_(vessels) tunica externa vasorum Wikipedia:Tunica_externa_(vessels) A tunica intima that is part of a artery. EMAPA:36293 EV:0100028 FMA:14272 SCTID:40022005 galen:IntimaOfArtery arterial intima tunica interna (intima)(arteriae) uberon UBERON:0005740 tunica intima of artery A tunica intima that is part of a artery. OBOL:automatic arterial intima EV:0100028 tunica interna (intima)(arteriae) FMA:14272 An outermost connective tissue covering of an organ, vessel, or other structure[WP]. BTO:0002010 FMA:45635 SCTID:30180000 Wikipedia:Adventitia tunica advetitia tunica externa uberon UBERON:0005742 adventitia http://upload.wikimedia.org/wikipedia/commons/e/e8/Illu_esophageal_layers.jpg An outermost connective tissue covering of an organ, vessel, or other structure[WP]. Wikipedia:Adventitia tunica advetitia Wikipedia:Adventitia tunica externa FMA:45635 Anatomical space that is an opening in a bone, usually for passage of blood vessels or nerves. in FMA and ZFA this is a conduit space, not a conduit. Note there may be some additional disambiguation required: foramen is used loosely in the sense of any opening (e.g. foramen primum). FMA appears to use cranial conduit (undefined) in the sense of any foramen of the skull (includes mental foramen, which is not in the cranium proper). foramen AAO:0010438 TAO:0001736 VHOG:0001760 ZFA:0005386 uberon UBERON:0005744 bone foramen http://upload.wikimedia.org/wikipedia/commons/8/81/Gray193.png Anatomical space that is an opening in a bone, usually for passage of blood vessels or nerves. TAO:curator in FMA and ZFA this is a conduit space, not a conduit. Note there may be some additional disambiguation required: foramen is used loosely in the sense of any opening (e.g. foramen primum). FMA appears to use cranial conduit (undefined) in the sense of any foramen of the skull (includes mental foramen, which is not in the cranium proper). FMA foramen ZFA:0005386 A acellular anatomical structure that is the bounding layer of a anatomical structure. FMA:63871 uberon UBERON:0005764 acellular membrane A acellular anatomical structure that is the bounding layer of a anatomical structure. OBOL:automatic An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina. this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell. AAO:0010596 FMA:63872 GAID:915 NCIT:C13191 SCTID:68989006 UMLS:C0004799 Wikipedia:Basement_membrane basement membrane of connective tissue membrana basalis uberon basement membrane UBERON:0005769 basement membrane of epithelium FMA An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina. Wikipedia:Basement_membrane http://orcid.org/0000-0002-6601-2165 http://palaeos.com/metazoa/porifera/homoscleromorpha.html UMLS:C0004799 ncithesaurus:Basement_Membrane basement membrane of connective tissue FMA:63872 membrana basalis Wikipedia:Basement_membrane basement membrane FMA:63872 Any portion of the aorta including the ascending and descending aorta, and aortic arch or a portion of the aortic orifice of the left ventricle. FMA:13087 NCIT:C34027 SCTID:119203005 UMLS:C0506947 aortic section uberon aortic segment portion of aorta segment of aorta UBERON:0005800 section of aorta Any portion of the aorta including the ascending and descending aorta, and aortic arch or a portion of the aortic orifice of the left ventricle. ncithesaurus:Aortic_Segment UMLS:C0506947 ncithesaurus:Aortic_Segment aortic segment FMA:13087 segment of aorta FMA:13087 The dorsal aorta is a blood vessel in a single-pass circulatory system that carries oxygenated blood from the gills to the rest of the body. In a single-pass circulatory system blood passes once through the heart to supply the body once. Each primitive aorta receives anteriorly a vein 'the vitelline vein' from the yolk-sac, and is prolonged backward on the lateral aspect of the notochord under the name of the dorsal aorta. The dorsal aortae give branches to the yolk-sac, and are continued backward through the body-stalk as the umbilical arteries to the villi of the chorion. The two dorsal aortae combine to become the descending aorta in later development[WP]. Principal unpaired, median artery of the trunk, leading from the paired roots (radices) of the dorsal aorta to the caudal artery. Kimmel et al, 1995.[TAO] The artery in vertebrate embryos that transports blood from the aortic arches to the trunk and limbs. In adult fish it is a major artery that carries oxygenated blood from the efferent branchial arteries to branches that supply the body organ. In adult tetrapods it arises from the systemic arch relationship loss: part_of axial vasculature (TAO:0001073)[TAO] When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG] AAO:0011029 BTO:0004673 EHDAA:402 EMAPA:18606 SCTID:338637006 TAO:0000014 VHOG:0000264 Wikipedia:Dorsal_aorta XAO:0000051 ZFA:0000014 DA aorta dorsalis uberon aortae dorsales dorsal aorta root dorsal aortae dorsal aortic root dorsal aortæ UBERON:0005805 dorsal aorta http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray459.png The dorsal aorta is a blood vessel in a single-pass circulatory system that carries oxygenated blood from the gills to the rest of the body. In a single-pass circulatory system blood passes once through the heart to supply the body once. GO:0035907 https://sourceforge.net/p/geneontology/ontology-requests/8525/ Each primitive aorta receives anteriorly a vein 'the vitelline vein' from the yolk-sac, and is prolonged backward on the lateral aspect of the notochord under the name of the dorsal aorta. The dorsal aortae give branches to the yolk-sac, and are continued backward through the body-stalk as the umbilical arteries to the villi of the chorion. The two dorsal aortae combine to become the descending aorta in later development[WP]. Wikipedia:Dorsal_aorta Principal unpaired, median artery of the trunk, leading from the paired roots (radices) of the dorsal aorta to the caudal artery. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000014 TAO ZFIN:curator The artery in vertebrate embryos that transports blood from the aortic arches to the trunk and limbs. In adult fish it is a major artery that carries oxygenated blood from the efferent branchial arteries to branches that supply the body organ. In adult tetrapods it arises from the systemic arch BTO:0004673 relationship loss: part_of axial vasculature (TAO:0001073)[TAO] 2012-08-14 TAO:0000014 TAO When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG] 2012-09-17 VHOG:0000264 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620 http://bgee.unil.ch/ DA ZFA:0000014 aorta dorsalis XAO:0000051 aortae dorsales Wikipedia:Dorsal_aorta dorsal aorta root VHOG:0000264 dorsal aortae Wikipedia:Dorsal_aorta dorsal aortic root VHOG:0000264 dorsal aortæ Wikipedia:Dorsal_aorta This is currently used loosely to refer to cervical, lumbar, etc as well as the metamerically repeated segments, which may correspond more closely with the ZFA neuromere term BIRNLEX:2665 FMA:62420 MA:0003080 SCTID:278748001 axial part of spinal cord axial regional part of spinal cord segment of spinal cord uberon spinal neuromeres UBERON:0005844 spinal cord segment axial part of spinal cord BIRNLEX:2665 axial regional part of spinal cord BIRNLEX:2665 segment of spinal cord FMA:62420 spinal neuromeres TAO:0001332 A spinal cord segment that adjacent_to a caudal region. FMA:256635 MA:0003084 SCTID:278753006 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1656 coccygeal segment of spinal cord coccygeal segments of spinal cord [1-3] pars coccygea medullae spinalis segmenta coccygea medullae spinalis [1-3] uberon segmenta coccygea UBERON:0005845 for spinal cord segments, we treat coccygeal/caudal as synonyms - we only differentiate where bone is concerned caudal segment of spinal cord A spinal cord segment that adjacent_to a caudal region. OBOL:automatic coccygeal segment of spinal cord FMA:256635 coccygeal segments of spinal cord [1-3] FMA:256635 pars coccygea medullae spinalis FMA:256635 FMA:TA segmenta coccygea medullae spinalis [1-3] FMA:256635 FMA:TA segmenta coccygea NeuroNames:1656 A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 EHDAA2_RETIRED:0003148 EHDAA:8979 mesenchyme condensation uberon UBERON:0005856 developing mesenchymal condensation AEO cjm AEO-modified-relation A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 mesenchyme condensation EMAPA:25351 Cell condensation that is an aggregation of mesenchymal cells that are committed to differentiate into chondroblasts and chondrocytes. isa cell condensation in VSAO; has_part chondroblast in AEO AEO:0000147 EHDAA2_RETIRED:0003147 EMAPA:32731 VSAO:0000092 XAO:0004022 cartilage condensation cartilagenous condensation chondrogenic condensation uberon UBERON:0005863 cartilaginous condensation AEO AEO Cell condensation that is an aggregation of mesenchymal cells that are committed to differentiate into chondroblasts and chondrocytes. GO:curator isa cell condensation in VSAO; has_part chondroblast in AEO VSAO cartilage condensation EMAPA:25353 cartilagenous condensation EHDAA2:0003147 chondrogenic condensation VSAO:0000092 UBERON:0008714 AEO:0000149 EHDAA2_RETIRED:0003149 pre muscle mass premuscle mass uberon UBERON:0005865 pre-muscle condensation AEO A delimited region of dense mesenchyme within looser mesenchyme whose cells are committed to become chondroblasts. A closely packed aggregation of mesenchymal cells just prior to their differentiation into embryonic cartilage. AEO:0000150 EHDAA2:0003150 EMAPA:32736 pre-chondrogenic condensation precartilage condensation precartilagenous condensation prechondrogenic condensation uberon UBERON:0005866 pre-cartilage condensation AEO AEO A delimited region of dense mesenchyme within looser mesenchyme whose cells are committed to become chondroblasts. AEO:0000150 AEO:JB A closely packed aggregation of mesenchymal cells just prior to their differentiation into embryonic cartilage. http://dictionary.reference.com/browse/precartilage the paired ventral prominences formed by bifurcation of the first pharyngeal arches in the embryo; the two prominences unite ventrally and fuse to form the mandible and lower lip check develops_from EHDAA2:0001061 EHDAA:5871 EMAPA:17355 FMA:293051 NCIT:C34204 UMLS:C1512982 Wikipedia:Mandibular_prominence uberon mandibular process mandibular swelling prominentia mandibularis UBERON:0005867 mandibular prominence the paired ventral prominences formed by bifurcation of the first pharyngeal arches in the embryo; the two prominences unite ventrally and fuse to form the mandible and lower lip ISBN:0-683-40008-8 MP:0010939 UMLS:C1512982 ncithesaurus:Mandibular_Prominence mandibular process Wikipedia:Mandibular_prominence mandibular swelling https://orcid.org/0000-0002-6601-2165 prominentia mandibularis Wikipedia:Mandibular_prominence Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occipital condyles. TODO - check An anatomical cluster that is located in the posterior region of the neurocranium and forms the margin of the foramen margin and occipital condyles.[AAO] Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occiptal condyle.[TAO] AAO:0010199 BTO:0004675 FMA:49187 SCTID:362618001 TAO:0001414 XAO:0003173 ZFA:0001414 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=2431 basicranial region occipital part of head occipital region of head uberon back of head UBERON:0005902 occipital region Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occipital condyles. TAO:0001414 UBERONREF:0000007 An anatomical cluster that is located in the posterior region of the neurocranium and forms the margin of the foramen margin and occipital condyles.[AAO] 2012-06-20 AAO:0010199 AAO AAO:EJS Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occiptal condyle.[TAO] 2012-08-14 TAO:0001414 TAO TAO:MAH basicranial region ZFA:0001414 occipital part of head FMA:49187 occipital region of head FMA:49187 back of head FMA:49187 Organ with organ cavity, which has as parts a serous membrane and a serous cavity . Examples: pleural sac, pericardial sac, tendon sheath, bursa.[FMA] EMAPA:16060 FMA:9689 MA:0000005 SCTID:362890006 uberon UBERON:0005906 See notes for serous membrane serous sac Organ with organ cavity, which has as parts a serous membrane and a serous cavity . Examples: pleural sac, pericardial sac, tendon sheath, bursa.[FMA] FMA:9689 https://github.com/obophenotype/uberon/issues/86 Epithelium that derives from the endoderm. Examples: urothelium, transitional epithelium of ureter, epithelium of prostatic gland.[FMA] FMA:69065 endoderm-derived epithelium endoepithelium uberon UBERON:0005911 endo-epithelium Epithelium that derives from the endoderm. Examples: urothelium, transitional epithelium of ureter, epithelium of prostatic gland.[FMA] FMA:69065 FMA:10483 bone organ zone uberon UBERON:0005913 zone of bone organ FMA bone organ zone FMA:10483 Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified]. Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO] AAO:0000963 EMAPA:17214 EMAPA:18043 MA:0000308 NCIT:C32172 SCTID:361725000 UMLS:C0222645 VSAO:0000056 Wikipedia:Axial_skeleton XAO:0004011 uberon skeleton axiale UBERON:0005944 axial skeleton plus cranial skeleton http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton http://upload.wikimedia.org/wikipedia/commons/8/8b/Axial_skeleton_diagram.svg Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified]. FMA:71221 VSAO:0000056 Wikipedia:Axial_skeleton https://github.com/obophenotype/uberon/issues/44 https://github.com/obophenotype/uberon/wiki/The-axial-skeleton Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO] 2012-08-14 VSAO:0000056 VSAO PSPUB:0000170 UMLS:C0222645 ncithesaurus:Axial_Skeleton skeleton axiale Wikipedia:Axial_skeleton An outflow tract that is part of a cardiac atrium. FMA:14141 outflow part of atrium uberon UBERON:0005946 outflow tract of atrium An outflow tract that is part of a cardiac atrium. OBOL:automatic outflow part of atrium FMA:14141 Anteriosuperior, smooth-walled portion of the cavity of the right ventricle, beginning at the supraventricular crest and terminating in the pulmonary trunk infundibulum EMAPA:37926 FMA:7216 NCIT:C61368 SCTID:244379003 UMLS:C1881209 RVOT conus arteriosus (infundibulum) infundibulum of right ventricle outflow tract of right ventricle pulmonary conus right ventricle pulmonary outflow tract right ventricular outflow tract uberon arterial cone conus arteriosus pulmonary cone pulmonary conus UBERON:0005953 outflow part of right ventricle PMID:17276708 Anteriosuperior, smooth-walled portion of the cavity of the right ventricle, beginning at the supraventricular crest and terminating in the pulmonary trunk MP:0010428 infundibulum Wikipedia:Conus_arteriosus EMAPA:37926 MA:th UMLS:C1881209 ncithesaurus:Infundibulum RVOT MP:0010428 conus arteriosus (infundibulum) FMA:7216 infundibulum of right ventricle FMA:7216 infundibulum of right ventricle MP:0010428 outflow tract of right ventricle FMA:7216 pulmonary conus FMA:7216 right ventricle pulmonary outflow tract MP:0010428 right ventricular outflow tract MP:0010428 arterial cone MP:0010428 conus arteriosus MP:0010428 pulmonary cone MP:0010428 pulmonary conus MP:0010428 Anterosuperior fibrous portion of the left ventricle that connects to the ascending aorta. EMAPA:37925 FMA:9473 SCTID:264070001 Wikipedia:Aortic_vestibule LVOT Sibson vestibule aortic vestibule heart left ventricle outflow tract left ventricular outflow left ventricular outflow tract outflow tract of left ventricle vestibulum aortae uberon UBERON:0005956 outflow part of left ventricle Anterosuperior fibrous portion of the left ventricle that connects to the ascending aorta. MP:0010429 EMAPA:37925 MA:th LVOT MP:0010429 Sibson vestibule MP:0010429 aortic vestibule FMA:9473 aortic vestibule MP:0010429 heart left ventricle outflow tract MP:0010429 left ventricular outflow FMA:9473 left ventricular outflow tract HP:0011103 outflow tract of left ventricle FMA:9473 vestibulum aortae FMA:9473 FMA:TA Outflow part of atrium which consists of wall and cavity of the outflow part of right atrium and the tricuspid valve.[FMA] FMA:9550 main part of right atrium outflow tract of right atrium uberon UBERON:0005965 outflow part of right atrium Outflow part of atrium which consists of wall and cavity of the outflow part of right atrium and the tricuspid valve.[FMA] FMA:9550 FMA:FMA main part of right atrium FMA:9550 outflow tract of right atrium FMA:9550 An outflow tract of atrium that is part of a left atrium. FMA:9551 main part of left atrium outflow tract of left atrium uberon UBERON:0005966 outflow part of left atrium An outflow tract of atrium that is part of a left atrium. OBOL:automatic main part of left atrium FMA:9551 outflow tract of left atrium FMA:9551 The vertical crest of the interior wall of the right atrium that lies to the right of the sinus of the vena cava and separates this from the remainder of the right atrium EMAPA:37837 FMA:9236 SCTID:277693004 Wikipedia:Crista_terminalis crista terminalis atrii dextri crista terminalis cordis crista terminalis of right atrium uberon UBERON:0005979 crista terminalis The vertical crest of the interior wall of the right atrium that lies to the right of the sinus of the vena cava and separates this from the remainder of the right atrium MP:0010495 EMAPA:37837 MA:th crista terminalis atrii dextri FMA:9236 FMA:TA crista terminalis cordis FMA:9236 crista terminalis of right atrium FMA:9236 The laminar structure of the heart uberon UBERON:0005983 heart layer The laminar structure of the heart MP:0010545 Any of the arteries or veins that supply blood to the heart or return blood from the heart muscles to the circulation TODO - change relation from part_of MESH:D003331 Wikipedia:Coronary_circulation uberon UBERON:0005985 coronary vessel Any of the arteries or veins that supply blood to the heart or return blood from the heart muscles to the circulation MP:0010551 The wall of the heart that separates the right atrium and left ventricle; and is located just above the septal cusp of the tricuspid valve EMAPA:37431 FMA:7136 SCTID:280151006 Wikipedia:Atrioventricular_septum membranous atrioventricular septum uberon UBERON:0005989 atrioventricular septum PMID:15797462 Wikipedia The wall of the heart that separates the right atrium and left ventricle; and is located just above the septal cusp of the tricuspid valve MP:0010592 EMAPA:37431 MA:th membranous atrioventricular septum FMA:7136 Anatomical structure embedded in or located in the integument that is part of the integumental system. Examples: hair, follicles, skin glands, claws, nails, feathers. add subclasses based on resolution of CARO tracker item. Also check: adnexal gland. Note that MP implicitly includes hypodermis. the tissue or structures associated with or embedded in the skin such as hair and hair follicles, sweat glands, sebaceous glands and claws or nails[MP:0010678] EMAPA:37883 Wikipedia:Skin_appendage body hair or bristle uberon adnexae cutis skin adnexa skin adnexal structure skin appendage UBERON:0006003 integumentary adnexa Anatomical structure embedded in or located in the integument that is part of the integumental system. Examples: hair, follicles, skin glands, claws, nails, feathers. http://code.google.com/p/caro2/issues/detail?id=5 http://orcid.org/0000-0002-6601-2165 the tissue or structures associated with or embedded in the skin such as hair and hair follicles, sweat glands, sebaceous glands and claws or nails[MP:0010678] MP:0010678 EMAPA:37883 MA:th body hair or bristle GO:GO adnexae cutis Wikipedia:Skin_appendage skin adnexa Wikipedia:Skin_appendage skin appendage Wikipedia:Skin_appendage uberon UBERON:0006056 posterior surface of head A bone that is part of a post-anal tail. MA has distinct classes for 'tail bone', 'caudal vertebra' and 'coccygeal vertebra' but these may all be equivalent. This class may be obsoleted in future. EMAPA:18042 MA:0000696 uberon tail bone tail vertebra UBERON:0006068 bone of tail A bone that is part of a post-anal tail. OBOL:automatic MA has distinct classes for 'tail bone', 'caudal vertebra' and 'coccygeal vertebra' but these may all be equivalent. This class may be obsoleted in future. MA tail bone MA:0000696 tail vertebra http://orcid.org/0000-0002-6601-2165 Subdivision of an organism along anterior-posterior axis that is the posteriormost region, extending past the anus (or cloaca, if present), consisting of a tail in some fully formed chordates (or a tail bud in embryos). In animals that have a sacral region, this is the region immediately posterior to this. This region is reduced in humans and corresponds to the coccyx We follow XAO is distinguishing the tail region from the tail; the tail bud is part of the tail region; the tail starts after the tail bud XAO:0000087 uberon post-anal caudal region post-anal tail region postsacral region tail region UBERON:0006071 caudal region Subdivision of an organism along anterior-posterior axis that is the posteriormost region, extending past the anus (or cloaca, if present), consisting of a tail in some fully formed chordates (or a tail bud in embryos). In animals that have a sacral region, this is the region immediately posterior to this. http://orcid.org/0000-0002-6601-2165 We follow XAO is distinguishing the tail region from the tail; the tail bud is part of the tail region; the tail starts after the tail bud XAO post-anal caudal region http://orcid.org/0000-0002-6601-2165 post-anal tail region http://orcid.org/0000-0002-6601-2165 postsacral region AAO:0000082 tail region AAO:0000082 That portion of the spine comprising the cervical vertebrae. The neck area of the spine. Anterior region of the vertebral column consisting of one to 19 or 20 vertebrae.[AAO] AAO:0000092 BTO:0004148 EHDAA2:0000238 EHDAA:5051 EMAPA:17215 FMA:24138 MA:0003154 NCIT:C69313 SCTID:260488005 UMLS:C0728985 axial skeleton cervical region cervical skeleton cervical spinal column cervical spine cervical vertebrae series cervical vertebral column uberon skeletal system of neck UBERON:0006072 cervical region of vertebral column FMA That portion of the spine comprising the cervical vertebrae. The neck area of the spine. http://medical-dictionary.thefreedictionary.com/ Anterior region of the vertebral column consisting of one to 19 or 20 vertebrae.[AAO] 2012-06-20 AAO:0000092 AAO AAO:Duellman_and_Trueb_1994 UMLS:C0728985 ncithesaurus:Cervical_Spine axial skeleton cervical region MA:0003154 cervical skeleton EHDAA2:0000238 cervical spinal column FMA:24138 cervical spine FMA:24138 cervical vertebral column FMA:24138 skeletal system of neck FMA:24138 That part of the spine comprising the thoracic vertebrae. Region of the vertebral column between the atlas and the sacrum consisting of seven to 285 vertebrae.[AAO] AAO:0000612 BTO:0004150 EHDAA:5063 EMAPA:17396 FMA:9140 MA:0003155 NCIT:C69315 SCTID:243931006 UMLS:C0581269 axial skeleton thoracic region columna vertebralis thoracicus thoracic spine thoracic vertebrae series thoracic vertebral column uberon UBERON:0006073 thoracic region of vertebral column FMA That part of the spine comprising the thoracic vertebrae. http://medical-dictionary.thefreedictionary.com/ Region of the vertebral column between the atlas and the sacrum consisting of seven to 285 vertebrae.[AAO] 2012-06-20 AAO:0000612 AAO AAO:Duellman_and_Trueb_1994 UMLS:C0581269 ncithesaurus:Thoracic_Spine axial skeleton thoracic region MA:0003155 columna vertebralis thoracicus FMA:9140 thoracic spine FMA:9140 thoracic vertebral column FMA:9140 Subdivision of vertebral column that corresponds to the caudal subdivision of the body, containing the caudal vertebrae. Region of the vertebral column posterior to the caudal-sacral region, that may consists of two or three to more than 100 vertebrae. These vertebrae exhibit a gradual reduction in the sizes of their transverse processes and zygapophyses, but these structures are never entirely absent. All caudal vertebrae bear haemal arches.[AAO] in AAO, this is posterior to the caudal-sacral region AAO:0000082 EMAPA:18043 MA:0003158 axial skeleton tail region caudal skeleton caudal vertebrae series uberon caudal region postsacral region tail region UBERON:0006076 caudal region of vertebral column Subdivision of vertebral column that corresponds to the caudal subdivision of the body, containing the caudal vertebrae. UBERONREF:0000006 Region of the vertebral column posterior to the caudal-sacral region, that may consists of two or three to more than 100 vertebrae. These vertebrae exhibit a gradual reduction in the sizes of their transverse processes and zygapophyses, but these structures are never entirely absent. All caudal vertebrae bear haemal arches.[AAO] 2012-06-20 AAO:0000082 AAO AAO:Duellman_and_Trueb_1994 in AAO, this is posterior to the caudal-sacral region AAO axial skeleton tail region MA:0003158 caudal skeleton UBERONREF:0000006 caudal vertebrae series http://purl.bioontology.org/ontology/provisional/a047a2d5-418f-4d9c-ad21-ee0b7c29c29d caudal region AAO:0000082 postsacral region AAO:0000082 tail region AAO:0000082 A collection of all skeletal elements in some subdivision of the vertebral column. FMA:16201 subdivision of vertebral skeleton vertebrae series vertebral column subdivision vertebral series uberon vertebral region vertebral subdivision UBERON:0006077 subdivision of vertebral column FMA A collection of all skeletal elements in some subdivision of the vertebral column. https://orcid.org/0000-0002-6601-2165 subdivision of vertebral skeleton https://orcid.org/0000-0002-6601-2165 vertebral column subdivision FMA:16201 The spiral septum that separates the truncus arteriosus into a ventral pulmonary trunk and the dorsal aorta[MP]. The aorticopulmonary septum is developmentally formed from neural crest, specifically the cardiac neural crest, and actively separates the aorta and pulmonary arteries and fuses with the interventricular septum within the heart during development. The actual mechanism of septation of the outflow tract is poorly understood, but is recognized as a dynamic process with contributions from contractile, hemodynamic, and extracellular matrix interactions. UBERON:0005999 CALOHA:TS-2409 EHDAA2:0000136 EHDAA:2592 EMAPA:16827 VHOG:0000502 Wikipedia:Aorticopulmonary_septum aortico-pulmonary septum aorticopulmonary septum septum aorticopulmonale uberon aortic septum spiral septum UBERON:0006207 aortico-pulmonary spiral septum http://upload.wikimedia.org/wikipedia/commons/b/b9/Gray470.png PMID:6844926 Wikipedia The spiral septum that separates the truncus arteriosus into a ventral pulmonary trunk and the dorsal aorta[MP]. The aorticopulmonary septum is developmentally formed from neural crest, specifically the cardiac neural crest, and actively separates the aorta and pulmonary arteries and fuses with the interventricular septum within the heart during development. The actual mechanism of septation of the outflow tract is poorly understood, but is recognized as a dynamic process with contributions from contractile, hemodynamic, and extracellular matrix interactions. MP:0010650 Wikipedia:Aorticopulmonary_septum aortico-pulmonary septum Wikipedia:Aorticopulmonary_septum aorticopulmonary septum Wikipedia:Aorticopulmonary_septum septum aorticopulmonale Wikipedia:Aorticopulmonary_septum aortic septum Wikipedia:Aorticopulmonary_septum spiral septum Wikipedia:Aorticopulmonary_septum The thin bilaminar membrane derived from the prechordal plate that is devoid of mesoderm and formed by the apposition of the stomodeal ectoderm with the foregut endoderm; after the embryonic head fold has evolved it lies at the caudal limit of the stomodeum, forming a septum between the primitive mouth and pharynx; the membrane eventually disappears, and thus a communication is established between the mouth and the future pharynx. EHDAA2:0000189 EHDAA:536 EMAPA:16259 FMA:313607 SCTID:361412007 VHOG:0000380 Wikipedia:Buccopharyngeal_membrane uberon oral membrane oral plate oropharyngeal membrane pharyngeal membrane UBERON:0006211 buccopharyngeal membrane http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png EHDAA2 The thin bilaminar membrane derived from the prechordal plate that is devoid of mesoderm and formed by the apposition of the stomodeal ectoderm with the foregut endoderm; after the embryonic head fold has evolved it lies at the caudal limit of the stomodeum, forming a septum between the primitive mouth and pharynx; the membrane eventually disappears, and thus a communication is established between the mouth and the future pharynx. MP:0012521 oral membrane MP:0012521 oral plate MP:0012521 oropharyngeal membrane Wikipedia:Buccopharyngeal_membrane pharyngeal membrane MP:0012521 EHDAA:1267 EMAPA:16342 RETIRED_EHDAA2:0000268 uberon UBERON:0006218 common atrial chamber The foremost region of the future forebrain that develops into the diencephalon. EFO:0003442 EHDAA2:0000600 EHDAA:844 EMAPA:16514 RETIRED_EHDAA2:0000386 TAO:0000574 ZFA:0000574 presumptive diencephalon uberon UBERON:0006222 future diencephalon EHDAA2 The foremost region of the future forebrain that develops into the diencephalon. UBERON:cjm Wikipedia:Diencephalon presumptive diencephalon TAO:0000574 An anatomical junctions that overlaps the foregut and midgut. Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[well established][VHOG] EHDAA2:0000569 EHDAA:526 EMAPA:16363 VHOG:0000291 uberon UBERON:0006235 foregut-midgut junction An anatomical junctions that overlaps the foregut and midgut. OBOL:automatic Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[well established][VHOG] 2012-09-17 VHOG:0000291 VHOG ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 http://bgee.unil.ch/ The embryonic precursor of the brain. The embryonic precursor of the brain and the set of mature brain structures that derive from it (CUMBO) BAMS:Enc BTO:0004726 EFO:0003431 EHDAA:300 EHDAA:830 EMAPA:16089 FMA:312967 RETIRED_EHDAA2:0000591 TAO:0000146 ZFA:0000146 brain rudiment presumptive brain encephalon uberon embryonic brain UBERON:0006238 future brain The embryonic precursor of the brain. NLX:94995 The embryonic precursor of the brain and the set of mature brain structures that derive from it (CUMBO) http://neurolex.org/wiki/Cumbo_terms brain rudiment TAO:0000146 presumptive brain ZFA:0000146 encephalon NLX:94995 embryonic brain BTO:0004726 A tendon that has the potential to develop into a central tendon. The cranial part of the septum transversum gives rise to the central tendon of the diaphragm and is the origin of the myoblasts that invade the pleuroperitoneal folds resulting in the formation of the muscular diaphragm. EHDAA2:0000593 EHDAA:4118 EMAPA:25035 uberon cranial derivative of septum transversum cranial part of septum transversum UBERON:0006239 future central tendon EHDAA2 mesenchyme cranial part Wikipedia A tendon that has the potential to develop into a central tendon. OBOL:automatic cranial derivative of septum transversum http://orcid.org/0000-0002-6601-2165 cranial part of septum transversum http://orcid.org/0000-0002-6601-2165 A presumptive structure that has the potential to develop into a forebrain. TODO. Add relationships to neural plate (both ZFA and EMAPA time this with the neural plate) BAMS:Pros EFO:0003423 EHDAA2:0000661 EHDAA:2643 EMAPA:16640 TAO:0000062 Wikipedia:Prosencephalon ZFA:0000062 future prosencephalon presumptive forebrain presumptive prosencephalon uberon prosencephalon UBERON:0006240 future forebrain A presumptive structure that has the potential to develop into a forebrain. OBOL:automatic presumptive forebrain ZFA:0000062 presumptive prosencephalon TAO:0000062 prosencephalon EHDAA2:0000661 EFO:0003438 EHDAA2:0000674 EHDAA:898 EMAPA:16092 EMAPA:16755 TAO:0000417 ZFA:0000417 presumptive spinal cord presumptive spinal cord neural keel presumptive spinal cord neural plate presumptive spinal cord neural rod uberon UBERON:0006241 future spinal cord EHDAA2 presumptive spinal cord ZFA:0000417 presumptive spinal cord neural keel TAO:0000417 presumptive spinal cord neural plate TAO:0000417 presumptive spinal cord neural rod TAO:0000417 An anatomical junctions that overlaps the mouth and foregut. EHDAA:534 EMAPA:16258 RETIRED_EHDAA2:0001205 VHOG:0000592 uberon UBERON:0006264 mouth-foregut junction An anatomical junctions that overlaps the mouth and foregut. OBOL:automatic The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG] EHDAA2:0001278 EHDAA:264 EMAPA:16101 NCIT:C34231 UMLS:C1518429 VHOG:0001212 uberon UBERON:0006267 notochordal plate EHDAA2 EHDAA2 The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. VHOG:0001212 The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG] 2012-09-17 VHOG:0001212 VHOG http://bgee.unil.ch/ UMLS:C1518429 ncithesaurus:Notochordal_Plate A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot EHDAA2:0001279 EHDAA:224 EMAPA:16102 FMA:293135 NCIT:C34232 UMLS:C1518430 VHOG:0001213 uberon chordamesoderm presumptive notochord UBERON:0006268 The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process EHDAA2 A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot http://www.med.umich.edu/lrc/coursepages/m1/embryology/embryo/05embryonicperiod.htm UMLS:C1518430 ncithesaurus:Notochordal_Process Each of the canals that links the peritoneal cavity and the caudal part of a pleural cavity. Each of the canal that links the peritoneal cavity and the caudal part of a pleural cavity. [ISBN:0124020607][VHOG] EHDAA2:0001481 EHDAA:4128 EMAPA:17704 EMAPA:17707 SCTID:361413002 VHOG:0001505 uberon pleuroperitoneal channel UBERON:0006279 pleuroperitoneal canal EHDAA2 EHDAA2 Each of the canals that links the peritoneal cavity and the caudal part of a pleural cavity. ISBN:0124020607 VHOG:0001505 Each of the canal that links the peritoneal cavity and the caudal part of a pleural cavity. [ISBN:0124020607][VHOG] 2012-09-17 VHOG:0001505 VHOG http://bgee.unil.ch/ pleuroperitoneal channel VHOG:0001505 Multi-tissue structure that is part of the heart tube and will become the cardiac ventricle. UBERON:0010226 embryonic ventricle EHDAA2:0001531 EMAPA:16350 FMA:71006 NCIT:C34160 SCTID:361524003 TAO:0002231 Wikipedia:Embryonic_ventricle ZFA:0001719 early heart ventricle embryonic heart ventricle future heart ventricle presumptive cardiac ventricle heart tube primitive ventricle primitive ventricle of heart primordial cardiac ventricle primordial ventricle uberon UBERON:0006283 The embryonic ventricle or primitive ventricle of the developing heart gives rise to the trabeculated parts of the left and right ventricles. In contrast, the smooth parts of the left and right ventricles originate from the embryological bulbus cordis. The primitive ventricle becomes divided by a septum, the septum inferius or ventricular septum, which grows upward from the lower part of the ventricle, its position being indicated on the surface of the heart by a furrow. Its dorsal part increases more rapidly than its ventral portion, and fuses with the dorsal part of the septum intermedium. For a time an interventricular foramen exists above its ventral portion, but this foramen is ultimately closed by the fusion of the aortic septum with the ventricular septum[WP] future cardiac ventricle ZFA EMAPA Multi-tissue structure that is part of the heart tube and will become the cardiac ventricle. ZFA:0001719 presumptive cardiac ventricle heart tube ZFA:0001719 primitive ventricle EHDAA2:0001531 primitive ventricle of heart EMAPA:16350 primordial cardiac ventricle FMA:71006 primordial ventricle FMA:71006 EHDAA:924 EMAPA:16663 RETIRED_EHDAA2:0002089 trigeminal V preganglion uberon trigeminal preganglion UBERON:0006304 See: https://github.com/obophenotype/mouse-anatomy-ontology/issues/13 and https://github.com/obophenotype/uberon/issues/693 -- consider merging into trigeminal ganglion, as this complicates the model future trigeminal ganglion EHDAA2 trigeminal V preganglion EMAPA:16663 trigeminal preganglion EMAPA:16663 A segment of the eyeball that is filled with refractive media BTO:0002085 EMAPA:37529 FMA:58071 MA:0002459 NCIT:C32301 SCTID:280540004 UMLS:C0459556 eye chamber eyeball chamber uberon chamber of eye UBERON:0006311 chamber of eyeball A segment of the eyeball that is filled with refractive media http://orcid.org/0000-0002-6601-2165 EMAPA:37529 MA:th UMLS:C0459556 ncithesaurus:Chamber_of_the_Eye eye chamber MA:0002459 eyeball chamber FMA:58071 chamber of eye BTO:0002085 Body substance in a liquid or semi-solid state in the eyeball which serves to refract light. ocular refraction MA:0001911 uberon UBERON:0006312 ocular refractive media Body substance in a liquid or semi-solid state in the eyeball which serves to refract light. http://orcid.org/0000-0002-6601-2165 Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not. fluid BIRNLEX:20 EMAPA:37441 FMA:280556 GAID:266 MESH:D001826 Wikipedia:Body_fluid galen:BodyFluid body fluid uberon UBERON:0006314 bodily fluid Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not. MESH:A12.207 Wikipedia:Body_fluid EMAPA:37441 MA:th body fluid GAID:266 A nucleus of brain that is part of a brainstem. EMAPA:32790 MA:0000821 uberon brain stem nucleus UBERON:0006331 brainstem nucleus A nucleus of brain that is part of a brainstem. OBOL:automatic brain stem nucleus EMAPA:32790 2 2 An artery that connects two larger arteries. EMAPA:18598 MA:0001938 NCIT:C52851 UMLS:C1707451 uberon UBERON:0006347 Grouping for anterior and posterior communicating artery An artery that connects two larger arteries. ncithesaurus:Communicating_Artery UMLS:C1707451 ncithesaurus:Communicating_Artery A portion of organism substance that secreted_by a zone of skin. MA:0002537 skin fluid/secretion uberon skin fluid skin substance UBERON:0006535 skin secretion A portion of organism substance that secreted_by a zone of skin. OBOL:automatic skin fluid/secretion MA:0002537 A portion of organism substance that is secreted by a female reproductive gland. MA:0002510 female reproductive system fluid/secretion uberon female reproductive system fluid female reproductive system secretion UBERON:0006537 female reproductive gland secretion A portion of organism substance that is secreted by a female reproductive gland. UBERON:cjm female reproductive system fluid/secretion MA:0002510 A portion of organism substance that secreted_by a respiratory system. EMAPA:36550 MA:0002533 NCIT:C13722 UMLS:C1514899 uberon respiratory system fluid respiratory system secretion UBERON:0006538 respiratory system fluid/secretion A portion of organism substance that secreted_by a respiratory system. OBOL:automatic UMLS:C1514899 ncithesaurus:Respiratory_System_Fluid_or_Secretion A tube that is part of a excretory system. uberon UBERON:0006555 excretory tube A tube that is part of a excretory system. OBOL:automatic The pharynx is the part of the digestive system immediately posterior to the mouth[GO]. currently this is an extremely generic class, encompassing both protostomes and deuterostomes. branchial pharyngeal FBbt:00005380 MAT:0000049 MIAA:0000049 uberon anterior part of foregut pharyngeal tube UBERON:0006562 pharynx The pharynx is the part of the digestive system immediately posterior to the mouth[GO]. GO:0060465 Tunica media of artery which is continuous with the myocardium of right ventricle.[FMA] FMA:85030 uberon UBERON:0006563 tunica media of pulmonary trunk Tunica media of artery which is continuous with the myocardium of right ventricle.[FMA] FMA:85030 FMA:FMA A myocardium that is part of a left ventricle of a heart. Myocardium of ventricle which is continuous with the tunica media of aorta. EMAPA:17339 FMA:9558 MA:0002983 SCTID:362021000 left ventricular myocardium myocardium of left ventricle uberon UBERON:0006566 left ventricle myocardium A myocardium that is part of a left ventricle of a heart. http://orcid.org/0000-0002-6601-2165 Myocardium of ventricle which is continuous with the tunica media of aorta. FMA:9558 left ventricular myocardium FMA:9558 myocardium of left ventricle FMA:9558 A myocardium that is part of a right ventricle of a heart. Myocardium of ventricle which is continuous with the tunica media of the pulmonary trunk. EMAPA:17342 FMA:9535 MA:0002984 SCTID:362020004 myocardium of right ventricle right ventricular myocardium uberon UBERON:0006567 right ventricle myocardium A myocardium that is part of a right ventricle of a heart. http://orcid.org/0000-0002-6601-2165 Myocardium of ventricle which is continuous with the tunica media of the pulmonary trunk. FMA:9535 myocardium of right ventricle FMA:9535 right ventricular myocardium FMA:9535 A nucleus of brain that is part of a diencephalon. TAO:0002191 ZFA:0001659 uberon UBERON:0006569 diencephalic nucleus A nucleus of brain that is part of a diencephalon. OBOL:automatic The pectinate line (anocutaneous line, dentate line, anorectal junction) is a line which divides the upper 2/3rds and lower 1/3rd of the anal canal. Developmentally, this line represents the hindgut-proctodeum junction. It is an important anatomical landmark, and several distinctions can be made based upon the location of a structure relative to this line: FMA also has FMA:29321 but it's not clear how this differs EMAPA:19159 FMA:75383 NCIT:C34245 SCTID:245445008 UMLS:C0821671 Wikipedia:Pectinate_line linea pectinata canalis analis pectinate line of anal canal uberon Hilton's 'white line' dentate line linea anocutanea recto-anal junction site of anal membrane UBERON:0006574 pectinate line http://upload.wikimedia.org/wikipedia/commons/7/7b/Hemorrhoid.png The pectinate line (anocutaneous line, dentate line, anorectal junction) is a line which divides the upper 2/3rds and lower 1/3rd of the anal canal. Developmentally, this line represents the hindgut-proctodeum junction. It is an important anatomical landmark, and several distinctions can be made based upon the location of a structure relative to this line: Wikipedia:Pectinate_line FMA also has FMA:29321 but it's not clear how this differs FMA UMLS:C0821671 ncithesaurus:Pectinate_Line linea pectinata canalis analis FMA:75383 FMA:TA pectinate line of anal canal FMA:75383 Hilton's 'white line' EMAPA:19159 dentate line Wikipedia:Pectinate_line linea anocutanea Wikipedia:Pectinate_line recto-anal junction Wikipedia:Pectinate_line site of anal membrane EMAPA:19159 Presumptive structure of the blastula that will develop into endoderm. AAO:0000471 EFO:0003437 TAO:0000416 ZFA:0000416 uberon UBERON:0006595 presumptive endoderm Presumptive structure of the blastula that will develop into endoderm. http://orcid.org/0000-0002-6601-2165 AAO:0000468 EFO:0003439 TAO:0000568 ZFA:0000568 future blood uberon UBERON:0006596 presumptive blood Portion of embryonic tissue determined by fate mapping to become a structure. Consider merging with anlage AAO:0000479 TAO:0001116 ZFA:0001116 future structure presumptive structures uberon UBERON:0006598 presumptive structure Portion of embryonic tissue determined by fate mapping to become a structure. GOC:CVS GOC:YMB ZFA:0001116 presumptive structures ZFA:0001116 Presumptive structure of the blastula that will develop into ectoderm. AAO:0000470 EFO:0003466 TAO:0001376 XAO:0004132 ZFA:0001376 uberon presumptive epidermis UBERON:0006601 presumptive ectoderm Presumptive structure of the blastula that will develop into ectoderm. http://orcid.org/0000-0002-6601-2165 presumptive epidermis ZFA:0001376 Presumptive structure of the blastula that will develop into mesoderm. AAO:0000476 EFO:0003467 TAO:0001377 ZFA:0001377 uberon UBERON:0006603 presumptive mesoderm Presumptive structure of the blastula that will develop into mesoderm. http://orcid.org/0000-0002-6601-2165 A region of muscle in many organs in the vertebrate body, adjacent to the submucosa membrane. It is responsible for gut movement such as peristalsis. currently this class conflates a generic layer of muscle and a specific layer found lining the digestive tract (the muscularis externa), typically composed of circular and longitudinal layers (although this varies) An outer layer of smooth muscle surrounding a hollow or tubular organ as the bladder, esophagus, large intestine, small intestine, stomach, ureter, uterus, and vagina that often consists of an inner layer of circular fibers serving to narrow the lumen of the organ and an outer layer of longitudinal fibers serving to shorten its length[BTO]. typically smooth muscle, but there may be exceptions - in the upper esophagus, part of the externa is skeletal muscle, rather than smooth muscle. BTO:0004838 SCTID:86915006 UMLS:C0225358 Wikipedia:Muscular_layer muscular layer muscularis layer tunica muscularis uberon muscular coat muscularis muscularis externa muscularis propria transverse muscular fibers tunica externa tunica muscularis UBERON:0006660 muscular coat A region of muscle in many organs in the vertebrate body, adjacent to the submucosa membrane. It is responsible for gut movement such as peristalsis. Wikipedia:Muscular_layer An outer layer of smooth muscle surrounding a hollow or tubular organ as the bladder, esophagus, large intestine, small intestine, stomach, ureter, uterus, and vagina that often consists of an inner layer of circular fibers serving to narrow the lumen of the organ and an outer layer of longitudinal fibers serving to shorten its length[BTO]. BTO:0004838 UMLS:C0225358 ncithesaurus:Muscle_Layer muscular layer OBOL:automatic muscularis layer FMA:45634 tunica muscularis BTO:0004838 muscular coat Wikipedia:Muscularis_externa muscularis externa BTO:0004838 muscularis propria Wikipedia:Muscularis_externa transverse muscular fibers Wikipedia:Muscularis_externa tunica externa BTO:0004838 tunica muscularis Wikipedia:Muscularis_externa On the interior surface of the temporal bone, behind the rough surface of the apex, is the large circular aperture of the carotid canal, which ascends at first vertically, and then, making a bend, runs horizontally forward and medialward. It transmits into the cranium, the internal carotid artery, and the carotid plexus of nerves. Sympathetics to the head also pass through the carotid canal. They have several motor functions: raise the eyelid (superior tarsal muscle), dilate pupil, innervate sweat glands of face and scalp and constricts blood vessels in head[WP]. EMAPA:18707 FMA:55805 Wikipedia:Carotid_canal uberon canalis caroticus UBERON:0006668 carotid canal http://upload.wikimedia.org/wikipedia/commons/4/4c/Gray141.png On the interior surface of the temporal bone, behind the rough surface of the apex, is the large circular aperture of the carotid canal, which ascends at first vertically, and then, making a bend, runs horizontally forward and medialward. It transmits into the cranium, the internal carotid artery, and the carotid plexus of nerves. Sympathetics to the head also pass through the carotid canal. They have several motor functions: raise the eyelid (superior tarsal muscle), dilate pupil, innervate sweat glands of face and scalp and constricts blood vessels in head[WP]. Wikipedia:Carotid_canal canalis caroticus Wikipedia:Carotid_canal the three-lobed cloverleaf-shaped aponeurosis situated at the center of the diaphragm; the central tendon is fused with the fibrous pericardium that provides attachment for the muscle fibers In mammals, the diaphragm muscle divides the thoracoabdominal cavity into thorax and abdomen. In most mammals, the diaphragm is a flat sheet with muscle fibers radiating outward from a central tendon, and the diaphragm's apposition to the cranial surface of the liver gives it a dome-shape. Muscle fiber contraction reduces the curvature of the dome, thereby expanding the thoracic cavity and aspirating air into the lungs.[well established][VHOG] EMAPA:17702 FMA:58279 NCIT:C34119 SCTID:244943002 UMLS:C0230162 VHOG:0001399 Wikipedia:Central_tendon_of_diaphragm central tendon centrum tendineum centrum tendineum diaphragmatis uberon UBERON:0006670 central tendon of diaphragm VHOG definitional the three-lobed cloverleaf-shaped aponeurosis situated at the center of the diaphragm; the central tendon is fused with the fibrous pericardium that provides attachment for the muscle fibers MGI:csmith MP:0012061 In mammals, the diaphragm muscle divides the thoracoabdominal cavity into thorax and abdomen. In most mammals, the diaphragm is a flat sheet with muscle fibers radiating outward from a central tendon, and the diaphragm's apposition to the cranial surface of the liver gives it a dome-shape. Muscle fiber contraction reduces the curvature of the dome, thereby expanding the thoracic cavity and aspirating air into the lungs.[well established][VHOG] 2012-09-17 VHOG:0001399 VHOG DOI:10.1016/j.resp.2006.06.003 http://bgee.unil.ch/ UMLS:C0230162 ncithesaurus:Central_Tendon_of_the_Diaphragm central tendon FMA:58279 centrum tendineum FMA:58279 centrum tendineum diaphragmatis FMA:58279 FMA:TA An anatomical boundary that adjacent_to a epithelium. FMA:70997 epithelium surface uberon UBERON:0006677 surface of epithelium An anatomical boundary that adjacent_to a epithelium. OBOL:automatic epithelium surface FMA:70997 A vein that is part of a vertebral column. EMAPA:18255 FMA:76735 MA:0002108 SCTID:181376008 Wikipedia:Spinal_veins vena spinalis uberon spinal branch UBERON:0006686 spinal vein A vein that is part of a vertebral column. OBOL:automatic vena spinalis FMA:76735 FMA:TA spinal branch FMA:76735 A conduit enclosed within the vertebral foramen of the vertebrae through which the spinal cord passes. TODO - check neural vs vertebral canal; embryonic vs adult? Canal formed by the vertebral centra ventrally, the pedicels laterally, and the neural arches dorsally that encloses and protects the spinal cord.[AAO] AAO:0000693 FMA:9680 GAID:242 NCIT:C33869 NCIT:C34221 SCTID:361746009 UMLS:C0037922 UMLS:C1522467 Wikipedia:Spinal_canal uberon c. vertebralis foramen vertebrale neural canal spinal canal spinal cavity vertebral canal UBERON:0006692 vertebral canal http://upload.wikimedia.org/wikipedia/commons/3/30/Gray82.png A conduit enclosed within the vertebral foramen of the vertebrae through which the spinal cord passes. Wikipedia:Spinal_canal http://orcid.org/0000-0002-6601-2165 Canal formed by the vertebral centra ventrally, the pedicels laterally, and the neural arches dorsally that encloses and protects the spinal cord.[AAO] 2012-06-20 AAO:0000693 AAO AAO:LAP UMLS:C0037922 ncithesaurus:Vertebral_Canal UMLS:C1522467 ncithesaurus:Neural_Canal c. vertebralis Wikipedia:Spinal_canal foramen vertebrale AAO:0000693 neural canal AAO:0000693 spinal canal AAO:0000693 spinal cavity Wikipedia:Spinal_canal vertebral canal Wikipedia:Spinal_canal the edge of the cornea where it joins the sclera; the limbus is a common site for the occurrence of corneal epithelial neoplasm EFO:0001403 EMAPA:37835 FMA:58342 GAID:896 MESH:D016850 SCTID:63716004 Wikipedia:Corneal_limbus ZFA:0005570 cornea limbus corneal limbus corneal-scleral limbus corneoscleral junction limbus corneae sclerocorneal junction sclerocorneal limbus uberon limbus corneae UBERON:0006761 This location has parts such as blood vessels etc. See PMC2868485, http://www.ncbi.nlm.nih.gov/pubmed/2695343 corneo-scleral junction http://upload.wikimedia.org/wikipedia/commons/3/3d/Limbus.png the edge of the cornea where it joins the sclera; the limbus is a common site for the occurrence of corneal epithelial neoplasm MP:0013477 EMAPA:37835 MA:th corneal limbus FMA:58342 corneal limbus GAID:896 corneal-scleral limbus PMID:17051547 corneoscleral junction GAID:896 limbus corneae Wikipedia:Corneal_limbus sclerocorneal junction FMA:58342 sclerocorneal limbus GAID:896 limbus corneae Wikipedia:Corneal_limbus An epithelium that is composed primarily of secretory cells. consider splitting epithelium from epithelial tissue BTO:0002991 NCIT:C43370 NCIT:C45715 UMLS:C0682578 UMLS:C1708242 uberon UBERON:0006799 glandular epithelium An epithelium that is composed primarily of secretory cells. http://orcid.org/0000-0002-6601-2165 UMLS:C0682578 ncithesaurus:Glandular_Epithelium UMLS:C1708242 ncithesaurus:Glandular_Epithelial_Tissue Loose connective tissue located at the outer and inner layers of organs. Examples: submucosal connective tissue, tunica adventitia of artery, papillary dermis, superficial fascia of dorsum of hand. Also known as loose connective tissue. A pliable, mesh-like tissue with a fluid matrix that functions to cushion and protect body organs.[AAO] relationship loss: subclass connective tissue proper (AAO:0000099)[AAO] cushions body organs AAO:0000027 FMA:63897 SCTID:68477002 loose areolar connective tissue uberon areolar tissue loose connective tissue UBERON:0006815 areolar connective tissue FMA FMA Loose connective tissue located at the outer and inner layers of organs. Examples: submucosal connective tissue, tunica adventitia of artery, papillary dermis, superficial fascia of dorsum of hand. FMA:63897 Also known as loose connective tissue. A pliable, mesh-like tissue with a fluid matrix that functions to cushion and protect body organs.[AAO] 2012-06-20 AAO:0000027 AAO AAO:LAP relationship loss: subclass connective tissue proper (AAO:0000099)[AAO] 2012-06-20 AAO:0000027 AAO cushions body organs AAO loose areolar connective tissue FMA:63897 loose connective tissue AAO:0000027 A subdivision of a the reproductive tract in a female organism that is the site of embryo development. uterus FBbt:00004924 TADS:0000421 WBbt:0006760 uberon UBERON:0006834 uterus or analog A subdivision of a the reproductive tract in a female organism that is the site of embryo development. http://orcid.org/0000-0002-6601-2165 uterus FBbt:00004924 A furrow or an incomplete tube. AEO:0000161 EHDAA2_RETIRED:0003161 uberon groove UBERON:0006846 surface groove A furrow or an incomplete tube. AEO:0000161 AEO:JB https://github.com/obophenotype/human-developmental-anatomy-ontology/issues/4 groove AEO:0000161 The distalmost portion of the digestive tract, derived from the hindgut, and terminating with the anus. this class is the superclass of 'rectum', which is currently reserved for the vertebrate structure. May be merged in future. FBbt:00005756 WBbt:0005773 rectum uberon rectal part of digestive tract terminal section of digestive tract UBERON:0006866 terminal part of digestive tract The distalmost portion of the digestive tract, derived from the hindgut, and terminating with the anus. http://orcid.org/0000-0002-6601-2165 rectum FBbt:00005756 A vasculature that is part of a organ. FMA:74612 organ vasculature set of blood vessels of organ uberon UBERON:0006876 vasculature of organ A vasculature that is part of a organ. OBOL:automatic organ vasculature FMA:74612 set of blood vessels of organ FMA:74612 A head mesenchyme that develops_from a mesoderm. merged in 'head mesoderm' from XAO/AAO and EFO here. Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme AAO:0011051 EFO:0003337 EFO:0003603 EHDAA2:0001118 EHDAA:655 EMAPA:16099 EMAPA_RETIRED:16270 FMA:293859 TAO:0000998 VHOG:0000185 XAO:0000053 ZFA:0000998 head mesenchyme derived from mesoderm head mesenchyme from head mesoderm head mesenchyme from mesoderm mesenchyme derived from head mesoderm mesenchyme from head mesoderm uberon cranial mesoderm head mesoderm UBERON:0006904 head mesenchyme from mesoderm ZFA EHDAA2 XAO A head mesenchyme that develops_from a mesoderm. OBOL:automatic head mesenchyme from head mesoderm EHDAA2:0001118 mesenchyme derived from head mesoderm EHDAA:1057 cranial mesoderm UBERON:0005280 head mesoderm AAO:0011051 UBERON:0005280 Mesenchyme that is part of a mandibular prominence. EHDAA2:0001062 EHDAA:5861 EHDAA:5873 EMAPA:17357 mesenchyme of mandibular process mesenchyme of mandibular prominence uberon UBERON:0006905 mandibular process mesenchyme Mesenchyme that is part of a mandibular prominence. OBOL:automatic mesenchyme of mandibular process EMAPA:17357 mesenchyme of mandibular prominence https://orcid.org/0000-0002-6601-2165 An anatomical space that surrounded_by a digestive tract. BTO:0000349 EMAPA:32908 FMA:45677 digestive tract lumen gut cavity gut lumen lumen of alimentary tract lumen of digestive tract lumen of gut uberon UBERON:0006909 lumen of digestive tract An anatomical space that surrounded_by a digestive tract. OBOL:automatic digestive tract lumen https://orcid.org/0000-0002-6601-2165 gut cavity BTO:0000349 gut lumen FMA:45677 lumen of alimentary tract https://orcid.org/0000-0002-6601-2165 lumen of digestive tract https://orcid.org/0000-0002-6601-2165 lumen of gut FMA:45677 An epithelium that is part of a lip. The thick, high squamous-stratified epithelium that covers the lips. It contains abundant melanocytes, many mucous cells and has well differentiated taste buds.[TAO] BTO:0004468 TAO:0005334 ZFA:0005334 uberon UBERON:0006913 lip epithelium An epithelium that is part of a lip. OBOL:automatic The thick, high squamous-stratified epithelium that covers the lips. It contains abundant melanocytes, many mucous cells and has well differentiated taste buds.[TAO] 2012-08-14 TAO:0005334 TAO ZFIN:ZDB-PUB-060921-12 An epithelium characterised by its most superficial layer consisting of squamous epithelial cells. FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium BTO:0002072 NCIT:C12848 SCTID:40118003 UMLS:C0221909 Wikipedia:Squamous_epithelium uberon UBERON:0006914 squamous epithelium An epithelium characterised by its most superficial layer consisting of squamous epithelial cells. Wikipedia:Squamous_epithelium FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium FBbt UMLS:C0221909 ncithesaurus:Squamous_Epithelium Multilaminar epithelium which consists of more than one layer of squamous cells only one layer of which is in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, epithelium of wall of esophagus.[FMA] FMA:45563 NCIT:C13180 UMLS:C0836131 Wikipedia:Stratified_squamous_epithelium epithelium stratificatum squamosum uberon UBERON:0006915 stratified squamous epithelium Multilaminar epithelium which consists of more than one layer of squamous cells only one layer of which is in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, epithelium of wall of esophagus.[FMA] FMA:45563 Wikipedia:Stratified_squamous_epithelium UMLS:C0836131 ncithesaurus:Stratified_Squamous_Epithelium epithelium stratificatum squamosum FMA:45563 A squamous epithelium that is part of a esophagus. MA introduces basal and squamous subtypes of esophagus epithelium; consider adding the FMA class 'epithelium of esophagus' here, because it is classified as squamous. BTO also has a singleton subclass BTO:0003635 CALOHA:TS-1250 EMAPA:35324 MA:0001567 NCIT:C49222 UMLS:C1707950 uberon esophageal squamous epithelium squamous epithelium of esophagus squamous oesophageal epithelium UBERON:0006920 esophagus squamous epithelium A squamous epithelium that is part of a esophagus. OBOL:automatic MA introduces basal and squamous subtypes of esophagus epithelium; consider adding the FMA class 'epithelium of esophagus' here, because it is classified as squamous. BTO also has a singleton subclass MA UMLS:C1707950 ncithesaurus:Esophageal_Squamous_Epithelium esophageal squamous epithelium OBOL:automatic squamous epithelium of esophagus OBOL:automatic squamous oesophageal epithelium MA:0001567 A squamous epithelium that is part of a stomach. EMAPA:35824 MA:0001611 uberon UBERON:0006921 stomach squamous epithelium A squamous epithelium that is part of a stomach. OBOL:automatic A glandular epithelium that lines the stomach. The stomach's glandular epithelium is characterized by the presence of gastric glands. we follow Kardong in treating the glandular epithelium as a distinct entity, and thus as an epithelium which has glands; FMA has 'epithelium of gastric gland', which is part of the gastric gland. EMAPA:17623 EMAPA:35814 FMA:63458 MA:0002784 epithelium of gastric gland uberon gastric gland epithelium UBERON:0006924 stomach glandular epithelium FMA A glandular epithelium that lines the stomach. The stomach's glandular epithelium is characterized by the presence of gastric glands. ISBN:0073040584 epithelium of gastric gland FMA:63458 gastric gland epithelium FMA:63458 Any gland that is part of the digestive system. AAO:0000130 BTO:0000345 uberon digestive gland UBERON:0006925 digestive system gland Any gland that is part of the digestive system. UBERON:cjm digestive gland BTO:0000345 Simple columnar epithelium that constitutes the secretory part of a gland. Examples: epithelium of stomach, luminal epithelium of lactiferous duct.[FMA] FMA:64800 NCIT:C13182 UMLS:C0225337 uberon UBERON:0006929 glandular columnar epithelium Simple columnar epithelium that constitutes the secretory part of a gland. Examples: epithelium of stomach, luminal epithelium of lactiferous duct.[FMA] FMA:64800 UMLS:C0225337 ncithesaurus:Columnar_Epithelium FMA:66809 uberon UBERON:0006930 glandular cuboidal epithelium stomach mucosa that is lined with glandular epithelium and part of a stomach glandular region. EMAPA:27167 MA:0001614 stomach glandular region glandular mucous membrane uberon UBERON:0006931 stomach glandular region mucosa stomach mucosa that is lined with glandular epithelium and part of a stomach glandular region. http://orcid.org/0000-0002-6601-2165 stomach glandular region glandular mucous membrane EMAPA:27167 Simple columnar epithelium made up of cells specialized to serve as sensory cells for the reception of external stimuli, as the sensory cells of the cochlea, vestibule, nasal mucosa, and tongue. note that the definition sourced from Dorlands say 'simple columnar', but FMA says atypical CALOHA:TS-0682 FMA:62410 SCTID:309045006 uberon neuroepithelium UBERON:0006934 sensory epithelium Simple columnar epithelium made up of cells specialized to serve as sensory cells for the reception of external stimuli, as the sensory cells of the cochlea, vestibule, nasal mucosa, and tongue. BTO:0000314 note that the definition sourced from Dorlands say 'simple columnar', but FMA says atypical FMA neuroepithelium BTO:0000314 The stroma of the ovary is a peculiar soft tissue, abundantly supplied with blood vessels, consisting for the most part of spindle-shaped cells with a small amount of ordinary connective tissue. These cells have been regarded by some anatomists as unstriped muscle cells, which, indeed, they most resemble; by others as connective-tissue cells. On the surface of the organ this tissue is much condensed, and forms a layer composed of short connective-tissue fibers, with fusiform cells between them. The stroma of the ovary may contain interstitial cells resembling those of the testis. CALOHA:TS-1246 EMAPA:28880 FMA:18626 MA:0002991 NCIT:C33638 SCTID:259306002 UMLS:C0737271 Wikipedia:Stroma_of_ovary interstitial tissue of ovary ovarian stroma ovary stroma stroma of the ovary stroma ovarica uberon stroma ovarii UBERON:0006960 ovary stroma FMA The stroma of the ovary is a peculiar soft tissue, abundantly supplied with blood vessels, consisting for the most part of spindle-shaped cells with a small amount of ordinary connective tissue. These cells have been regarded by some anatomists as unstriped muscle cells, which, indeed, they most resemble; by others as connective-tissue cells. On the surface of the organ this tissue is much condensed, and forms a layer composed of short connective-tissue fibers, with fusiform cells between them. The stroma of the ovary may contain interstitial cells resembling those of the testis. Wikipedia:Stroma_of_ovary UMLS:C0737271 ncithesaurus:Stroma_of_the_Ovarian_Cortex interstitial tissue of ovary FMA:18626 ovarian stroma FMA:18626 ovary stroma MA:0002991 stroma of the ovary Wikipedia:Stroma_of_ovary stroma ovarica FMA:18626 stroma ovarii Wikipedia:Stroma_of_ovary The vascular cord is the primordial vasculature that will develop into blood vessels by the process of tubulogenesis[GO]. The vascular cord is composed of angioblast or vascular endothelial cells in a solid linear mass called a cord. The cord then undergoes tubulogenesis to form the lumen of the vessels[ZFA]. EFO:0003709 TAO:0005077 ZFA:0005077 uberon UBERON:0006965 vascular cord The vascular cord is the primordial vasculature that will develop into blood vessels by the process of tubulogenesis[GO]. The vascular cord is composed of angioblast or vascular endothelial cells in a solid linear mass called a cord. The cord then undergoes tubulogenesis to form the lumen of the vessels[ZFA]. GO:0072360 ZFA:0005077 A capillary that is part of the coronary system. ZFA:0005813 heart capillary uberon UBERON:0006966 coronary capillary A capillary that is part of the coronary system. http://orcid.org/0000-0002-6601-2165 heart capillary GO:0003248 A two dimensional anatomical structure that is the boundary between an anatomical structure and an anatomical substance, an anatomical space or the organism's environment. Examples include the surface of your skin, the surface of the lining of your gut; the surface of the endothelium of you aorta that is in contact with blood.n BILA:0000010 CARO:0001002 EHDAA2_RETIRED:0003192 FMA:24137 NCIT:C34022 UMLS:C1515977 uberon UBERON:0006984 Old definition: 'Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures.' Note, in the new definition, the space referred to is not necessarily an anatomical space. It may be the outside of an organism. anatomical surface via morphological boundary in CARO A two dimensional anatomical structure that is the boundary between an anatomical structure and an anatomical substance, an anatomical space or the organism's environment. Examples include the surface of your skin, the surface of the lining of your gut; the surface of the endothelium of you aorta that is in contact with blood.n CARO:0001002 UMLS:C1515977 ncithesaurus:Anatomic_Surface The splanchnic mesoderm in the cardiogenic region where the heart develops; it gives rise to endocardial heart tubes that fuse to form the primordial cardiac tube, the heart primordium[web]. Two migratory heart primordia that move ventrally during the course of neurulation, and then fuse[XAO]. consider FBbt:00005541 ! cardiogenic mesoderm review EHDAA2 placement AAO:0011021 BILA:0000051 EFO:0000315 EHDAA2:0000214 EHDAA:385 FMA:293143 SCTID:360387000 VHOG:0001641 XAO:0000235 cardiogenic splanchnopleure uberon cardiac mesoderm cardiogenic mesoderm cardiogenic region heart primordia UBERON:0007005 cardiogenic splanchnic mesoderm The splanchnic mesoderm in the cardiogenic region where the heart develops; it gives rise to endocardial heart tubes that fuse to form the primordial cardiac tube, the heart primordium[web]. Two migratory heart primordia that move ventrally during the course of neurulation, and then fuse[XAO]. XAO:0000235 http://www.drugs.com/dict/cardiogenic-mesoderm.html https://github.com/obophenotype/insect_neuroanatomy_ontology/issues/7 cardiogenic splanchnopleure EHDAA2:0000214 cardiac mesoderm XAO:0000235 cardiogenic mesoderm http://www.drugs.com/dict/cardiogenic-mesoderm.html cardiogenic region http://orcid.org/0000-0002-6601-2165 heart primordia XAO:0000235 Organism at the cleavage stage. BILA:0000058 uberon UBERON:0007010 cleaving embryo Organism at the cleavage stage. OBOL:automatic The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis BILA:0000084 NCIT:C34268 SCTID:360394002 UMLS:C1514442 future digestive tract future digestive tube future gut primitive gut uberon embryonic digestive tube primordial digestive tube primordial gut UBERON:0007026 presumptive gut The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis NCBIBook:NBK10107 UMLS:C1514442 ncithesaurus:Primordial_Gut BILA:0000142 uberon UBERON:0007037 mechanosensory system Cranial neural crest that migrates into the mandibular arch. TAO:0007064 XAO:0000024 ZFA:0007064 uberon UBERON:0007098 mandibular neural crest ZFA ZFA Cranial neural crest that migrates into the mandibular arch. ZFA:0007064 A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified]. note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis FBbt:00003154 SPD:0000130 TADS:0000147 http://www.sciencemag.org/content/313/5795/1922/F1.large.jpg dorsal tube heart uberon adult heart UBERON:0007100 Gene notes: Bmp, Nkx, Gata primary circulatory organ GO uses blood circulation generically to include the haemolymphatic fluid of arthropods A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified]. GO:0007507 dorsal tube Wikipedia:Heart heart GO:0007507 adult heart FBbt:00003154 Ganglion which is located in the trunk. EFO:0000901 MAT:0000344 MIAA:0000344 TAO:0001573 ZFA:0001573 body ganglion trunk ganglia uberon UBERON:0007134 trunk ganglion Ganglion which is located in the trunk. ZFIN:curator body ganglion MAT:0000344 trunk ganglia ZFA:0001573 An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO] EFO:0003497 TAO:0000131 ZFA:0000131 uberon presumptive central nervous system UBERON:0007135 neural keel An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. ZFIN:ZDB-PUB-961014-576 An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000131 TAO ZFIN:curator presumptive central nervous system ZFA:0000131 An internal carotid artery that branching_part_of a left common carotid artery plus branches. EMAPA:16329 FMA:4062 SCTID:161452006 arteria caritis interna sinistra uberon UBERON:0007142 left internal carotid artery An internal carotid artery that branching_part_of a left common carotid artery plus branches. OBOL:automatic arteria caritis interna sinistra FMA:4062 An internal carotid artery that branching_part_of a right common carotid artery plus branches. EMAPA:16330 FMA:3949 SCTID:161251001 arteria carotis interna dextra uberon UBERON:0007143 right internal carotid artery An internal carotid artery that branching_part_of a right common carotid artery plus branches. OBOL:automatic arteria carotis interna dextra FMA:3949 An embryonic structure that will either develop into a post-anal tail or recede into a vestigial remnant of the tail. By the fourth week a clear tail is seen in the human embryo. It recedes after a few weeks and these tissues form what is commonly known as the tailbone (coccyx). EMAPA:16748 FMA:85540 embryo tail tail of embryo uberon embryonic tail UBERON:0007144 embryonic post-anal tail An embryonic structure that will either develop into a post-anal tail or recede into a vestigial remnant of the tail. http://orcid.org/0000-0002-6601-2165 embryo tail FMA:85540 tail of embryo FMA:85540 embryonic tail FMA:85540 An anatomical cavity that surrounded_by a midgut. EMAPA:18377 FMA:54366 midgut lumen uberon UBERON:0007147 lumen of midgut An anatomical cavity that surrounded_by a midgut. OBOL:automatic midgut lumen FMA:54366 An anatomical cavity that surrounded_by a hindgut. EMAPA:18396 FMA:54367 hindgut lumen uberon UBERON:0007148 lumen of hindgut An anatomical cavity that surrounded_by a hindgut. OBOL:automatic hindgut lumen FMA:54367 An anatomical cavity that surrounded_by a anal canal. EMAPA:18836 FMA:17357 anal canal lumen uberon UBERON:0007158 lumen of anal canal An anatomical cavity that surrounded_by a anal canal. OBOL:automatic anal canal lumen FMA:17357 An anatomical cavity that surrounded_by a colon. EMAPA:18945 FMA:18374 SCTID:362156004 colon lumen uberon colonic lumen UBERON:0007159 lumen of colon An anatomical cavity that surrounded_by a colon. OBOL:automatic colon lumen FMA:18374 colonic lumen FMA:18374 A lamina propria that is part of a colonic mucosa. EMAPA:27395 FMA:15657 MA:0003196 SCTID:113284008 colonic lamina propria lamina propria mucosae of colon lamina propria of colonic mucosa lamina propria of colonic mucous membrane uberon UBERON:0007177 lamina propria of mucosa of colon A lamina propria that is part of a colonic mucosa. OBOL:automatic colonic lamina propria FMA:15657 lamina propria mucosae of colon FMA:15657 lamina propria of colonic mucosa FMA:15657 lamina propria of colonic mucous membrane FMA:15657 A mesothelium that is part of a serous pericardium. BTO:0003157 EMAPA:16133 FMA:18149 SCTID:67300002 mesothelium of pericardium pericardial mesothelium serous pericardium mesothelium uberon UBERON:0007188 mesothelium of serous pericardium A mesothelium that is part of a serous pericardium. OBOL:automatic mesothelium of pericardium FMA:18149 pericardial mesothelium FMA:18149 serous pericardium mesothelium FMA:18149 The stroma of the bone marrow is all tissue not directly involved in the primary function of hematopoiesis. The yellow bone marrow belongs here, and makes the majority of the bone marrow stroma, in addition to stromal cells located in the red bone marrow. Yellow bone marrow is found in the Medullary cavity. Still, the stroma is indirectly involved in hematopoiesis, since it provides the hematopoietic microenvironment that facilitates hematopoiesis by the parenchymal cells. For instance, they generate colony stimulating factors, affecting hematopoiesis. CALOHA:TS-0085 FMA:21426 Wikipedia:Bone_marrow#Stroma bone marrow stroma uberon UBERON:0007195 stroma of bone marrow The stroma of the bone marrow is all tissue not directly involved in the primary function of hematopoiesis. The yellow bone marrow belongs here, and makes the majority of the bone marrow stroma, in addition to stromal cells located in the red bone marrow. Yellow bone marrow is found in the Medullary cavity. Still, the stroma is indirectly involved in hematopoiesis, since it provides the hematopoietic microenvironment that facilitates hematopoiesis by the parenchymal cells. For instance, they generate colony stimulating factors, affecting hematopoiesis. Wikipedia:Bone_marrow#Stroma bone marrow stroma FMA:21426 The vasculature consisting of brachiocephalic arteries and veins. uberon UBERON:0007204 brachiocephalic vasculature The vasculature consisting of brachiocephalic arteries and veins. http://orcid.org/0000-0002-6601-2165 Mesenchyme that develops_from a cranial neural crest. EFO:0003572 EHDAA2:0000735 EMAPA:16169 EMAPA:16271 EMAPA_RETIRED:16271 TAO:0000787 ZFA:0000787 head mesenchyme from cranial neural crest head mesenchyme from neural crest head neural crest derived mesenchyme uberon UBERON:0007213 mesenchyme derived from head neural crest ZFA Mesenchyme that develops_from a cranial neural crest. OBOL:automatic head mesenchyme from neural crest EHDAA2:0000735 Mesenchyme that develops_from a trunk neural crest. EHDAA2:0002093 EMAPA:16182 TAO:0000999 ZFA:0000999 trunk mesenchyme from neural crest trunk neural crest derived mesenchyme uberon UBERON:0007214 mesenchyme derived from trunk neural crest Mesenchyme that develops_from a trunk neural crest. OBOL:automatic trunk mesenchyme from neural crest EHDAA2:0002093 relationship to Meckel's cartilage to be added Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG] EHDAA2:0000031 EHDAA:583 EMAPA:16382 VHOG:0000510 ventral pharyngeal arch 1 uberon ventral mandibular arch ventral visceral arch 1 UBERON:0007237 1st arch mandibular component EHDAA2 Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG] 2012-09-17 VHOG:0000510 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) http://bgee.unil.ch/ ventral pharyngeal arch 1 VHOG:0000510 ventral mandibular arch VHOG:0000510 ventral visceral arch 1 VHOG:0000510 A tunica media that is part of a artery. EMAPA:36294 EV:0100029 FMA:14273 NCIT:C49321 SCTID:84300001 UMLS:C1710627 arterial media tunica media (arteriae) uberon UBERON:0007239 tunica media of artery A tunica media that is part of a artery. OBOL:automatic UMLS:C1710627 ncithesaurus:Venous_System_Smooth_Muscle_Tissue arterial media EV:0100029 tunica media (arteriae) FMA:14273 A tunica adventitia that is part of a artery. EMAPA:36295 EV:0100030 FMA:14274 SCTID:113261001 arterial adventitia tunica externa (adventitia)(arteriae) uberon UBERON:0007240 tunica adventitia of artery FMA A tunica adventitia that is part of a artery. OBOL:automatic arterial adventitia EV:0100030 tunica externa (adventitia)(arteriae) FMA:14274 A tunica adventitia that is part of a vein. EMAPA:36310 EV:0100034 FMA:14355 SCTID:13202006 tunica externa (adventitia)(venae) venous adventitia uberon UBERON:0007241 tunica adventitia of vein A tunica adventitia that is part of a vein. OBOL:automatic tunica externa (adventitia)(venae) FMA:14355 venous adventitia EV:0100034 A tunica intima that is part of a vein. EMAPA:36308 EV:0100032 FMA:14353 SCTID:2436009 tunica interna (intima)(venae) venous intima uberon UBERON:0007242 tunica intima of vein A tunica intima that is part of a vein. OBOL:automatic tunica interna (intima)(venae) FMA:14353 venous intima EV:0100032 A tunica media that is part of a vein. EMAPA:36309 EV:0100033 FMA:14354 SCTID:42049001 tunica media (venae) venous media uberon UBERON:0007243 tunica media of vein A tunica media that is part of a vein. OBOL:automatic tunica media (venae) FMA:14354 venous media EV:0100033 Gray matter of the central nervous system which is a collection of clustered nuclei. FMA:256381 FMA:84059 uberon cluster of neural nuclei neural nuclei nuclear complex UBERON:0007245 nuclear complex of neuraxis Gray matter of the central nervous system which is a collection of clustered nuclei. http://orcid.org/0000-0002-6601-2165 Any of the nuclei that comprise the superior olivary complex (superior olive). This includes both the primary nuclei such as the lateral and medial nuclei, as well as periolivary nuclei. this class exists largely for consistency with the FMA. It is defined trivially with respect to the SOC. The class may be removed in future. FMA:72246 SCTID:369024009 superior olivary complex nucleus uberon UBERON:0007247 nucleus of superior olivary complex Any of the nuclei that comprise the superior olivary complex (superior olive). This includes both the primary nuclei such as the lateral and medial nuclei, as well as periolivary nuclei. http://orcid.org/0000-0002-6601-2165 superior olivary complex nucleus FMA:72246 Any collection of muscles that is part of a pelvic appendage. currently defined by location rather than attachment Musculature that is part of the pelvic fin.[TAO] TAO:0000258 ZFA:0000258 pelvic fin musculature uberon UBERON:0007270 pelvic appendage musculature Any collection of muscles that is part of a pelvic appendage. OBOL:automatic Musculature that is part of the pelvic fin.[TAO] 2012-08-14 TAO:0000258 TAO TAO:curator pelvic fin musculature ZFA:0000258 Any collection of muscles that is part of an appendage. currently defined by location rather than attachment TAO:0000207 ZFA:0000207 fin musculature uberon UBERON:0007271 appendage musculature Any collection of muscles that is part of an appendage. OBOL:automatic fin musculature ZFA:0000207 The collection of all skeletal elements in a pelvic appendage region. uberon UBERON:0007273 pelvic appendage skeleton VSAO The collection of all skeletal elements in a pelvic appendage region. https://orcid.org/0000-0002-6601-2165 The rhombencephalon (or hindbrain) is a developmental categorization of portions of the central nervous system in vertebrates. The rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. In the human embryo eight rhombomeres can be distinguished, from caudal to rostral: Rh7-Rh1 and the isthmus (the most rostral rhombomere). A rare disease of the rhombencephalon, 'rhombencephalosynapsis' is characterized by a missing vermis resulting in a fused cerebellum. Patients generally present with cerebellar ataxia. The caudal rhombencephalon has been generally considered as the initiation site for neural tube closure. TODO - unify naming conventions The embryonic rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. Rhombomeres Rh7-Rh4 form the myelencephalon that will give the medulla oblongata. Rhombomeres Rh3-Rh1 form the metencephalon that will form the pons and the cerebellum[NPX:PDR]. BAMS:HB CALOHA:TS-2118 EFO:0003440 EHDAA2:0001630 FMA:295640 TAO:0000569 Wikipedia:Rhombencephalon ZFA:0000569 presumptive rhombencephalon uberon embryonic rhombencephalon future hindbrain rhombencephalon UBERON:0007277 presumptive hindbrain XAO-abduced cjm The rhombencephalon (or hindbrain) is a developmental categorization of portions of the central nervous system in vertebrates. The rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. In the human embryo eight rhombomeres can be distinguished, from caudal to rostral: Rh7-Rh1 and the isthmus (the most rostral rhombomere). A rare disease of the rhombencephalon, 'rhombencephalosynapsis' is characterized by a missing vermis resulting in a fused cerebellum. Patients generally present with cerebellar ataxia. The caudal rhombencephalon has been generally considered as the initiation site for neural tube closure. Wikipedia:Rhombencephalon The embryonic rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. Rhombomeres Rh7-Rh4 form the myelencephalon that will give the medulla oblongata. Rhombomeres Rh3-Rh1 form the metencephalon that will form the pons and the cerebellum[NPX:PDR]. NPX:PDR presumptive rhombencephalon ZFA:0000569 embryonic rhombencephalon CALOHA:TS-2118 future hindbrain https://orcid.org/0000-0002-6601-2165 rhombencephalon EHDAA2:0001630 Portion of tissue that is part of the heart tube and will become the sinus venosus. TAO:0002234 ZFA:0001722 uberon UBERON:0007278 presumptive sinus venosus ZFA Portion of tissue that is part of the heart tube and will become the sinus venosus. ZFA:0001722 A presumptive structure that has the potential to develop into a endocardium. Portion of tissue that is part of the heart tube and will become the endocardium.[TAO] TAO:0002233 ZFA:0001724 uberon UBERON:0007280 presumptive endocardium A presumptive structure that has the potential to develop into a endocardium. OBOL:automatic Portion of tissue that is part of the heart tube and will become the endocardium.[TAO] 2012-08-14 TAO:0002233 TAO ZFIN:curator Embryonic structure that gives rise to the midbrain hindbrain boundary. EFO:0003446 TAO:0001187 XAO:0004086 ZFA:0001187 presumptive MHB presumptive midbrain-hindbrain boundary uberon UBERON:0007281 presumptive midbrain hindbrain boundary ZFA Embryonic structure that gives rise to the midbrain hindbrain boundary. ZFA:0001187 presumptive MHB https://orcid.org/0000-0002-6601-2165 presumptive midbrain-hindbrain boundary ZFA:0001187 A presumptive structure that has the potential to develop into a presomitic mesoderm. EFO:0003421 TAO:0000053 ZFA:0000053 uberon presumptive segmental plates UBERON:0007282 presumptive segmental plate https://github.com/obophenotype/uberon/wiki/The-neural-crest EDHAA2 A presumptive structure that has the potential to develop into a presomitic mesoderm. OBOL:automatic presumptive segmental plates ZFA:0000053 A presumptive structure that has the potential to develop into a neural plate. consider merging Region of the gastrula which gives rise to the neural plate.[TAO] EFO:0003424 TAO:0000063 ZFA:0000063 prospective neuroectoderm prospective vegetal ectoderm uberon UBERON:0007284 presumptive neural plate A presumptive structure that has the potential to develop into a neural plate. OBOL:automatic Region of the gastrula which gives rise to the neural plate.[TAO] 2012-08-14 TAO:0000063 TAO ZFIN:curator prospective neuroectoderm ZFA:0000063 prospective vegetal ectoderm ZFA:0000063 The part of the blastula that has the potential to develop into a paraxial mesoderm. EFO:0003443 TAO:0000591 XAO:0004134 ZFA:0000591 future paraxial mesenchyme future paraxial mesoderm uberon UBERON:0007285 presumptive paraxial mesoderm https://github.com/obophenotype/uberon/issues/1277 The part of the blastula that has the potential to develop into a paraxial mesoderm. UBERON:cjm https://github.com/obophenotype/uberon/issues/1277 future paraxial mesenchyme UBERON:cjm A presumptive structure that has the potential to develop into a forebrain-midbrain boundary. EFO:0003463 TAO:0001368 ZFA:0001368 uberon UBERON:0007288 presumptive forebrain midbrain boundary A presumptive structure that has the potential to develop into a forebrain-midbrain boundary. OBOL:automatic A blood vessel that is part of a limb/fin. TAO:0005299 ZFA:0005299 fin blood vessel limb blood vessel uberon UBERON:0007301 appendage blood vessel A blood vessel that is part of a limb/fin. OBOL:automatic fin blood vessel ZFA:0005299 limb blood vessel A vasculature that is part of a chordate pharynx. TAO:0005003 ZFA:0005003 branchial vasculature uberon UBERON:0007303 pharyngeal vasculature A vasculature that is part of a chordate pharynx. OBOL:automatic branchial vasculature ZFA:0005003 A vasculature that is part of a limb/fin. TAO:0005095 ZFA:0005095 fin vasculature uberon UBERON:0007304 appendage vasculature A vasculature that is part of a limb/fin. OBOL:automatic fin vasculature ZFA:0005095 The epidermis is the entire outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species[GO]. this grouping class exists primarily to align with GO - see GO:0008544. BSA:0000073 BTO:0000313 FBbt:00004993 HAO:0000298 TADS:0000109 WBbt:0005733 Wikipedia:Epidermis_(zoology) epidermis epidermis (sensu Metazoa) outer epidermal layer outer epithelial layer uberon hypoderm hypodermis UBERON:0007376 outer epithelium The epidermis is the entire outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species[GO]. GO:0008544 epidermis GO:0008544 hypoderm BTO:0000313 hypodermis GO:0008544 WBbt:0005733 Outermost layer of cells surrounding the embryo. Outermost monolayer of cells surrounding the embryo that become very flattened in the blastula and give rise to the periderm. Sometimes used synonymously with periderm. Kimmel et al, 1995.[TAO] relationship loss: develops_from superficial blastomere (TAO:0001484)[TAO] Originally this tissue is one cell layer thick but in most vertebrates it soon becomes a two layered structure. The outer layer gives rise to the periderm. EFO:0003425 TAO:0000086 ZFA:0000086 EVL enveloping layer uberon UBERON:0007383 enveloping layer of ectoderm Outermost layer of cells surrounding the embryo. http://orcid.org/0000-0002-6601-2165 Outermost monolayer of cells surrounding the embryo that become very flattened in the blastula and give rise to the periderm. Sometimes used synonymously with periderm. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000086 TAO ZFIN:curator relationship loss: develops_from superficial blastomere (TAO:0001484)[TAO] 2012-08-14 TAO:0000086 TAO EVL ZFA:0000086 enveloping layer ZFIN:ZDB-PUB-961014-576 A cartilage tissue that is part of a paired limb or fin. Cartilage which is part of one of the paired fins.[TAO] TAO:0001543 ZFA:0001543 uberon UBERON:0007389 paired limb/fin cartilage A cartilage tissue that is part of a paired limb or fin. http://orcid.org/0000-0002-6601-2165 Cartilage which is part of one of the paired fins.[TAO] 2012-08-14 TAO:0001543 TAO ZFIN:curator A cartilage tissue that is part of a pelvic appendage. Cartilage which is part of the pelvic fin.[TAO] TAO:0001459 ZFA:0001459 uberon pelvic fin cartilage UBERON:0007391 pelvic appendage cartilage tissue A cartilage tissue that is part of a pelvic appendage. OBOL:automatic Cartilage which is part of the pelvic fin.[TAO] 2012-08-14 TAO:0001459 TAO ZFIN:curator pelvic fin cartilage TAO:0001459 A nucleus of brain that spans a midbrain tegmentum. this class groups together any nuclei in the tegmentum region, possibly including disparate structures across species UBERON:0012277 FMA:258768 ZFA:0005577 tegmental nuclei tegmental nucleus uberon UBERON:0007414 nucleus of midbrain tegmentum A nucleus of brain that spans a midbrain tegmentum. OBOL:automatic tegmental nuclei tegmental nucleus ZFA:0005577 The space within an epithelial sphere. EHDAA2:0003079 AEO:0000079 cavity of vesicle uberon UBERON:0007473 lumen of epithelial sac The space within an epithelial sphere. AEO:JB cavity of vesicle AEO:0000079 A tissue whose predominant feature is extracellular matrix which may or may not be highly hydrated or calcified. EHDAA2:0003081 AEO:0000081 EHDAA2:0003081 uberon UBERON:0007475 matrix-based tissue A tissue whose predominant feature is extracellular matrix which may or may not be highly hydrated or calcified. AEO:JB An epithelial tube that is open at one end only. AEO:0000115 EHDAA2:0003115 uberon UBERON:0007499 epithelial sac AEO An epithelial tube that is open at one end only. AEO:JB UBERONREF:0000001 An epithelial tube open at both ends that allows fluid flow. AEO_RETIRED:0000116 RETIRED_EHDAA2:0003116 uberon UBERON:0007500 epithelial tube open at both ends AEO An epithelial tube open at both ends that allows fluid flow. AEO:JB UBERONREF:0000001 A closed epithelium with a lumen. EHDAA2:0003119 AEO:0000119 EHDAA2:0003119 uberon UBERON:0007503 epithelial vesicle AEO A closed epithelium with a lumen. AEO:JB Mesenchyme with little extracellular matrix. EHDAA2:0003146 AEO:0000146 EHDAA2:0003146 uberon UBERON:0007524 dense mesenchyme tissue AEO AEO Mesenchyme with little extracellular matrix. AEO:JB Mesenchymal cells that are migrating. this class will be an important part of the NC reorganization EHDAA2:0003152 AEO:0000152 EHDAA2:0003152 uberon UBERON:0007530 migrating mesenchyme population Mesenchymal cells that are migrating. AEO:JB Simple columnar epithelium in which the luminal side of the cells bears cilia. Examples: epithelium of trachea, epithelium of uterine tube.[FMA] In humans, Ciliated columnar epithelial cells are found mainly in the tracheal and bronchial regions of the pulmonary system and also in the fallopian tubes of the female reproductive system Ciliated columnar epithelium in the pulmonary system is interspersed with goblet cells that secrete mucous to form a mucosal layer apical to the epithelial layer. The rowing-like action of epithelial cilia work in tandem with goblet cells to propel mucus away from the lungs, preventing particulate matter from causing infection[http://www.bio.davidson.edu/people/kabernd/berndcv/lab/epithelialinfoweb/ciliated%20columnar%20epithelium.html] FMA:64798 uberon UBERON:0007592 ciliated columnar epithelium FMA Simple columnar epithelium in which the luminal side of the cells bears cilia. Examples: epithelium of trachea, epithelium of uterine tube.[FMA] FMA:64798 Epithelium bearing vibratile cilia on the free surface. uberon UBERON:0007601 ciliated epithelium Epithelium bearing vibratile cilia on the free surface. http://medical-dictionary.thefreedictionary.com/ciliated+epithelium A thin, loose vascular connective tissue that makes up the membranes surrounding joints and the sheaths protecting tendons (particularly flexor tendons in the hands and feet) where they pass over bony prominences. Synovial tissue contains synovial cells, which secrete a viscous liquid called synovial fluid; this liquid contains protein and hyaluronic acid and serves as a lubricant and nutrient for the joint cartilage surfaces[BTO]. Synovial tissue can be found in tendons (tissues that connect muscle to bone), bursae (fluid-filled, cushioning sacs found in spaces between tendons, ligaments, and bones), and the cavity (hollow enclosed area) that separates the bones of a freely movable joint, such as the knee or elbow[BTO]. BTO:0001338 CALOHA:TS-0998 FMA:66762 synovium stratum synoviale synovial layer synovial membrane uberon synovial tissue UBERON:0007616 layer of synovial tissue BTO A thin, loose vascular connective tissue that makes up the membranes surrounding joints and the sheaths protecting tendons (particularly flexor tendons in the hands and feet) where they pass over bony prominences. Synovial tissue contains synovial cells, which secrete a viscous liquid called synovial fluid; this liquid contains protein and hyaluronic acid and serves as a lubricant and nutrient for the joint cartilage surfaces[BTO]. Synovial tissue can be found in tendons (tissues that connect muscle to bone), bursae (fluid-filled, cushioning sacs found in spaces between tendons, ligaments, and bones), and the cavity (hollow enclosed area) that separates the bones of a freely movable joint, such as the knee or elbow[BTO]. BTO:0001338 http://www.britannica.com/EBchecked/topic/578563/synovial-tissue synovium CALOHA:TS-0998 stratum synoviale FMA:TA synovial layer FMA:66762 synovial membrane FMA:66762 synovial tissue BTO:0001338 An anatomical cavity that surrounded_by a synovial joint. FMA:11356 articular cavity (synovial joint) cavitas articularis (junctura synovialis) cavity of synovial joint uberon joint cavity synovial cavity UBERON:0007617 synovial cavity of joint An anatomical cavity that surrounded_by a synovial joint. OBOL:automatic articular cavity (synovial joint) FMA:11356 cavitas articularis (junctura synovialis) FMA:11356 cavity of synovial joint FMA:11356 joint cavity FMA:11356 synovial cavity FMA:11356 epithelial layer of the retina, ciliary body, or iris composed of cells containing pigment granules. GAID:907 MESH:D010857 uberon eye pigment epithelium UBERON:0007625 pigment epithelium of eye epithelial layer of the retina, ciliary body, or iris composed of cells containing pigment granules. MP:0005200 eye pigment epithelium MESH:A09.371.670 A neural nucleus that is part of a medulla oblongata. FMA:258772 SCTID:304943004 uberon UBERON:0007635 nucleus of medulla oblongata A neural nucleus that is part of a medulla oblongata. OBOL:automatic The sensory trigeminal nerve nuclei are the largest of the cranial nerve nuclei, and extend through the whole of the midbrain, pons and medulla. There is also a distinct trigeminal motor nucleus that is medial to the chief sensory nucleus[WP]. in MA and FMA this is part of the pons / pontime tegmentum. We weaken this to overlaps to avoid inconsistency. In NIF this is a composite structure spanning multiple regions, which is more appropriate. BIRNLEX:4096 BM:V CALOHA:TS-2077 DHBA:266441713 FMA:71248 HBA:9203 UMLS:C0040999 Wikipedia:Trigeminal_nerve_nuclei http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=2021 trigeminal nuclei uberon nuclei trigemini UBERON:0007641 trigeminal nuclear complex http://upload.wikimedia.org/wikipedia/commons/3/30/Gray696.png FMA FMA The sensory trigeminal nerve nuclei are the largest of the cranial nerve nuclei, and extend through the whole of the midbrain, pons and medulla. There is also a distinct trigeminal motor nucleus that is medial to the chief sensory nucleus[WP]. Wikipedia:Trigeminal_nerve_nuclei in MA and FMA this is part of the pons / pontime tegmentum. We weaken this to overlaps to avoid inconsistency. In NIF this is a composite structure spanning multiple regions, which is more appropriate. MA UMLS:C0040999 BIRNLEX:4096 trigeminal nuclei FMA:71248 nuclei trigemini Wikipedia:Trigeminal_nerve_nuclei 2 An anatomical structure that connects two structures junction FMA:5898 SCTID:91833003 anatomical junction uberon UBERON:0007651 anatomical junction FMA An anatomical structure that connects two structures http://code.google.com/p/caro2/issues/detail?id=15 Anlagen are populations of contiguous cells, typically arranged in one plane, that are morphologically indistinct, but that already correspond in extent to a later organ/tissue. field AEO:0000170 EFO:0001649 EHDAA2:0003170 FBbt:00005426 Wikipedia:Anlage_(biology) developmental field uberon future organ organ field UBERON:0007688 anlage FBbt AEO FBbt Anlagen are populations of contiguous cells, typically arranged in one plane, that are morphologically indistinct, but that already correspond in extent to a later organ/tissue. FBbt:00005426 JB:DEF http://flybase.org/reports/FBrf0178740.html . EFO:0003626 EHDAA2:0001457 EHDAA:962 EMAPA:32754 FMA:293087 TAO:0001104 ZFA:0001104 early pharyngeal arch endoderm uberon pharyngeal arch endoderm pharyngeal endoderm pharyngeal region endoderm UBERON:0007690 relation conflict: ZFA vs EHDAA2. Note EHDAA2 term renamed to 'early PA endoderm' early pharyngeal endoderm cjm . http://dev.biologists.org/content/128/22/4573.full early pharyngeal arch endoderm EHDAA2:0001457 pharyngeal endoderm ZFA:0001104 pharyngeal region endoderm EHDAA2:0001456 The minute opening of a taste bud on the surface of the oral mucosa through which the gustatory hairs of the specialised neuroepithelial gustatory cells project. FMA:63589 NCIT:C33738 SCTID:368724008 UMLS:C0226971 porus gustatorius taste pore uberon UBERON:0007691 gustatory pore Taste:bud.svg FMA FMA The minute opening of a taste bud on the surface of the oral mucosa through which the gustatory hairs of the specialised neuroepithelial gustatory cells project. http://www.mondofacto.com/facts/dictionary?gustatory+pore UMLS:C0226971 ncithesaurus:Taste_Pore porus gustatorius http://www.mondofacto.com/facts/dictionary?gustatory+pore taste pore FMA:63589 A bone that is part of a reproductive organ. baculum uberon os penis/os clitoris UBERON:0007719 bone of reproductive organ A bone that is part of a reproductive organ. OBOL:automatic https://github.com/obophenotype/uberon/issues/1158 Wikipedia A gland that is part of a epidermis. FMA:59153 epidermal gland gland of epidermis uberon UBERON:0007771 epidermis gland A gland that is part of a epidermis. OBOL:automatic gland of epidermis FMA:59153 Any bodily fluid that has passed through a membrane such as the capillary wall, as a result of unbalanced hydrostatic and osmotic forces transudative characteristically low in protein and cellular content (unless there has been secondary concentration) FMA:12276 GAID:1195 MESH:D005122 ncithesaurus:Transudate uberon plasma ultrafiltrate UBERON:0007779 transudate Any bodily fluid that has passed through a membrane such as the capillary wall, as a result of unbalanced hydrostatic and osmotic forces http://medical-dictionary.thefreedictionary.com/transudate Any fluid produced by a serous gland. serous fluid Wikipedia:Serous_fluid serosal fluid serous gland fluid uberon UBERON:0007794 secretion of serous gland Any fluid produced by a serous gland. UBERON:cjm serosal fluid Wikipedia:Serous_fluid Anatomical system that consists of all blood and lymph vessels. consider merging with vasculature The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]. in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system BTO:0001085 CALOHA:TS-2053 EHDAA2:0004520 EMAPA:35905 MA:0002718 NCIT:C33854 UMLS:C0489903 uberon UBERON:0007798 vascular system MA Anatomical system that consists of all blood and lymph vessels. http://orcid.org/0000-0002-6601-2165 The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]. ncithesaurus:Vascular_System in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system MA UMLS:C0489903 ncithesaurus:Vascular_System Adipose tissue that is located in the abdominal region. This includes any subcutaneous fat, visceral fat or encapsulated adipose tissue depots. CALOHA:TS-0002 EFO:0003771 uberon abdominal adipose tissue abdominal fat intra-abdominal fat UBERON:0007808 adipose tissue of abdominal region Adipose tissue that is located in the abdominal region. This includes any subcutaneous fat, visceral fat or encapsulated adipose tissue depots. CALOHA:paula MGI:csmith http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/259 abdominal adipose tissue BTO:0004041 abdominal fat BTO:0004041 intra-abdominal fat BTO:0004041 The anteriormost subdivision of the body that includes the head, jaws, pharyngeal region and the neck (if present). In vertebrates this is the subdivision that includes the cervical vertebrae. CALOHA:TS-2356 EV:0100009 FMA:280881 MA:0000006 NCIT:C12418 SCTID:361355005 UMLS:C0460004 WikipediaCategory:Head_and_neck galen:HeadAndNeck uberon cephalic area cephalic part of animal cephalic region head and neck head or neck UBERON:0007811 craniocervical region MA The anteriormost subdivision of the body that includes the head, jaws, pharyngeal region and the neck (if present). In vertebrates this is the subdivision that includes the cervical vertebrae. https://orcid.org/0000-0002-6601-2165 UMLS:C0460004 ncithesaurus:Head_and_Neck cephalic area https://github.com/obophenotype/uberon/issues/379 cephalic part of animal Wikipedia:Head cephalic region https://github.com/obophenotype/uberon/issues/379 head and neck FMA:280881 A tail that extends from the posterior tip of the organism to the anus, contains muscle and skeleton. Anatomical structure that is the terminal, flexible posterior appendage of the organism.[AAO] Organism subdivision which is the part of the body posterior to the vent which includes the anal and caudal fins.[TAO] present at some time in chordate life history (eg in Urochordates, present only in free-swimming larvae). Function: propellor locomotion (in some species) AAO:0010338 EMAPA:16748 MA:0000008 NCIT:C77663 TAO:0001117 UMLS:C0039259 XAO:0003026 ZFA:0001117 muscular postanal tail postanal tail post-anal fin tail uberon post-vent region UBERON:0007812 post-anal tail possible exception in hemichordates cjm A tail that extends from the posterior tip of the organism to the anus, contains muscle and skeleton. https://orcid.org/0000-0002-6601-2165 Anatomical structure that is the terminal, flexible posterior appendage of the organism.[AAO] 2012-06-20 AAO:0010338 AAO AAO:EJS Organism subdivision which is the part of the body posterior to the vent which includes the anal and caudal fins.[TAO] 2012-08-14 TAO:0001117 TAO ZFIN:curator UMLS:C0039259 ncithesaurus:Tail post-anal fin tail http://purl.oboibrary.org/obo/uberon/tracker/185 post-vent region TAO:0001117 An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). this encompasses non-skeletal tissue An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There are only two instances of appendage girdle regions per organism.[VSAO] UBERON:0007824 girdle girdle region EMAPA:37854 FMA:24874 VSAO:0000303 uberon fin girdle fin girdle region limb girdle limb girdle region UBERON:0007823 appendage girdle region An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). UBERONREF:0000003 https://orcid.org/0000-0002-6601-2165 An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There are only two instances of appendage girdle regions per organism.[VSAO] 2012-08-14 VSAO:0000303 VSAO https://orcid.org/0000-0002-6601-2165 EMAPA:37854 MA:th fin girdle fin girdle region limb girdle limb girdle region A bone that is part of a appendage girdle region. EMAPA:35379 MA:0000291 girdle bone uberon UBERON:0007828 girdle bone/zone A bone that is part of a appendage girdle region. OBOL:automatic girdle bone MA:0000291 A bone element or fused bone that is part of pelvic girdle. check sacrum, coccyx (MA does NOT include these) typically the ilium, ischium and pubis. These can alternately be considered individual bones, or zones of a single fused bone EMAPA:18028 MA:0000293 NCIT:C33287 SCTID:426214007 UMLS:C0030786 bone of pelvic girdle pelvic girdle bone uberon UBERON:0007830 pelvic girdle bone/zone MA A bone element or fused bone that is part of pelvic girdle. https://orcid.org/0000-0002-6601-2165 UMLS:C0030786 ncithesaurus:Pelvic_Bone pelvic girdle bone MA:0000293 Skeletal subdivision consisting of a set of bones linking the axial series to the hindlimb zeugopodium and offering anchoring areas for hindlimb and caudal musculature. need to resolve whether this is a paired structure or a single belt (Paired in FMA - implicitly paired in VSAO) Anatomical cluster by which the hind limbs are supported and attached to the vertebral column.[AAO] Anatomical cluster that consists of the paired basipterygia which support the pelvic fin.[TAO] Girdle skeleton consisting of a set of bones linking the axial series to the hindlimb/fin skeleton and offering anchoring areas for hindlimb/fin and caudal musculature.[VSAO] The pelvic girdle is never joined by contributions of dermal bone. From its first appearance in placoderms, the pelvic girdle is exclusively endoskeletal. It arose from pterygiophores, perhaps several times, in support of the fin.[well established][VHOG] Note that the VSAO and many ontologies use the label 'pelvic girdle' to denote the skeletal region specifically. We place the EHDAA2 class here, note that this includes the pre-cartilage condensation as parts AAO:0000426 AAO:0000768 EFO:0000947 EHDAA2:0001426 EHDAA:7149 EHDAA:8324 EMAPA:18028 FMA:87592 MAT:0000182 MIAA:0000182 TAO:0000565 VHOG:0000305 VSAO:0000155 Wikipedia:Pelvis XAO:0003064 ZFA:0000565 galen:PelvicGirdle http://people.eku.edu/ritchisong/pectoralgirdles.gif pelvic girdle skeleton skeletal parts of pelvic girdle skeleton of pelvic girdle uberon pelvic girdle UBERON:0007832 pelvic girdle skeleton http://upload.wikimedia.org/wikipedia/commons/f/fe/Gray242.png PMID:21455939 Skeletal subdivision consisting of a set of bones linking the axial series to the hindlimb zeugopodium and offering anchoring areas for hindlimb and caudal musculature. VSAO:0000155 Wikipedia:Pelvis Anatomical cluster by which the hind limbs are supported and attached to the vertebral column.[AAO] 2012-06-20 AAO:0000426 AAO AAO:LAP Anatomical cluster that consists of the paired basipterygia which support the pelvic fin.[TAO] 2012-08-14 TAO:0000565 TAO TAO:wd Girdle skeleton consisting of a set of bones linking the axial series to the hindlimb/fin skeleton and offering anchoring areas for hindlimb/fin and caudal musculature.[VSAO] 2012-08-14 VSAO:0000155 VSAO https://orcid.org/0000-0002-6601-2165 The pelvic girdle is never joined by contributions of dermal bone. From its first appearance in placoderms, the pelvic girdle is exclusively endoskeletal. It arose from pterygiophores, perhaps several times, in support of the fin.[well established][VHOG] 2012-09-17 VHOG:0000305 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.333 http://bgee.unil.ch/ Note that the VSAO and many ontologies use the label 'pelvic girdle' to denote the skeletal region specifically. We place the EHDAA2 class here, note that this includes the pre-cartilage condensation as parts VSAO pelvic girdle skeleton VSAO:0000155 skeletal parts of pelvic girdle https://orcid.org/0000-0002-6601-2165 skeleton of pelvic girdle https://orcid.org/0000-0002-6601-2165 pelvic girdle VSAO:0000155 Bone element that arises as a result of intramembranous ossification. Bone element that arises as a result of intramembranous ossification.[VSAO] Intramembranous bone that forms deep in the organism.[TAO] AEO:0000085 EHDAA2:0003085 TAO:0001645 VSAO:0000023 XAO:0004014 ZFA:0001636 uberon membrane bones UBERON:0007842 membrane bone VSAO Bone element that arises as a result of intramembranous ossification. GO_REF:0000034 VSAO:0000023 http://dx.plos.org/10.1371/journal.pone.0051070 https://github.com/obophenotype/uberon/issues/267 Bone element that arises as a result of intramembranous ossification.[VSAO] 2012-08-14 VSAO:0000023 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 PSPUB:0000170 Intramembranous bone that forms deep in the organism.[TAO] 2012-08-14 TAO:0001645 TAO TAO:wd membrane bones ZFA:0001636 Skeletal element that is composed of cartilage tissue and may be permanent or transient. TAO still mixes tissue and element AAO:0011130 CALOHA:TS-0118 EMAPA:32730 FMA:55107 VSAO:0000000 XAO:0004013 ZFA:0001501 cartilage organ cartilaginous element chondrogenic element uberon cartilage UBERON:0007844 cartilage element VSAO VSAO VSAO Skeletal element that is composed of cartilage tissue and may be permanent or transient. GO_REF:0000034 PSPUB:0000170 VSAO:0000000 http://dx.plos.org/10.1371/journal.pone.0051070 TAO still mixes tissue and element TAO cartilage organ FMA:55107 cartilaginous element https://orcid.org/0000-0002-6601-2165 chondrogenic element VSAO:0000000 cartilage VSAO:0000000 Connective tissue, which consists of fibroblasts, the intercellular matrix of which contains a regular network of collagen and elastic fiber bundles. Examples: bone (tissue), cartilage (tissue), dense regular connective tissue. the connective tissue hierarchy largely follows FMA with definitions from VSAO. Note that in FMA, loose-CT is irregular-CT. This means regular-CT is necessarily equivalent to dense-regular-CT (assuming a JEPD classification). FMA:20103 uberon UBERON:0007845 regular connective tissue FMA Connective tissue, which consists of fibroblasts, the intercellular matrix of which contains a regular network of collagen and elastic fiber bundles. Examples: bone (tissue), cartilage (tissue), dense regular connective tissue. FMA:20103 Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts). Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts).[VSAO] Regular connective tissue, the intercellular matrix of which consists predominantly of collagen fiber bundles arranged in parallel arrays.[FMA] FMA:64781 NCIT:C33453 SCTID:22560007 UMLS:C0225333 VSAO:0000050 Wikipedia:Dense_regular_connective_tissue XAO:0004030 dense fibrous connective tissue dense regular collagenous connective tissue dense regular collagenous tissue regular dense connective tissue typus regularis (textus connectivus collagenosus compactus) uberon UBERON:0007846 dense regular connective tissue FMA ncithesaurus Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts). GO_REF:0000034 PSPUB:0000170 VSAO:0000050 http://dx.plos.org/10.1371/journal.pone.0051070 Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts).[VSAO] 2012-08-14 VSAO:0000050 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 PSPUB:0000170 Regular connective tissue, the intercellular matrix of which consists predominantly of collagen fiber bundles arranged in parallel arrays.[FMA] 2012-08-29 FMA:64781 FMA UMLS:C0225333 ncithesaurus:Regular_Dense_Connective_Tissue dense fibrous connective tissue FMA:64781 dense regular collagenous connective tissue FMA:64781 dense regular collagenous tissue FMA:64781 typus regularis (textus connectivus collagenosus compactus) FMA:64781 A bone that is part of a craniocervical region. EMAPA:37245 MA:0000569 head or neck bone uberon cranial bone UBERON:0007914 bone of craniocervical region MA MA A bone that is part of a craniocervical region. OBOL:automatic EMAPA:37245 MA:th head or neck bone MA:0000569 The irregular bones are bones which, from their peculiar form, cannot be grouped as long bone, short bone, flat bone or sesamoid bone. Irregular bones serve various purposes in the body, such as protection of nervous tissue, affording multiple anchor points for skeletal muscle attachment (as with the sacrum), and maintaining pharynx and trachea support, and tongue attachment (such as the hyoid bone). They consist of cancellous tissue enclosed within a thin layer of compact bone. The irregular bones are: the vertebrC&, sacrum, coccyx, temporal, sphenoid, ethmoid, zygomatic, maxilla, mandible, palatine, inferior nasal concha, and hyoid. FMA:7477 NCIT:C32881 SCTID:421560006 UMLS:C0502414 Wikipedia:Irregular_bone os irregulare uberon os irregulare UBERON:0008001 irregular bone FMA The irregular bones are bones which, from their peculiar form, cannot be grouped as long bone, short bone, flat bone or sesamoid bone. Irregular bones serve various purposes in the body, such as protection of nervous tissue, affording multiple anchor points for skeletal muscle attachment (as with the sacrum), and maintaining pharynx and trachea support, and tongue attachment (such as the hyoid bone). They consist of cancellous tissue enclosed within a thin layer of compact bone. The irregular bones are: the vertebrC&, sacrum, coccyx, temporal, sphenoid, ethmoid, zygomatic, maxilla, mandible, palatine, inferior nasal concha, and hyoid. Wikipedia:Irregular_bone UMLS:C0502414 ncithesaurus:Irregular_Bone os irregulare Wikipedia:Irregular_bone A skeletal joint that is part of a appendage girdle region. MA:0001505 girdle joint uberon UBERON:0008114 joint of girdle MA A skeletal joint that is part of a appendage girdle region. OBOL:automatic girdle joint OBOL:automatic A anatomical surface that is part of a cartilage element. FMA:76668 cartilage surface uberon UBERON:0008115 surface of cartilage A anatomical surface that is part of a cartilage element. OBOL:automatic cartilage surface FMA:76668 A bone that is hollow or contains many air cells, such as the mastoid process of the temporal bone[TMD]. subclasses of this should be checked for taxonomic consistency Skeletal pneumaticity is the presence of air spaces within bones. Skeletal pneumaticity exists only in synapsids and archosaurs. It is generally produced during development by excavation of bone by pneumatic diverticula (air sacs) from an air-filled space such as the lungs or nasal cavity. Pneumatization is highly variable between individuals, and bones not normally pneumatized can become pneumatized in pathological development. Pneumatization occurs in the skulls of mammals, crocodilians and birds among extant groups, as well as extinct archosaurs including the dinosaurs and pterosaurs. Pneumatic spaces include the paranasal sinuses and some of the mastoid cells[WP]. [Wikipedia:Skeletal_pneumaticity] FMA:7478 SCTID:333008005 Wikipedia:Skeletal_pneumaticity galen:PneumaticBone os pneumaticum pneumatic bone uberon hollow bone UBERON:0008193 pneumatized bone A bone that is hollow or contains many air cells, such as the mastoid process of the temporal bone[TMD]. http://www.medilexicon.com/medicaldictionary.php?t=11303 os pneumaticum FMA:7478 pneumatic bone FMA:7478 The part of the ventral body cavity that is within the pelvis. EMAPA:37235 FMA:9738 MA:0003089 SCTID:281903009 Wikipedia:Pelvic_cavity space of pelvic compartment uberon cavitas pelvis UBERON:0008203 pelvic cavity http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg The part of the ventral body cavity that is within the pelvis. UBERON:cjm EMAPA:37235 MA:th space of pelvic compartment FMA:9738 cavitas pelvis Wikipedia:Pelvic_cavity Musculature system of the pharyngeal and head regions. in MA this is restricted to skeletal muscles EMAPA:37259 MA:0000571 TAO:0000328 ZFA:0000328 head or neck muscle uberon head muscles head or neck muscle UBERON:0008229 craniocervical region musculature MA MA Musculature system of the pharyngeal and head regions. ZFA:0000328 ZFA:curator in MA this is restricted to skeletal muscles MA EMAPA:37259 MA:th head or neck muscle MA:0000571 head muscles ZFA:0000328 head or neck muscle MA:0000571 Subdivision of thorax, which in humans is the posterior part of the thorax and is demarcated from the chest by the external surface of the posterolateral part of the rib cage and the anterior surface of the thoracic vertebral column; together with the chest, it constitutes the thorax. EMAPA:37234 FMA:24217 MA:0000028 SCTID:362666008 dorsum of thorax posterior part of thorax thoracic back thoracic part of back upper back uberon back of thorax UBERON:0008231 dorsal thoracic segment of trunk FMA MA FMA Subdivision of thorax, which in humans is the posterior part of the thorax and is demarcated from the chest by the external surface of the posterolateral part of the rib cage and the anterior surface of the thoracic vertebral column; together with the chest, it constitutes the thorax. FMA:24217 EMAPA:37234 MA:th dorsum of thorax FMA:24217 posterior part of thorax FMA:24217 thoracic back FMA:24217 thoracic part of back FMA:24217 upper back MA:0000028 back of thorax FMA:24217 A muscle of back that is part of a dorsal thoracic segment of trunk. EMAPA:37261 MA:0000508 SCTID:305071003 uberon UBERON:0008243 upper back muscle MA MA A muscle of back that is part of a dorsal thoracic segment of trunk. OBOL:automatic EMAPA:37261 MA:th An endothelium that is part of a heart [Automatically generated definition]. this class includes any endothelia that are part of the heart. This might include the endocardial epithelia, as well as endothelia of vessels that are considered strictly part of the heart (e.g. outflow tract). As a grouping class, this may lack utility, and pending review this class may be obsoleted. For annotation consider a more specific class. BTO:0004293 uberon cardiac endothelium UBERON:0008307 heart endothelium An endothelium that is part of a heart [Automatically generated definition]. OBOL:automatic cardiac endothelium BTO:0004293 A vertebral foramen that is part of a cervical vertebra. FMA:13480 SCTID:280833008 uberon UBERON:0008429 cervical vertebral foramen A vertebral foramen that is part of a cervical vertebra. OBOL:automatic A vertebral foramen that is part of a thoracic vertebra. FMA:9143 SCTID:280834002 uberon UBERON:0008432 thoracic vertebral foramen A vertebral foramen that is part of a thoracic vertebra. OBOL:automatic A transient embryonic complex that comprises the pharyngeal arches, bulges of tissues of mesoderm and neural crest derivation through which pass nerves and pharyngeal arch arteries. The arches are separated internally by pharyngeal pouches, evaginations of foregut endoderm, and externally by pharyngeal clefts, invaginations of surface ectoderm. The development of the system ends when the stucture it contributes to are forming, which may include (depending on species) the thymus, thyroid, parathyroids, maxilla, mandible, aortic arch, cardiac outflow tract, external and middle ear[GO,modified]. Currently defined in a vertebrate specific manner. The arch system has origins in basal deuterostomes, consider generalizing EHDAA2:0000187 FMA:293041 NCIT:C34248 UMLS:C1519038 embryonic pharyngeal complex pharyngeal apparatus pharyngeal system uberon pharyngeal arch complex pharyngeal arch region pharyngeal arches and clefts pharyngeal complex UBERON:0008814 pharyngeal arch system A transient embryonic complex that comprises the pharyngeal arches, bulges of tissues of mesoderm and neural crest derivation through which pass nerves and pharyngeal arch arteries. The arches are separated internally by pharyngeal pouches, evaginations of foregut endoderm, and externally by pharyngeal clefts, invaginations of surface ectoderm. The development of the system ends when the stucture it contributes to are forming, which may include (depending on species) the thymus, thyroid, parathyroids, maxilla, mandible, aortic arch, cardiac outflow tract, external and middle ear[GO,modified]. GO:0060037 GOC:dph UMLS:C1519038 ncithesaurus:Pharyngeal_Apparatus pharyngeal system GO:0060037 pharyngeal arch region EHDAA2:0000187 A head that is part of a embryo. CALOHA:TS-0246 FBbt:00000155 FMA:293011 uberon UBERON:0008816 embryonic head A head that is part of a embryo. OBOL:automatic A brain that develops_from a neural tube. a reasoner should automatically classify all the vertebrate ontology brain classes here vertebrate brain uberon UBERON:0008823 neural tube derived brain https://github.com/obophenotype/uberon/issues/338 ZFA FMA A brain that develops_from a neural tube. OBOL:automatic https://github.com/obophenotype/uberon/issues/338 The smooth muscle layer of the stomach wall that functions to churn and mix food and gastric secretions as well as to move food along the digestive tract to the intestines the muscularis externa in the stomach differs from that of other GI organs in that it has three layers of smooth muscle instead of two FMA:14909 SCTID:362132003 gastric muscularis muscle layer of stomach muscularis externa of stomach tunica muscularis (gaster) tunica muscularis gastris uberon UBERON:0008856 stomach muscularis externa MA-abduced The smooth muscle layer of the stomach wall that functions to churn and mix food and gastric secretions as well as to move food along the digestive tract to the intestines MP:0010779 the muscularis externa in the stomach differs from that of other GI organs in that it has three layers of smooth muscle instead of two WP gastric muscularis FMA:14909 muscle layer of stomach FMA:14909 muscularis externa of stomach FMA:14909 tunica muscularis (gaster) FMA:14909 Any skeletal muscle organ in the hypodermis / superficial fascia We follow MP and treat this as part of the hypodermis, although some sources may consider the hypodermis to be superficial to this UBERON:0010934 EMAPA:18188 MA:0003140 hypodermal muscle layer hypodermis muscle layer superficial fascia muscular layer panniculus carnosus uberon UBERON:0008876 hypodermis skeletal muscle layer MP-def Any skeletal muscle organ in the hypodermis / superficial fascia ISBN:0123813611 MP:0011157 hypodermal muscle layer MP:0011157 hypodermis muscle layer MP:0011157 panniculus carnosus MP:0011157 Bone tissue that is an unmineralized bone matrix deposited by osteoblasts prior to the mineralization of bone tissue. Bone tissue that is an unmineralized bone matrix deposited by osteoblasts prior to the mineralization of bone tissue.[VSAO] Newly formed organic bone matrix secreted by osteoblasts, that exists prior to calcification; it is comprised mainly of type I collagen fibers, chondroitin sulfate and osteocalci[ISBN:0-683-40008-8]n Note that in VSAO this was classified both as tissue and acellular extracellular matrix. Consider also the AEO class 'bone condensation'. is_a intercellular matrix in FMA. EMAPA:37923 FMA:66830 NCIT:C33228 SCTID:39365008 UMLS:C0682561 VSAO:0000046 Wikipedia:Osteoid XAO:0004035 galen:Osteoid osteoid tissue pre-bone prebone prebone tissue uberon UBERON:0008883 osteoid Active:osteoblasts.jpg VSAO Bone tissue that is an unmineralized bone matrix deposited by osteoblasts prior to the mineralization of bone tissue. GO_REF:0000034 VSAO:0000046 http://dx.plos.org/10.1371/journal.pone.0051070 Bone tissue that is an unmineralized bone matrix deposited by osteoblasts prior to the mineralization of bone tissue.[VSAO] 2012-08-14 VSAO:0000046 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 PSPUB:0000170 Newly formed organic bone matrix secreted by osteoblasts, that exists prior to calcification; it is comprised mainly of type I collagen fibers, chondroitin sulfate and osteocalci[ISBN:0-683-40008-8]n ISBN:0-683-40008-8 MP:0010924 Note that in VSAO this was classified both as tissue and acellular extracellular matrix. Consider also the AEO class 'bone condensation'. is_a intercellular matrix in FMA. VSAO EMAPA:37923 MA:th UMLS:C0682561 ncithesaurus:Osteoid osteoid tissue http://orcid.org/0000-0002-6601-2165 pre-bone PSPUB:0000170 prebone VSAO:curator prebone tissue FMA:66830 MP:0002113 The part of the cardiovascular system consisting of all pulmonary arteries and all pulmonary veins. Subdivision of cardiovascular system which has as its parts the pulmonary arterial and venous tree organs.[FMA] FMA:45621 Wikipedia:Pulmonary_circulation pulmonary circulatory system pulmonary system uberon UBERON:0008886 pulmonary vascular system Obol The part of the cardiovascular system consisting of all pulmonary arteries and all pulmonary veins. ISBN:0073040584 Wikipedia:Pulmonary_circulation Subdivision of cardiovascular system which has as its parts the pulmonary arterial and venous tree organs.[FMA] FMA FMA:45621 pulmonary circulatory system FMA:45621 pulmonary system ISBN:0073040584 Subdivision of endoskeleton derived from pharyngeal arches Anatomical cluster that is part of the cranium and consists of the jaws, hyoid and branchial arches.[TAO] Anatomical cluster that is part of the cranium and consists of the jaws, hyoid, and branchial arches.[AAO] The part of the skull derived from the embryonic pharyngeal arches. [Biology_Online][VHOG] The skull of ancestral tetrapods has the three basic components that we have been considering: (1) chondrocranium, (2) splanchnocranium, and (3) dermatocranium (reference 1); Each part of the skull arises from a separate phylogenetic source. The most ancient part is the splanchnocranium (visceral cranium), which first arose to support pharyngeal slits in protochordates (reference 2).[well established][VHOG] VSAO labels this term 'pharyngeal arch' (2012-06-01) - however, it clearly means pharyngeal arch skeleton. many sources define this as the part of the endoskeletal that is from pharyngeal arches - this would make it part-disjoint from dermatocranium. However, there are many bones in AOs that have part-paths to both AAO:0010157 TAO:0001216 VHOG:0000315 VSAO:0000149 Wikipedia:Facial_skeleton XAO:0003176 ZFA:0001216 pharyngeal endoskeleton viscerocranium uberon branchial arch skeleton gill arch skeleton pharyngeal arch pharyngeal arch skeleton pharyngeal skeleton visceral cranium visceral skeletal system visceral skeleton UBERON:0008895 splanchnocranium http://upload.wikimedia.org/wikipedia/commons/7/77/Illu_facial_bones.jpg https://github.com/obophenotype/uberon/issues/83 redundant Grays PMID:11237469 Subdivision of endoskeleton derived from pharyngeal arches ISBN:0073040584 Wikipedia:Facial_skeleton https://orcid.org/0000-0002-6601-2165 Anatomical cluster that is part of the cranium and consists of the jaws, hyoid and branchial arches.[TAO] 2012-08-14 TAO:0001216 TAO ZFIN:curator Anatomical cluster that is part of the cranium and consists of the jaws, hyoid, and branchial arches.[AAO] 2012-06-20 AAO:0010157 AAO AAO:EJS The part of the skull derived from the embryonic pharyngeal arches. [Biology_Online][VHOG] 2012-09-17 VHOG:0000315 VHOG http://bgee.unil.ch/ The skull of ancestral tetrapods has the three basic components that we have been considering: (1) chondrocranium, (2) splanchnocranium, and (3) dermatocranium (reference 1); Each part of the skull arises from a separate phylogenetic source. The most ancient part is the splanchnocranium (visceral cranium), which first arose to support pharyngeal slits in protochordates (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000315 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.242, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.235 http://bgee.unil.ch/ VSAO labels this term 'pharyngeal arch' (2012-06-01) - however, it clearly means pharyngeal arch skeleton. VSAO pharyngeal endoskeleton http://orcid.org/0000-0002-6601-2165 viscerocranium VHOG:0000315 Wikipedia:Viscerocranium ZFA:0001216 pharyngeal arch VSAO:0000149 pharyngeal arch skeleton ZFA:0001216 pharyngeal skeleton ZFA:0001216 visceral cranium http://orcid.org/0000-0002-6601-2165 visceral skeletal system http://orcid.org/0000-0002-6601-2165 visceral skeleton UBERONREF:0000007 Skeletal element that forms superficially in the organism, usually in association with the ectoderm[VSAO]. Intramembranous bone that forms superficially in the organism.[TAO] other AOs are not yet in sync with this classification AAO:0010769 TAO:0001590 VSAO:0000130 Wikipedia:Dermal_bone XAO:0004015 ZFA:0001590 uberon dermal bones UBERON:0008907 dermal bone wd VSAO VSAO Skeletal element that forms superficially in the organism, usually in association with the ectoderm[VSAO]. GO_REF:0000034 VSAO:0000130 http://dx.plos.org/10.1371/journal.pone.0051070 https://github.com/obophenotype/uberon/issues/267 Intramembranous bone that forms superficially in the organism.[TAO] 2012-08-14 TAO:0001590 TAO TAO:wd dermal bones ZFA:0001590 Bone element that is adjacent to the notochord. We go with the latest VSAO in making this a subtype of bone, and add a logical definition based on the textual definition in VSAO. We also include the subtyping under 'replacement bone', for consistency with ZFA Replacement bone that forms within the connective tissue surrounding the notochord.[TAO] AAO:0010777 TAO:0001639 VSAO:0000307 ZFA:0001629 perichordal bones uberon perichordal bone UBERON:0008909 perichordal bone not in VSAO ZFA Bone element that is adjacent to the notochord. GO_REF:0000034 VSAO:0000307 http://dx.plos.org/10.1371/journal.pone.0051070 Replacement bone that forms within the connective tissue surrounding the notochord.[TAO] 2012-08-14 TAO:0001639 TAO TAO:wd perichordal bones ZFA:0001629 perichordal bone ZFA:0001629 A parenchyma that is part of a lung. EMAPA:35522 FMA:27360 MA:0003168 SCTID:201712001 respiratory portion of lung uberon parenchyma of lung pulmonary parenchyma UBERON:0008946 lung parenchyma FMA FMA A parenchyma that is part of a lung. OBOL:automatic respiratory portion of lung FMA:27360 parenchyma of lung BTO:0000763 pulmonary parenchyma EMAPA:35522 EHDAA2:0004069 NCIT:C34283 UMLS:C1514898 uberon UBERON:0008947 respiratory primordium Obol UMLS:C1514898 ncithesaurus:Respiratory_Primordium System pertaining to blood vessels in the brain. UBERON:0005284 BTO:0003840 EFO:0003491 EMAPA:35186 FMA:242007 FMA:61935 SCTID:362029003 TAO:0000099 ZFA:0000099 brain vasculature cerebrovascular system intracerebral vasculature uberon UBERON:0008998 vasculature of brain System pertaining to blood vessels in the brain. BTO:0003840 cerebrovascular system BTO:0003840 intracerebral vasculature FMA:61935 A zone of skin that is part of a dorsal thoracic segment of trunk. EMAPA:37280 MA:0000510 SCTID:304890003 uberon UBERON:0009015 upper back skin MA A zone of skin that is part of a dorsal thoracic segment of trunk. OBOL:automatic EMAPA:37280 MA:th Vein that drains left lung and returns blood to the heart. A vein that returns oxygenated blood from the left lung to the left atrium of the heart[ncithesaurus:Left_Pulmonary_Vein]. EMAPA:37165 MA:0002207 NCIT:C48946 SCTID:304057004 UMLS:C0226670 uberon UBERON:0009030 left pulmonary vein Vein that drains left lung and returns blood to the heart. http://orcid.org/0000-0002-6601-2165 A vein that returns oxygenated blood from the left lung to the left atrium of the heart[ncithesaurus:Left_Pulmonary_Vein]. ncithesaurus:Left_Pulmonary_Vein EMAPA:37165 MA:th UMLS:C0226670 ncithesaurus:Left_Pulmonary_Vein Vein that drains right lung and returns blood to the heart. A vein that returns oxygenated blood from the right lung to the left atrium of the heart[ncithesaurus:Right_Pulmonary_Vein]. EMAPA:37379 MA:0002208 NCIT:C48947 SCTID:304056008 UMLS:C0226669 uberon UBERON:0009032 right pulmonary vein Vein that drains right lung and returns blood to the heart. http://orcid.org/0000-0002-6601-2165 A vein that returns oxygenated blood from the right lung to the left atrium of the heart[ncithesaurus:Right_Pulmonary_Vein]. ncithesaurus:Right_Pulmonary_Vein EMAPA:37379 MA:th UMLS:C0226669 ncithesaurus:Right_Pulmonary_Vein A gonad prior to differentiating into a definitive testis or ovary. EHDAA2:0000716 NCIT:C34192 UMLS:C1512703 uberon gonad rudiment UBERON:0009117 typically part of the embryo - however, in male tammar wallabies the gonads are indifferent at the neonatal stage[8827321] indifferent gonad A gonad prior to differentiating into a definitive testis or ovary. http://www.medterms.com/script/main/art.asp?articlekey=8981 UMLS:C1512703 ncithesaurus:Indifferent_Gonad Epibranchial placode between geniculate and nodose. Associated with 2nd branchial cleft. EHDAA2:0004207 TAO:0001296 XAO:0004212 ZFA:0001296 epibranchial placode 2 glossopharyngeal IX placode glossopharyngeal epibranchial placode glossopharyngeal placode uberon UBERON:0009125 Taxonomic equivalence to EHDAA2 class made on basis of shared development: gives rise to glossopharyngeal ganglion petrosal placode ZFA Epibranchial placode between geniculate and nodose. Associated with 2nd branchial cleft. NCBIBook:NBK53175 epibranchial placode 2 EHDAA2:0004207 glossopharyngeal IX placode ISBN:0471888893 glossopharyngeal epibranchial placode XAO:0004212 glossopharyngeal placode ISBN:0471888893 ZFA:0001296 Cranial ganglion which develops from an epibranchial placode. TAO:0001555 ZFA:0001555 epibranchial ganglia uberon UBERON:0009127 Epibranchial ganglia orchestrate the development of the cranial neurogenic crest epibranchial ganglion ZFA NCBIBook:NBK53175 Cranial ganglion which develops from an epibranchial placode. PMID:20133851 ZFIN:curator epibranchial ganglia ZFA:0001555 Endocardium that is part of the right atrium. EHDAA2:0000274 FMA:7281 NCIT:C102339 SCTID:3194006 VHOG:0001228 endocardium of right atrium right atrial endocardium uberon right atrium endocardial tissue UBERON:0009129 right atrium endocardium EHDAA2 EHDAA2 Endocardium that is part of the right atrium. http://orcid.org/0000-0002-6601-2165 endocardium of right atrium FMA:7281 right atrial endocardium FMA:7281 right atrium endocardial tissue VHOG:0001228 A fold of tissue which extends into the peritoneal cavity of the developing embryo and participates in the separation of the pleural and peritoneal cavities. In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart [of other tetrapods] is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG] UBERON:0009146 EHDAA2:0001483 EMAPA:17709 NCIT:C34256 SCTID:361429005 UMLS:C1283968 VHOG:0000757 Wikipedia:Pleuroperitoneal pleuroperitoneal fold pleuroperitoneal membranes uberon UBERON:0009133 pleuroperitoneal membrane EHDAA2 A fold of tissue which extends into the peritoneal cavity of the developing embryo and participates in the separation of the pleural and peritoneal cavities. Wikipedia:Pleuroperitoneal http://medical-dictionary.thefreedictionary.com/pleuroperitoneal+membrane In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart [of other tetrapods] is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG] 2012-09-17 VHOG:0000757 VHOG ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206 http://bgee.unil.ch/ UMLS:C1283968 ncithesaurus:Pleuroperitoneal_Membrane pleuroperitoneal fold VHOG:0000757 pleuroperitoneal membranes EHDAA2:0001483 A vein that is part of a craniocervical region. EHDAA2:0004542 SCTID:32945007 craniocervical vein head and neck veins vein of head and neck uberon UBERON:0009141 craniocervical region vein A vein that is part of a craniocervical region. OBOL:automatic head and neck veins EHDAA2:0004542 Sum total of mesenchyme in the embryo. consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm) UBERON:0003313 EHDAA2:0001113 EHDAA:177 EMAPA:16097 uberon UBERON:0009142 entire embryonic mesenchyme EHDAA2 Sum total of mesenchyme in the embryo. https://github.com/obophenotype/human-developmental-anatomy-ontology/issues/7 EMAPA:16549 RETIRED_EHDAA2:0001454 pharyngeal region uberon UBERON:0009145 pharyngeal region of foregut EHDAA2 pharyngeal region EMAPA:16549 EHDAA2:0004021 uberon UBERON:0009196 indifferent external genitalia cjm An ectoderm that is part of a buccopharyngeal membrane. EHDAA2:0000190 EMAPA:16260 uberon UBERON:0009479 ectoderm of buccopharyngeal membrane An ectoderm that is part of a buccopharyngeal membrane. OBOL:automatic An endoderm that is part of a buccopharyngeal membrane. EHDAA2:0000191 EMAPA:16261 uberon UBERON:0009480 endoderm of buccopharyngeal membrane An endoderm that is part of a buccopharyngeal membrane. OBOL:automatic Mesenchyme that is part of a foregut-midgut junction. EHDAA2:0000570 EMAPA:16364 uberon UBERON:0009482 associated mesenchyme of foregut-midgut junction Mesenchyme that is part of a foregut-midgut junction. OBOL:automatic A portion of mesenchymal tissue associated with an individual pharyngeal arch. this represents a part of the entire arch mesenchyme (UBERON:0010046), and is therefore a superclass of the individual arch mesenchyme classes. Alternate definition: primordial embryonic connective tissue associated with the branchial arches, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to facial and cranial nerve-associated structures. EMAPA:32755 FMA:295694 branchial arch mesenchyme pharyngeal arch mesenchyme uberon UBERON:0009494 pharyngeal arch mesenchymal region EHDAA2 cjm A portion of mesenchymal tissue associated with an individual pharyngeal arch. https://orcid.org/0000-0002-6601-2165 this represents a part of the entire arch mesenchyme (UBERON:0010046), and is therefore a superclass of the individual arch mesenchyme classes. Alternate definition: primordial embryonic connective tissue associated with the branchial arches, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to facial and cranial nerve-associated structures. MP:0011262 branchial arch mesenchyme MP:0011262 pharyngeal arch mesenchyme https://orcid.org/0000-0002-6601-2165 An epithelium that is part of a foregut-midgut junction. EHDAA2:0000573 EMAPA:16564 uberon UBERON:0009497 epithelium of foregut-midgut junction EHDAA2 EHDAA2 An epithelium that is part of a foregut-midgut junction. OBOL:automatic Mesenchyme that is part of a developing hindgut. EHDAA2:0000780 EMAPA:16716 hindgut associated mesenchyme uberon UBERON:0009503 mesenchyme of hindgut Mesenchyme that is part of a developing hindgut. OBOL:automatic hindgut associated mesenchyme EHDAA2:0000780 An endoderm that is part of a anal region. EHDAA2:0004020 EMAPA:17177 uberon UBERON:0009521 anal membrane endodermal component An endoderm that is part of a anal region. OBOL:automatic An endoderm that is part of a foregut-midgut junction. EHDAA2:0000572 EMAPA:18403 uberon UBERON:0009550 endoderm of foregut-midgut junction An endoderm that is part of a foregut-midgut junction. OBOL:automatic A submucosa that is part of a intestine. FMA:15696 submucosa of intestine uberon UBERON:0009566 intestinal submucosa FMA A submucosa that is part of a intestine. OBOL:automatic submucosa of intestine FMA:15696 Subdivision of vertebral column that corresponds to the trunk of the body, containing the trunk/presacral vertebrae. In organisms that have a thoracic and lumbar distinction, this corresponds to the sum of both of these regions. Region of the vertebral column between the atlas and the sacrum consisting of seven to 285 vertebrae.[AAO] AAO:0000612 FMA:72066 NCIT:C92597 SCTID:281699004 thoracolumbar column thoracolumbar region of vertebral column thoracolumbar vertebrae set thoracolumbar vertebral column trunk vertebrae series trunk vertebral column uberon presacral region thoracolumbar region trunk region trunk skeleton trunk spine UBERON:0009568 trunk region of vertebral column Subdivision of vertebral column that corresponds to the trunk of the body, containing the trunk/presacral vertebrae. In organisms that have a thoracic and lumbar distinction, this corresponds to the sum of both of these regions. UBERONREF:0000006 Region of the vertebral column between the atlas and the sacrum consisting of seven to 285 vertebrae.[AAO] 2012-06-20 AAO:0000612 AAO AAO:Duellman_and_Trueb_1994 thoracolumbar vertebrae set FMA:72066 presacral region AAO:0000612 thoracolumbar region AAO:0000612 trunk region AAO:0000612 FMA:25054 SCTID:22943007 region of trunk trunk subdivision uberon UBERON:0009569 subdivision of trunk region of trunk FMA:25054 trunk subdivision FMA:25054 A sulcus limitans of neural tube that is part of a future spinal cord. EHDAA2:0001265 EMAPA:17584 VHOG:0001548 spinal cord lateral wall sulcus limitans uberon UBERON:0009570 spinal cord sulcus limitans A sulcus limitans of neural tube that is part of a future spinal cord. OBOL:automatic spinal cord lateral wall sulcus limitans EHDAA2:0001265 A sulcus limitans of neural tube that is part of a future medulla oblongata. EHDAA2:0001100 EMAPA:17561 uberon UBERON:0009576 medulla oblongata sulcus limitans EHDAA2 A sulcus limitans of neural tube that is part of a future medulla oblongata. OBOL:automatic A sulcus limitans of neural tube that is part of a future metencephalon. EHDAA2:0001161 EMAPA:17567 uberon UBERON:0009577 metencephalon sulcus limitans A sulcus limitans of neural tube that is part of a future metencephalon. OBOL:automatic A sulcus limitans of neural tube that is part of a future myelencephalon. EHDAA2:0001945 uberon UBERON:0009578 myelencephalon sulcus limitans A sulcus limitans of neural tube that is part of a future myelencephalon. OBOL:automatic EHDAA2:0000397 EMAPA:16906 VHOG:0000912 diencephalon lateral wall mantle layer mantle layer lateral wall diencephalon uberon UBERON:0009580 diencephalon mantle layer mantle layer lateral wall diencephalon VHOG:0000912 EHDAA2:0001172 EMAPA:16977 VHOG:0000910 mantle layer lateral wall midbrain midbrain lateral wall mantle layer uberon mantle layer lateral wall mesencephalon UBERON:0009581 midbrain mantle layer mantle layer lateral wall midbrain VHOG:0000910 mantle layer lateral wall mesencephalon VHOG:0000910 EMAPA:17580 VHOG:0000911 mantle layer lateral wall spinal cord spinal cord lateral wall mantle layer uberon UBERON:0009583 spinal cord mantle layer mantle layer lateral wall spinal cord VHOG:0000911 Mesenchyme that is part of a 1st arch mandibular component. UBERON:0010043 EHDAA2:0000034 EMAPA:16385 mesenchymal region of mandibular component of first pharyngeal arch mesenchyme of mandibular component uberon mandibular component mesenchyme mandibular mesenchyme UBERON:0009584 1st arch mandibular mesenchyme EMAPA Mesenchyme that is part of a 1st arch mandibular component. OBOL:automatic mesenchymal region of mandibular component of first pharyngeal arch https://orcid.org/0000-0002-6601-2165 mesenchyme of mandibular component EMAPA:16385 Mesenchyme that is part of a developing left lung. EHDAA2:0000944 EMAPA:16730 EMAPA:17654 left lung mesenchyme uberon UBERON:0009602 left lung associated mesenchyme Mesenchyme that is part of a developing left lung. OBOL:automatic left lung mesenchyme EMAPA:17654 Mesenchyme that is part of a developing right lung. EHDAA2:0001739 EMAPA:17662 right lung mesenchyme uberon UBERON:0009603 right lung associated mesenchyme Mesenchyme that is part of a developing right lung. OBOL:automatic right lung mesenchyme EMAPA:17662 A neural plate that develops_from a future forebrain. TAO:0007018 ZFA:0007018 uberon UBERON:0009610 forebrain neural plate ZFA ZFA A neural plate that develops_from a future forebrain. OBOL:automatic A neural plate that develops_from a presumptive midbrain. TAO:0007019 ZFA:0007019 uberon UBERON:0009611 midbrain neural plate ZFA ZFA A neural plate that develops_from a presumptive midbrain. OBOL:automatic A neural plate that develops_from a presumptive hindbrain. TAO:0007022 ZFA:0007022 uberon UBERON:0009614 hindbrain neural plate ZFA ZFA A neural plate that develops_from a presumptive hindbrain. OBOL:automatic TODO - developmental relationships for lines TAO:0007044 ZFA:0007044 MHB neural plate midbrain-hindbrain boundary neural plate uberon UBERON:0009615 midbrain hindbrain boundary neural plate ZFA https://github.com/obophenotype/uberon/issues/438 Bgee:AN MHB neural plate https://orcid.org/0000-0002-6601-2165 midbrain-hindbrain boundary neural plate ZFA:0007044 A presumptive structure that has the potential to develop into a midbrain. TODO - unify naming conventions BAMS:MES EFO:0003432 EHDAA2:0000615 EMAPA:16140 TAO:0000148 Wikipedia:Mesencephalon ZFA:0000148 presumptive mesencephalon uberon early midbrain future midbrain mesencephalon UBERON:0009616 presumptive midbrain ZFA ZFA A presumptive structure that has the potential to develop into a midbrain. OBOL:automatic presumptive mesencephalon ZFA:0000148 early midbrain https://orcid.org/0000-0002-6601-2165 future midbrain https://orcid.org/0000-0002-6601-2165 mesencephalon EHDAA2:0000615 Bilateral mesenchymal mesoderm parallel and immediately adjacent to the neural tube/notochord; it generates a subset of extra-ocular, and other head, muscles. A major contributor to neurocranium [PMID:16313393] EHDAA2:0000736 EHDAA:364 EMAPA:16171 cephalic paraxial mesenchyme cephalic paraxial mesoderm cranial paraxial mesenchyme cranial paraxial mesoderm head paraxial mesenchyme uberon somitomere somitomeric mesoderm UBERON:0009617 head paraxial mesoderm EHDAA2 Bilateral mesenchymal mesoderm parallel and immediately adjacent to the neural tube/notochord; it generates a subset of extra-ocular, and other head, muscles. PMID:21610022 cephalic paraxial mesenchyme https://orcid.org/0000-0002-6601-2165 cephalic paraxial mesoderm https://orcid.org/0000-0002-6601-2165 cranial paraxial mesenchyme https://orcid.org/0000-0002-6601-2165 cranial paraxial mesoderm https://orcid.org/0000-0002-6601-2165 head paraxial mesenchyme EHDAA2:0000736 https://github.com/obophenotype/uberon/issues/30 EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon trunk paraxial mesenchyme UBERON:0009618 trunk paraxial mesoderm EHDAA2 trunk and cervical paraxial mesenchyme EHDAA2:0002094 trunk paraxial mesenchyme https://github.com/obophenotype/uberon/issues/30 A somite that is part of a tail. AAO:0010383 EMAPA:16860 XAO:0003143 uberon UBERON:0009621 tail somite A somite that is part of a tail. OBOL:automatic EMAPA:37092 MA:0001987 NCIT:C52947 UMLS:C1708633 labial artery uberon UBERON:0009657 artery of lip EMAPA:37092 MA:th UMLS:C1708633 ncithesaurus:Labial_Artery labial artery MA:0001987 Nucleus located in the midbrain. SCTID:279285003 TAO:0002209 ZFA:0001665 uberon UBERON:0009661 midbrain nucleus Nucleus located in the midbrain. ZFIN:curator Nucleus located within the hindbrain. TAO:0002177 ZFA:0001658 uberon UBERON:0009662 hindbrain nucleus Nucleus located within the hindbrain. ZFIN:curator A nucleus of brain that is part of a telencephalon. TAO:0002178 ZFA:0001660 uberon UBERON:0009663 telencephalic nucleus A nucleus of brain that is part of a telencephalon. OBOL:automatic An anatomical space that surrounded_by a embryonic cloaca. EHDAA2:0004586 uberon UBERON:0009669 embryonic cloacal lumen An anatomical space that surrounded_by a embryonic cloaca. OBOL:automatic An anatomical space that surrounded_by a rectum. EHDAA2:0004587 EMAPA:18388 FMA:14598 SCTID:259740004 lumen of rectum uberon UBERON:0009670 rectal lumen cjm EHDAA2 An anatomical space that surrounded_by a rectum. OBOL:automatic lumen of rectum FMA:14598 Any endocardium that is part of the right ventricle of the heart. Endocardium of ventricle which is continuous tricuspid valve, pulmonary valve and with the tunica intima of the pulmonary trunk. EHDAA2:0002188 EMAPA:17341 FMA:9536 NCIT:C102343 SCTID:8911002 VHOG:0001235 right ventricle endocardium right ventricular endocardium uberon endocardial lining of right ventricle right ventricle endocardial tissue UBERON:0009712 endocardium of right ventricle EHDAA2 FMA Any endocardium that is part of the right ventricle of the heart. http://orcid.org/0000-0002-6601-2165 Endocardium of ventricle which is continuous tricuspid valve, pulmonary valve and with the tunica intima of the pulmonary trunk. FMA:9536 right ventricle endocardium VHOG:0001235 right ventricular endocardium FMA:9536 endocardial lining of right ventricle EMAPA:17341 right ventricle endocardial tissue VHOG:0001235 Any endocardium that is part of the left ventricle of the heart. Endocardium of ventricle which is continuous with mitral valve, aortic valve, atrioventricular septum and the tunica intima of the aorta. EHDAA2:0002182 EMAPA:17338 FMA:9559 SCTID:191004004 VHOG:0001233 left ventricle endocardium left ventricular endocardium uberon endocardial lining of left ventricle left ventricle endocardial tissue UBERON:0009713 endocardium of left ventricle FMA Any endocardium that is part of the left ventricle of the heart. http://orcid.org/0000-0002-6601-2165 Endocardium of ventricle which is continuous with mitral valve, aortic valve, atrioventricular septum and the tunica intima of the aorta. FMA:9559 left ventricle endocardium VHOG:0001233 left ventricular endocardium FMA:9559 endocardial lining of left ventricle EMAPA:17338 left ventricle endocardial tissue VHOG:0001233 An anatomical cavity that surrounded_by a stomodeum. lumen of stomatodaeum lumen of stomodeum stomatodeal cavity uberon UBERON:0009715 stomodeal lumen An anatomical cavity that surrounded_by a stomodeum. OBOL:automatic EHDAA2:0004621 EMAPA:32754 FMA:293087 uberon pharyngeal arch endoderm UBERON:0009722 entire pharyngeal arch endoderm EHDAA2 pharyngeal arch endoderm EHDAA2:0004621 The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing cardiac structures decide whether to merge with cardiac mesoderm. In EHDAA2 this lasts CS12->unbounded, includes mesenchyme of individual components as parts EHDAA2:0004162 EMAPA:36438 heart mesenchyme uberon UBERON:0009751 cardiac mesenchyme The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing cardiac structures MP:0011264 heart mesenchyme EMAPA:36438 A ganglion that is part of a abdominal segment of trunk. SCTID:280508003 uberon UBERON:0009758 abdominal ganglion A ganglion that is part of a abdominal segment of trunk. OBOL:automatic A serous sac that has the pleura and the pleural cavity as parts. despite its name the class EHDAA2:0004737 is not a true cavity, it corresponds to what we call the sac EHDAA2:0004737 FMA:9690 SCTID:361996004 uberon UBERON:0009778 pleural sac FMA FMA-abduced-lr A serous sac that has the pleura and the pleural cavity as parts. https://github.com/obophenotype/uberon/issues/86 despite its name the class EHDAA2:0004737 is not a true cavity, it corresponds to what we call the sac EHDAA2 The many-lobed berry cluster of cells that is the terminous of a gland where the secretion is produced is acinar in form. acinar acinus FMA:55588 Wikipedia:Acinus uberon acini UBERON:0009842 glandular acinus http://upload.wikimedia.org/wikipedia/commons/9/99/Gray1105.png The many-lobed berry cluster of cells that is the terminous of a gland where the secretion is produced is acinar in form. Wikipedia:Acinus acinus FMA:55588 acini Wikipedia:Acinus An epithelium that is part of a embryonic cloaca. cloacal epithelium EHDAA2:0004585 uberon UBERON:0009846 embryonic cloacal epithelium EHDAA2 EHDAA2 An epithelium that is part of a embryonic cloaca. OBOL:automatic cloacal epithelium EHDAA2:0004585 Branch or outpocketing of the digestive tract. FBbt:00100316 uberon diverticulum of gut intestinal pouch UBERON:0009854 digestive tract diverticulum Branch or outpocketing of the digestive tract. https://orcid.org/0000-0002-6601-2165 diverticulum of gut FBbt:00100316 galen:Diverticulum pouch uberon diverticulum UBERON:0009856 sac A division of the stomach. The stomach can be divided based on mucosal histology (glandular epithelium and gastric glands) and the relative position and type of gastric gland. We follow Kardong in defining stomach regions by gland, but we also include 'body of stomach'. In future we may want to have different partitions of the stomach UBERON:0009034 EMAPA:35821 FMA:14558 MA:0002561 SCTID:245415005 Wikipedia:Stomach#Sections gastric zone region of stomach section of stomach uberon UBERON:0009870 zone of stomach http://upload.wikimedia.org/wikipedia/commons/2/29/Regions_of_stomach.svg A division of the stomach. The stomach can be divided based on mucosal histology (glandular epithelium and gastric glands) and the relative position and type of gastric gland. ISBN:0073040584 Wikipedia:Stomach#Sections gastric zone FMA:14558 EFO:0003704 TAO:0005041 ZFA:0005041 ALPM uberon UBERON:0009881 anterior lateral plate mesoderm ZFA ALPM ZFA:0005041 One of a number of vertical folds, produced by an infolding of the mucous membrane and some of the muscular tissue in the upper half of the lumen of the anal canal[WP] FMA:15713 NCIT:C32067 SCTID:245444007 UMLS:C0227428 Wikipedia:Anal_columns column of Morgagni uberon columnae anales UBERON:0009882 anal column https://upload.wikimedia.org/wikipedia/commons/0/01/Gray1078.png One of a number of vertical folds, produced by an infolding of the mucous membrane and some of the muscular tissue in the upper half of the lumen of the anal canal[WP] Wikipedia:Anal_columns UMLS:C0227428 ncithesaurus:Anal_Column column of Morgagni FMA:15713 columnae anales Wikipedia:Anal_columns A specific region of the lateral mesoderm that will form the majority of the mesodermal component of the right ventricle, arterial pole (outflow tract) and venous pole (inflow tract). extra-cardiac population of mesodermal progenitors that gives rise to the right ventricle and outflow tract[PMID:17276708]. In general, the two studies in chick concluded that the contribution of the SHF was to the outflow tract, whereas the mouse work suggested that the second lineage contributed more broadly to the heart, including the outflow tract and much or all of the right ventricle [11-14]. These different conclusions may represent differences in the experimental approaches used or may represent bona fide differences in the contribution of the second lineage to the hearts of birds compared to mammals [11]. Alternatively, the secondary/anterior heart fields described in the chick may represent a subset of a broader field that makes a more substantial contribution to the heart, as the mouse studies suggested in mouse has left ventricular identity[PMID:22855565] XAO:0004186 anterior heart field anterior/second heart field second heart field uberon SHF UBERON:0009889 secondary heart field GO:0003129 PMID:17276708 PMID:17276708 A specific region of the lateral mesoderm that will form the majority of the mesodermal component of the right ventricle, arterial pole (outflow tract) and venous pole (inflow tract). GO:0003139 GOC:mtg_heart GOC:rl extra-cardiac population of mesodermal progenitors that gives rise to the right ventricle and outflow tract[PMID:17276708]. PMID:17276708 In general, the two studies in chick concluded that the contribution of the SHF was to the outflow tract, whereas the mouse work suggested that the second lineage contributed more broadly to the heart, including the outflow tract and much or all of the right ventricle [11-14]. These different conclusions may represent differences in the experimental approaches used or may represent bona fide differences in the contribution of the second lineage to the hearts of birds compared to mammals [11]. Alternatively, the secondary/anterior heart fields described in the chick may represent a subset of a broader field that makes a more substantial contribution to the heart, as the mouse studies suggested PMID:17276708 anterior heart field PMID:17276708 anterior/second heart field Geisha:syn NCBITaxon:8782 second heart field XAO:0004186 SHF XAO:0004186 Mesenchyme that is part of a developing face. EMAPA:35337 FMA:302884 face mesenchyme mesenchyme of face uberon UBERON:0009891 facial mesenchyme Mesenchyme that is part of a developing face. OBOL:automatic EHDAA2:0001315 EHDAA:1122 uberon UBERON:0009920 optic neural crest EHDAA2 EHDAA2 A multicellular organism that existence_starts_with a post-embryonic stage. MA:0002405 postnatal organism TS28 mouse post-hatching organism post-natal organism postnatal mouse uberon UBERON:0009953 post-embryonic organism https://github.com/obophenotype/uberon/issues/667 A multicellular organism that existence_starts_with a post-embryonic stage. OBOL:automatic TS28 mouse MA:0002405 post-hatching organism https://orcid.org/0000-0002-6601-2165 post-natal organism https://orcid.org/0000-0002-6601-2165 postnatal mouse MA:0002405 Cranial ectodermal placode with potential to develop into a component of the nervous system, such as nerves or ganglia. Includes: trigeminal, otic, lateral line and epibranchial placodes. While some sensory placodes (otic and olfactory) may have homologues in basal chordates (Wada et al., 1998), the so-called neurogenenic placodes (trigeminal, otic, lateral line and epibranchial placodes) appear to have emerged at a later time (Shimeld and Holland, 2000) EFO:0003460 TAO:0001309 Wikipedia:Neurogenic_placodes XAO:0004620 ZFA:0001309 neurogenic placodes uberon placodae neurogenicae UBERON:0009955 neurogenic placode cjm Cranial ectodermal placode with potential to develop into a component of the nervous system, such as nerves or ganglia. PMID:11523831 http://orcid.org/0000-0002-6601-2165 While some sensory placodes (otic and olfactory) may have homologues in basal chordates (Wada et al., 1998), the so-called neurogenenic placodes (trigeminal, otic, lateral line and epibranchial placodes) appear to have emerged at a later time (Shimeld and Holland, 2000) NCBIBook:NBK53171 neurogenic placodes ZFA:0001309 placodae neurogenicae Wikipedia:Neurogenic_placodes An anatomical structure that has more than one cell as a part. CARO:0010000 FBbt:00100313 multicellular structure uberon UBERON:0010000 multicellular anatomical structure CARO An anatomical structure that has more than one cell as a part. CARO:0010000 multicellular structure FBbt:00100313 A small cluster of cells of various types which form a discrete structure, largely delimited by a morphological boundary and whose components work together to make the whole structure capable of a specific function. CARO:0010001 FBbt:00007229 uberon UBERON:0010001 Examples include arthropod sensilla. cell cluster organ CARO CARO FBbt A small cluster of cells of various types which form a discrete structure, largely delimited by a morphological boundary and whose components work together to make the whole structure capable of a specific function. CARO:0010001 Mesenchyme that is part of a pharyngeal arch 6. EHDAA2:0004076 EMAPA:32765 FMA:318209 6th pharyngeal arch mesenchyme uberon 6th branchial arch mesenchyme pharyngeal arch 6 mesenchyme UBERON:0010031 6th arch mesenchyme Mesenchyme that is part of a pharyngeal arch 6. OBOL:automatic An organ of the digestive tract that is capable of retaining and storing food This is a very broad functionally defined grouping class that collects disparate structures from insects to vertebrates BSA:0000123 TADS:0000172 TGMA:0001041 uberon UBERON:0010039 food storage organ An organ of the digestive tract that is capable of retaining and storing food https://orcid.org/0000-0002-6601-2165 Mesenchyme that is part of a pharyngeal arch 1. EMAPA:16128 mesenchyme of 1st arch uberon UBERON:0010042 1st arch mesenchyme Mesenchyme that is part of a pharyngeal arch 1. OBOL:automatic mesenchyme of 1st arch EMAPA:16128 The sum total of mesenchymal tissue in the pharyngeal arch region. Pharyngeal mesenchyme is undifferentiated, loose connective tissue derived mostly from mesoderm, and also contains ectodermally derived neural crest cells. EHDAA2:0001459 EMAPA:16550 XAO:0004524 associated mesenchyme of pharyngeal region entire branchial arch associated mesenchyme pharyngeal arch associated mesenchyme uberon UBERON:0010046 entire pharyngeal arch associated mesenchyme EHDAA2 EHDAA2 cjm The sum total of mesenchymal tissue in the pharyngeal arch region. Pharyngeal mesenchyme is undifferentiated, loose connective tissue derived mostly from mesoderm, and also contains ectodermally derived neural crest cells. XAO:0004524 https://orcid.org/0000-0002-6601-2165 associated mesenchyme of pharyngeal region EMAPA:16550 entire branchial arch associated mesenchyme https://orcid.org/0000-0002-6601-2165 pharyngeal arch associated mesenchyme EHDAA2:0001459 Gland of the epithelium lining the oral cavity. The most common are the salivary glands. Note that Kardong classifies lacrimal glands here. EHDAA2 includes pituitary primordium, as this develops from oral mucosa UBERON:0003293 EHDAA2:0001327 EHDAA:2181 EMAPA:16572 EMAPA:16723 VHOG:0000652 buccal gland uberon gland of oral opening gland of oral region mouth gland oral cavity gland oral region gland UBERON:0010047 oral gland Gland of the epithelium lining the oral cavity. The most common are the salivary glands. ISBN:0073040584 Note that Kardong classifies lacrimal glands here. EHDAA2 includes pituitary primordium, as this develops from oral mucosa EHDAA2 An anatomical space with at least one opening to another space or the exterior. AEO:0000221 EHDAA2:0004616 uberon UBERON:0010064 open anatomical space cjm An anatomical space with at least one opening to another space or the exterior. AEO:0000221 An epithelium consisting of cuboidal epithelial cells. TODO - coordinate with CL, add cuboidal cell in NCIT this is glandular NCIT:C32415 UMLS:C0682577 Wikipedia:Cuboidal_epithelium uberon UBERON:0010077 cuboidal epithelium An epithelium consisting of cuboidal epithelial cells. Wikipedia:Cuboidal_epithelium in NCIT this is glandular NCIT UMLS:C0682577 ncithesaurus:Cuboidal_Epithelium Mesenchyme that has the potential to develop into a dermis. check development EHDAA2:0000598 uberon UBERON:0010083 future dermis EHDAA2 EHDAA2 XAO Mesenchyme that has the potential to develop into a dermis. OBOL:automatic A structure that will develop into a diaphragm. EHDAA2:0000599 uberon UBERON:0010084 future diaphragm EHDAA2 PMID:23586979 PMID:23586979 A structure that will develop into a diaphragm. http://orcid.org/0000-0002-6601-2165 A developing anatomical structure that has the potential to develop into a metencephalon. EHDAA2:0000623 uberon UBERON:0010092 future metencephalon A developing anatomical structure that has the potential to develop into a metencephalon. OBOL:automatic A developing anatomical structure that has the potential to develop into a myelencephalon. EHDAA2:0000640 uberon UBERON:0010096 future myelencephalon A developing anatomical structure that has the potential to develop into a myelencephalon. OBOL:automatic A gray matter that has the potential to develop into a superior salivatory nucleus. EHDAA2:0004644 uberon UBERON:0010125 future superior salivatory nucleus A gray matter that has the potential to develop into a superior salivatory nucleus. OBOL:automatic Any portion of cardiac muscle tissue that is part of the conducting system of heart or the Purkinje fibers. EHDAA2:0004528 FMA:83378 specialized conducting tissue of heart specialized muscle tissue of heart uberon UBERON:0010131 conducting tissue of heart Any portion of cardiac muscle tissue that is part of the conducting system of heart or the Purkinje fibers. http://orcid.org/0000-0002-6601-2165 specialized conducting tissue of heart FMA:83378 specialized muscle tissue of heart FMA:83378 any of the organized aggregations of cells that function as secretory or excretory organs and that release hormones in response to neural stimuli MA:0000720 neuroendocrine system gland uberon UBERON:0010133 neuroendocrine gland any of the organized aggregations of cells that function as secretory or excretory organs and that release hormones in response to neural stimuli ISBN:0-683-40008-8 MP:0000631 An anatomical cavity that surrounded_by a blood vessel. FMA:312610 SCTID:91747007 blood vessel lumen uberon UBERON:0010161 lumen of blood vessel An anatomical cavity that surrounded_by a blood vessel. OBOL:automatic The distal end of the tail EMAPA:37760 MA:0002848 XAO:0004057 tail tip uberon end of tail UBERON:0010162 post-anal tail tip MA The distal end of the tail http://orcid.org/0000-0002-6601-2165 EMAPA:37760 MA:th tail tip MA:0002848 end of tail MA:0002848 A roughly circular bulge in a surface. requires review AEO:0000205 EHDAA2:0003250 FMA:82506 uberon UBERON:0010188 protuberance FMA A roughly circular bulge in a surface. EHDAA2:0003250 the paired arterial structures of the embryo that supplies each developing somite via efferent segmental arteries; the dorsal aortae articulate with the umbilical arteries, which return mixed blood to the villi of the chorion for reoxygenation EHDAA2:0000410 EMAPA:18606 MA:0000476 paired dorsal aortae uberon UBERON:0010190 pair of dorsal aortae EHDAA2 EHDAA2 the paired arterial structures of the embryo that supplies each developing somite via efferent segmental arteries; the dorsal aortae articulate with the umbilical arteries, which return mixed blood to the villi of the chorion for reoxygenation ISBN:0-914294-08-3 MP:0004787 paired dorsal aortae EHDAA2:0000410 EHDAA2:0004512 uberon UBERON:0010191 aortic system Wikipedia One of the laterally paired arteries that supply the gonads. Wikipedia:Gonadal_artery gonadal artery uberon UBERON:0010192 genital artery One of the laterally paired arteries that supply the gonads. ISBN:0073040584 Wikipedia:Gonadal_artery An anatomical boundary that corresponds to some physical discontinuity. CARO:0001004 uberon UBERON:0010199 One might argue that all boundaries are actually fiat in the sense that there must be some fiat element at a fine enough scale of granularity. This ontology choses to ignore this issue as below the level of granularity relevant to anatomy. (DOS121102) bona-fide anatomical boundary CARO An anatomical boundary that corresponds to some physical discontinuity. CARO:0001004 A vasculature that is part of a post-anal tail. isa blood vessel in XAO TAO:0005037 XAO:0004151 ZFA:0005037 post-vent vasculature uberon tail vasculature UBERON:0010204 tail vasculature A vasculature that is part of a post-anal tail. OBOL:automatic isa blood vessel in XAO XAO post-vent vasculature ZFA:0005037 tail vasculature ZFA:0005037 Apparatus located between the lungs and the buccal cavity. This apparatus is composed of a pair of arytenoid cartilages that are supported by the cricoid ring. check this. See also https://github.com/obophenotype/uberon/wiki/The-axial-skeleton AAO:0000267 EHDAA2:0000904 laryngeal cartilage system uberon UBERON:0010212 laryngeal apparatus EHDAA2 Apparatus located between the lungs and the buccal cavity. This apparatus is composed of a pair of arytenoid cartilages that are supported by the cricoid ring. AAO:0000267 laryngeal cartilage system EHDAA2:0000904 uberon UBERON:0010213 laryngeal pre-cartilage condensation EHDAA2-abstracted EHDAA2-abstracted EHDAA2:0004085 uberon UBERON:0010221 Many sources say: thyroid cartilage from arch 4 other laryngeal cartilage (cricoid/arytenoid) from 6? laryngeal associated mesenchyme EHDAA2 EHDAA2 Wikipedia Wikipedia Wikipedia A nuclear complex which in mammals consists of four parts, the hypothalamus, epithalamus, ventral thalamus, and dorsal thalamus[WP,modified]. EHDAA2:0004469 FMA:258745 uberon UBERON:0010225 thalamic complex A nuclear complex which in mammals consists of four parts, the hypothalamus, epithalamus, ventral thalamus, and dorsal thalamus[WP,modified]. Wikipedia:Thalamus#Thalamic_nuclei Multi-tissue structure that is part of the heart tube and will become the cardiac atrium. FMA:71005 TAO:0002228 ZFA:0001718 presumptive atrium heart tube primordial atrium primordial cardiac atrium uberon UBERON:0010227 future cardiac atrium ZFA Multi-tissue structure that is part of the heart tube and will become the cardiac atrium. ZFA:0001718 presumptive atrium heart tube ZFA:0001718 primordial atrium FMA:71005 primordial cardiac atrium FMA:71005 The core globe-shaped component of the camera-type eye. See notes for camera-type eye FMA:12513 MIAA:0000283 SCTID:244486005 VHOG:0001616 Wikipedia:Globe_(human_eye) bulbus oculi eye globe eyeball uberon eye globe UBERON:0010230 eyeball of camera-type eye FMA The core globe-shaped component of the camera-type eye. UBERON:cjm eye globe VHOG:0001616 eyeball FMA:12513 eye globe HP:0100886 MIAA:0000283 Mesenchyme that develops_from a neural crest and is part of a 1st arch mandibular mesenchyme. EHDAA2:0000037 uberon UBERON:0010252 1st arch mandibular mesenchyme from neural crest inferred EHDAA2 EHDAA2 Mesenchyme that develops_from a neural crest and is part of a 1st arch mandibular mesenchyme. OBOL:automatic Mesenchyme that develops_from a neural crest and is part of a 3rd arch mesenchyme. In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] EHDAA2:0000083 EMAPA:16404 VHOG:0000571 3rd pharyngeal arch mesenchyme derived from neural crest mesenchyme derived from neural crest of mesenchyme of 3rd arch neural crest derived arch 3 mesenchyme pharyngeal arch 3 mesenchyme from neural crest uberon branchial arch 3 mesenchyme from neural crest UBERON:0010255 3rd arch mesenchyme from neural crest EHDAA2 Mesenchyme that develops_from a neural crest and is part of a 3rd arch mesenchyme. OBOL:automatic In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] 2012-09-17 VHOG:0000571 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) http://bgee.unil.ch/ 3rd pharyngeal arch mesenchyme derived from neural crest VHOG:0000571 mesenchyme derived from neural crest of mesenchyme of 3rd arch EMAPA:16404 Mesenchyme that develops_from a neural crest and is part of a 4th arch mesenchyme. In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] EHDAA2:0000098 EMAPA:16772 VHOG:0000580 4th pharyngeal arch mesenchyme derived from neural crest mesenchyme derived from neural crest of mesenchyme of 4th arch neural crest derived arch 4 mesenchyme pharyngeal arch 4 mesenchyme from neural crest uberon branchial arch 4 mesenchyme from neural crest UBERON:0010256 4th arch mesenchyme from neural crest EHDAA2 EHDAA2 Mesenchyme that develops_from a neural crest and is part of a 4th arch mesenchyme. OBOL:automatic In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG] 2012-09-17 VHOG:0000580 VHOG DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) http://bgee.unil.ch/ 4th pharyngeal arch mesenchyme derived from neural crest VHOG:0000580 mesenchyme derived from neural crest of mesenchyme of 4th arch EMAPA:16772 Mesenchyme that develops_from a neural crest and is part of a 6th arch mesenchyme. EHDAA2:0004077 neural crest derived arch 6 mesenchyme pharyngeal arch 6 mesenchyme from neural crest uberon branchial arch 6 mesenchyme from neural crest UBERON:0010257 6th arch mesenchyme from neural crest EHDAA2 EHDAA2 Mesenchyme that develops_from a neural crest and is part of a 6th arch mesenchyme. OBOL:automatic Mesenchyme that develops_from a rhombencephalon neural crest. EHDAA2:0004423 uberon UBERON:0010258 mesenchyme from rhombencephalic neural crest EHDAA2 Mesenchyme that develops_from a rhombencephalon neural crest. OBOL:automatic Mesenchyme that develops_from a neural crest and is part of a 1st arch mesenchyme. EMAPA:16129 mesenchyme derived from neural crest of mesenchyme of 1st arch neural crest derived arch 1 mesenchyme pharyngeal arch 1 mesenchyme from neural crest uberon branchial arch 1 mesenchyme from neural crest UBERON:0010259 1st arch mesenchyme from neural crest Mesenchyme that develops_from a neural crest and is part of a 1st arch mesenchyme. OBOL:automatic mesenchyme derived from neural crest of mesenchyme of 1st arch EMAPA:16129 Any anatomical space that is part of a vertebral column. AAO:0000700 vertebral column opening vertebral conduit uberon UBERON:0010276 space in vertebral column Any anatomical space that is part of a vertebral column. OBOL:automatic vertebral column opening AAO:0000700 Portion of tissue that is dorsolateral to the floor plate and part of the midbrain. DHBA:12322 EFO:0003567 EHDAA2:0004375 TAO:0000761 ZFA:0000761 basal plate midbrain basal plate midbrain region uberon UBERON:0010285 midbrain basal plate EHDAA2 EHDAA2 ZFA Portion of tissue that is dorsolateral to the floor plate and part of the midbrain. ZFA:0000761 basal plate midbrain TAO:0000761 basal plate midbrain region ZFA:0000761 Portion of neural tube that gives rise to the midbrain. we follow ZFA in temporally dividing midbrain NT from presumptive midbrain, but in future this may be collapsed TAO:0007039 ZFA:0007039 uberon UBERON:0010286 midbrain neural tube ZFA Portion of neural tube that gives rise to the midbrain. ZFA:0007039 . Wikipedia:Sclera#Histology uberon UBERON:0010291 layer of sclera cjm . Wikipedia:Sclera#Histology An endothelium that is part of a sclera. uberon UBERON:0010294 scleral endothelium Wikipedia An endothelium that is part of a sclera. OBOL:automatic A stroma that is part of a sclera. subsantia propria FMA:58365 NCIT:C33652 SCTID:368851004 UMLS:C1704397 scleral stroma stroma of sclera subsantia propria sclerae substantia propria sclerae uberon UBERON:0010295 substantia propria of sclera Wikipedia A stroma that is part of a sclera. OBOL:automatic UMLS:C1704397 ncithesaurus:Substantia_Propria scleral stroma FMA:58365 stroma of sclera FMA:58365 subsantia propria sclerae FMA:58365 substantia propria sclerae FMA:58365 FMA:TA Mesenchyme surrounding the developing optic cup which develops into the sclera. The mesenchyme surrounding the developing optic cup differentiates into the sclera, the dense fibrous coat of the eye.. http://www.ncbi.nlm.nih.gov/pubmed/16496288 uberon UBERON:0010299 scleral mesenchyme Mesenchyme surrounding the developing optic cup which develops into the sclera. PMID:16496288 https://orcid.org/0000-0002-6601-2165 An epithelium that is part of a extraembryonic structure. extra-embryonic epithelium uberon UBERON:0010303 extraembryonic epithelium An epithelium that is part of a extraembryonic structure. OBOL:automatic Developing anatomical structure that develops into the eyeball and associated structures. Multi-tissue structure that consists of the structures that develop into the retina and lens.[TAO] TAO:0002201 ZFA:0001678 future eye uberon UBERON:0010312 immature eye definitional Developing anatomical structure that develops into the eyeball and associated structures. ZFA:0001678 Multi-tissue structure that consists of the structures that develop into the retina and lens.[TAO] 2012-08-14 TAO:0002201 TAO ZFIN:curator An anatomical structure that develops from the neural crest. Grouping term for query purposes uberon UBERON:0010313 neural crest-derived structure An anatomical structure that develops from the neural crest. https://orcid.org/0000-0002-6601-2165 An anatomical structure that has some part that develops from the neural crest. Grouping term for query purposes uberon UBERON:0010314 structure with developmental contribution from neural crest An anatomical structure that has some part that develops from the neural crest. https://orcid.org/0000-0002-6601-2165 uberon UBERON:0010316 germ layer / neural crest A skeletal element that is part of a orbital region. uberon eye skeleton ocular skeleton skeletal element of orbital region UBERON:0010321 skeletal element of eye region A skeletal element that is part of a orbital region. OBOL:automatic Skeletal subdivision of the head including skull (cranium plus mandible), pharyngeal and/or hyoid apparatus. we use 'cranial skeletal system', so that we can include the skull, which has joints/sutures as parts (recall, we follow FMA in distinguishing between the skeleton and skeletal system - only the latter includes joints) that the cranial skeleton includes the pharyngeal arch skeleton. It is thus more inclusive that the cranium itself, and extends beyond the head in tetrapods. The AAO class called 'skull' belongs here, as it includes the whole splanchnocranium Bony structure that encases the central nervous system and the primary sense organs of sight, olfaction, hearing, and equilibrium.[AAO] Skeletal system which is part of the skull, including the splanchnocranium, chondrocranium, and dermatocranium.[TAO] AAO:0000109 AAO:0000971 AAO:0010185 TAO:0000737 VSAO:0000049 XAO:0003075 ZFA:0000737 cranial skeleton osteocranium uberon cranium UBERON:0010323 cranial skeletal system Skeletal subdivision of the head including skull (cranium plus mandible), pharyngeal and/or hyoid apparatus. GO_REF:0000034 PSPUB:0000170 VSAO:0000049 http://dx.plos.org/10.1371/journal.pone.0051070 Bony structure that encases the central nervous system and the primary sense organs of sight, olfaction, hearing, and equilibrium.[AAO] 2012-06-20 AAO:0000109 AAO AAO:LAP Skeletal system which is part of the skull, including the splanchnocranium, chondrocranium, and dermatocranium.[TAO] 2012-08-14 TAO:0000737 TAO ZFIN:curator cranium ZFA:0000737 Mesenchyme that is part of a limb/fin bud. uberon UBERON:0010329 paired limb/fin bud mesenchyme EHDAA2-abduced Mesenchyme that is part of a limb/fin bud. OBOL:automatic Mesenchyme that develops_from a neural crest and is part of a mandibular process mesenchyme. EHDAA2:0004603 uberon UBERON:0010336 mandibular process mesenchyme from neural crest EHDAA2 EHDAA2 Mesenchyme that develops_from a neural crest and is part of a mandibular process mesenchyme. OBOL:automatic Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a mandibular process mesenchyme. EHDAA2:0004604 uberon UBERON:0010337 mandibular process mesenchyme from head mesenchyme EHDAA2 EHDAA2 Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a mandibular process mesenchyme. OBOL:automatic Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mandibular mesenchyme. EHDAA2:0000036 uberon UBERON:0010339 1st arch mandibular mesenchyme from head mesenchyme EHDAA2 Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mandibular mesenchyme. OBOL:automatic Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mesenchyme. EMAPA:16130 mesenchyme derived from head mesoderm of mesenchyme of 1st arch uberon UBERON:0010341 1st arch mesenchyme from head mesenchyme EMAPA Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mesenchyme. OBOL:automatic mesenchyme derived from head mesoderm of mesenchyme of 1st arch EMAPA:16130 Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 3rd arch mesenchyme. EHDAA2:0000082 EMAPA:16403 head mesenchyme derived arch 3 mesenchyme mesenchyme derived from head mesoderm of mesenchyme of 3rd arch pharyngeal arch 3 mesenchyme from head mesenchyme uberon branchial arch 3 mesenchyme from head mesenchyme UBERON:0010344 3rd arch mesenchyme from head mesenchyme EHDAA2 Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 3rd arch mesenchyme. OBOL:automatic mesenchyme derived from head mesoderm of mesenchyme of 3rd arch EMAPA:16403 Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 4th arch mesenchyme. EHDAA2:0000097 EMAPA:16771 head mesenchyme derived arch 4 mesenchyme mesenchyme derived from head mesoderm of mesenchyme of 4th arch pharyngeal arch 4 mesenchyme from head mesenchyme uberon branchial arch 4 mesenchyme from head mesenchyme UBERON:0010345 4th arch mesenchyme from head mesenchyme EHDAA2 Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 4th arch mesenchyme. OBOL:automatic mesenchyme derived from head mesoderm of mesenchyme of 4th arch EMAPA:16771 Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 6th arch mesenchyme. EHDAA2:0004078 head mesenchyme derived arch 6 mesenchyme pharyngeal arch 6 mesenchyme from head mesenchyme uberon branchial arch 6 mesenchyme from head mesenchyme UBERON:0010347 6th arch mesenchyme from head mesenchyme EHDAA2 Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 6th arch mesenchyme. OBOL:automatic Mesenchyme that develops_from a neural crest and is part of a entire pharyngeal arch associated mesenchyme. arch mesenchyme from neural crest branchial arch mesenchyme from neural crest neural crest derived arch mesenchyme uberon UBERON:0010359 Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme pharyngeal arch mesenchyme from neural crest Mesenchyme that develops_from a neural crest and is part of a entire pharyngeal arch associated mesenchyme. OBOL:automatic Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a entire pharyngeal arch associated mesenchyme. arch mesenchyme from head mesenchyme branchial arch mesenchyme from head mesenchyme head mesenchyme derived arch mesenchyme uberon UBERON:0010360 Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme pharyngeal arch mesenchyme from head mesenchyme Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a entire pharyngeal arch associated mesenchyme. OBOL:automatic Skeletal subdivision that undergoes indirect development and includes elements that develop as a replacement or substitution of other elements or tissues. An endoskeleton is an internal support structure of an animal, composed of mineralized tissue. Endoskeleton develops within the skin or in the deeper body tissues. The vertebrate is basically an endoskeleton made up of two types of tissues (bone and cartilage). During early embryonic development the endoskeleton is composed of notochord and cartilage. The notochord in most vertebrates is replaced by vertebral column and cartilage is replaced by bone in most adults. In three phyla and one subclass of animals, endoskeletons of various complexity are found: Chordata, Echinodermata, Porifera, and Coleoidea. An endoskeleton may function purely for support (as in the case of sponges), but often serves as an attachment site for muscle and a mechanism for transmitting muscular forces. A true endoskeleton is derived from mesodermal tissue. Such a skeleton is present in echinoderms and chordates. The poriferan 'skeleton' consists of microscopic calcareous or siliceous spicules or a spongin network. The Coleoidae do not have a true endoskeleton in the evolutionary sense; here, a mollusk exoskeleton evolved into several sorts of internal structure, the 'cuttlebone' of cuttlefish being the best-known version. Yet they do have cartilaginous tissue in their body, even if it is not mineralized, especially in the head, where it forms a primitive cranium. The endoskeleton gives shape,support and protection to the body and provides a mean of locomotion.[Wikipedia:Endoskeleton]t VSAO:0000037 Wikipedia:Endoskeleton XAO:0004026 replacement skeleton uberon UBERON:0010362 endoskeleton VSAO Skeletal subdivision that undergoes indirect development and includes elements that develop as a replacement or substitution of other elements or tissues. GO_REF:0000034 PSPUB:0000170 VSAO:0000037 http://dx.plos.org/10.1371/journal.pone.0051070 An endoskeleton is an internal support structure of an animal, composed of mineralized tissue. Endoskeleton develops within the skin or in the deeper body tissues. The vertebrate is basically an endoskeleton made up of two types of tissues (bone and cartilage). During early embryonic development the endoskeleton is composed of notochord and cartilage. The notochord in most vertebrates is replaced by vertebral column and cartilage is replaced by bone in most adults. In three phyla and one subclass of animals, endoskeletons of various complexity are found: Chordata, Echinodermata, Porifera, and Coleoidea. An endoskeleton may function purely for support (as in the case of sponges), but often serves as an attachment site for muscle and a mechanism for transmitting muscular forces. A true endoskeleton is derived from mesodermal tissue. Such a skeleton is present in echinoderms and chordates. The poriferan 'skeleton' consists of microscopic calcareous or siliceous spicules or a spongin network. The Coleoidae do not have a true endoskeleton in the evolutionary sense; here, a mollusk exoskeleton evolved into several sorts of internal structure, the 'cuttlebone' of cuttlefish being the best-known version. Yet they do have cartilaginous tissue in their body, even if it is not mineralized, especially in the head, where it forms a primitive cranium. The endoskeleton gives shape,support and protection to the body and provides a mean of locomotion.[Wikipedia:Endoskeleton]t Wikipedia:Endoskeleton replacement skeleton VSAO:curator A skeletal element that has the potential to participate in endochondral ossification, and may participate in intramembranous ossification. VSAO:0000139 XAO:0004017 ZFA:0005620 endochondral replacement element uberon UBERON:0010363 endochondral element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern VSAO A skeletal element that has the potential to participate in endochondral ossification, and may participate in intramembranous ossification. GO_REF:0000034 PSPUB:0000170 VSAO:0000139 http://dx.plos.org/10.1371/journal.pone.0051070 endochondral replacement element VSAO:0000139 Skeletal subdivision that undergoes direct development and includes elements that either develop in association with the basement membrane of the ectoderm or are homologous with such elements; includes dermatocranium, components of the appendicular skeleton, teeth and tooth-like elements of the oropharynx, and integumentary elements. exoskeleton VSAO:0000035 XAO:0004025 uberon dermal skeletal system dermoskeleton desmoskeleton UBERON:0010364 This ontology covers metazoa, so we do not use exoskeleton as primary label, as in VSAO dermal skeleton VSAO Skeletal subdivision that undergoes direct development and includes elements that either develop in association with the basement membrane of the ectoderm or are homologous with such elements; includes dermatocranium, components of the appendicular skeleton, teeth and tooth-like elements of the oropharynx, and integumentary elements. GO_REF:0000034 PSPUB:0000170 VSAO:0000035 http://dx.plos.org/10.1371/journal.pone.0051070 exoskeleton VSAO:curator dermal skeletal system VSAO:curator dermoskeleton VSAO:curator desmoskeleton VSAO:curator Epithelium composed of cells that develops from the ectoderm[FMA,modified]. FMA:69064 ectoderm-derived epithelium uberon UBERON:0010371 ecto-epithelium Epithelium composed of cells that develops from the ectoderm[FMA,modified]. FMA:69064 Mesenchyme that develops_from a somatopleure. the way this class is defined also includes extraembryonic mesenchyme such as the amniotic mesenchyme; in future this may be restricted to embryonic derivatives EHDAA2:0001120 uberon UBERON:0010377 mesenchyme from somatopleure EHDAA2 EHDAA2 Mesenchyme that develops_from a somatopleure. OBOL:automatic Mesenchyme that develops_from a splanchnopleure. EHDAA2:0001122 uberon UBERON:0010378 mesenchyme from splanchnopleure EHDAA2 EHDAA2 Mesenchyme that develops_from a splanchnopleure. OBOL:automatic Any layer of the epidermis that is superior to the stratum basale suprabasal layer EMAPA:35315 MA:0000808 suprabasal cell layer of skin suprabasal layer of epidermis uberon UBERON:0010402 epidermis suprabasal layer Any layer of the epidermis that is superior to the stratum basale MP:0001233 PMID:10469309 http://orcid.org/0000-0002-6601-2165 suprabasal layer MP:0001233 The integrated unit (of the eye) that consists of the conjunctiva, the corneal surface, and the ocular mucosal adnexa including the lid margins and the meibomian gland openings, the lacrimal glands and the lacrimal drainage system, all which are critical to maintain ocular surface integrity and provide protection from external antigens and pathogenic microorganisms. EMAPA:35336 MA:0002486 eye surface eye surface region ocular surface uberon UBERON:0010409 ocular surface region The integrated unit (of the eye) that consists of the conjunctiva, the corneal surface, and the ocular mucosal adnexa including the lid margins and the meibomian gland openings, the lacrimal glands and the lacrimal drainage system, all which are critical to maintain ocular surface integrity and provide protection from external antigens and pathogenic microorganisms. MP:0013754 eye surface MA:0002486 The ciliary processes are formed by the inward folding of the various layers of the choroid, i.e. , the choroid proper and the lamina basalis, and are received between corresponding foldings of the suspensory ligament of the lens. FMA:76551 SCTID:280860001 Wikipedia:Ciliary_processes ciliary processes ciliary processes set processus ciliares set of ciliary processes uberon ciliary process processus ciliares UBERON:0010427 ciliary processes http://upload.wikimedia.org/wikipedia/commons/b/b2/Gray875.png The ciliary processes are formed by the inward folding of the various layers of the choroid, i.e. , the choroid proper and the lamina basalis, and are received between corresponding foldings of the suspensory ligament of the lens. Wikipedia:Ciliary_processes ciliary processes FMA:76551 ciliary processes set FMA:76551 processus ciliares FMA:TA set of ciliary processes FMA:76551 ciliary process Wikipedia:Ciliary_processes processus ciliares Wikipedia:Ciliary_processes A bone that is shaped as a broad flat plate and composed of two thin layers of compact tissue enclosing between them a variable quantity of cancellous tissue, which is the location of red bone marrow. In an adult mammal, most red blood cells are formed in flat bones Flat bones are those bones which are found where the principal requirement is either extensive protection or the provision of broad surfaces for muscular attachment FMA:7476 NCIT:C32616 SCTID:332907008 UMLS:C0222649 Wikipedia:Flat_bone galen:FlatBone uberon os planum UBERON:0010428 Examples: cranium, the ilium, sternum, rib cage, the sacrum and the scapula; the occipital, parietal, frontal, nasal, lacrimal, vomer, scapula, os coxC&, sternum, and ribs flat bone FMA A bone that is shaped as a broad flat plate and composed of two thin layers of compact tissue enclosing between them a variable quantity of cancellous tissue, which is the location of red bone marrow. Wikipedia:Flat_bone UMLS:C0222649 ncithesaurus:Flat_Bone os planum Wikipedia:Flat_bone A simple columnar epithelium that looks stratified but is not, because its cells are arranged with their nuclei at different levels. Pseudostratified epithelia function in secretion or absorption. If a specimen looks stratified but has cilia, then it is a pseudostratified ciliated epithelium, since stratified epithelia do not have cilia. glandular in NCIT; we consider the two NCIT terms synonymous FMA:45572 NCIT:C33419 NCIT:C49316 UMLS:C0836138 UMLS:C1514590 Wikipedia:Pseudostratified_columnar_epithelium uberon UBERON:0010498 pseudostratified columnar epithelium FMA A simple columnar epithelium that looks stratified but is not, because its cells are arranged with their nuclei at different levels. Wikipedia:Pseudostratified_columnar_epithelium http://medical-dictionary.thefreedictionary.com/pseudostratified+epithelium glandular in NCIT; we consider the two NCIT terms synonymous NCIT UMLS:C0836138 ncithesaurus:Pseudostratified_Columnar_Epithelium UMLS:C1514590 ncithesaurus:Pseudostratified_Epithelium Epithelium composed of a single layer of cells, appearing as layered because the column-shaped cells vary in height so the nuclei are at different levels. The basal portions of all the cells are in contact with the basement membrane. It lines the respiratory system and the male reproductive tract. The cilia in the respiratory tract are motile, while the stereocilia in the male reproductive tract are immobile. FMA:13146 NCIT:C13181 UMLS:C0506992 epithelium pseudostratificatum columnare ciliatum (trachea et bronchi) uberon UBERON:0010499 pseudostratified ciliated columnar epithelium Epithelium composed of a single layer of cells, appearing as layered because the column-shaped cells vary in height so the nuclei are at different levels. The basal portions of all the cells are in contact with the basement membrane. It lines the respiratory system and the male reproductive tract. The cilia in the respiratory tract are motile, while the stereocilia in the male reproductive tract are immobile. NCIT:NCIT UMLS:C0506992 ncithesaurus:Pseudostratified_Columnar_Ciliated_Epithelium epithelium pseudostratificatum columnare ciliatum (trachea et bronchi) FMA:13146 Skeletal element that forms as a replacement or substitution of another element or tissue. VSAO:0000135 XAO:0004016 ZFA:0005624 uberon UBERON:0010522 replacement element VSAO cjm Skeletal element that forms as a replacement or substitution of another element or tissue. GO_REF:0000034 PSPUB:0000170 VSAO:0000135 http://dx.plos.org/10.1371/journal.pone.0051070 A vessel of the microcirculature, lying between the arterioles and venules; includes capillaries (blood and lymphatic), metarterioles and arteriovenous anastomoses. MESH:A07.231.432 TAO:0005251 ZFA:0005251 uberon microcirculatory vessels UBERON:0010523 microcirculatory vessel ZFA A vessel of the microcirculature, lying between the arterioles and venules; includes capillaries (blood and lymphatic), metarterioles and arteriovenous anastomoses. MESH:A07.231.432 ZFA:0005251 http://orcid.org/0000-0002-6601-2165 microcirculatory vessels TAO:0005251 An organ cavity that surrounded_by a bone. FMA:24021 bone organ cavity uberon UBERON:0010527 cavity of bone organ An organ cavity that surrounded_by a bone. OBOL:automatic bone organ cavity FMA:24021 FMA:24028 air space of bone uberon UBERON:0010528 pneumatic cavity of bone FMA air space of bone FMA:24028 An organism subdivision that includes both an appendage and its associated girdle region. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO] Anatomical group that consists of the soft and skeletal tissues of the appendicular region of the body and the appendage proper.[VSAO] It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO] note that the FMA uses the term 'limb' to refer to the entire appendage complex (free limb plus girdle region) haendel 2012-04-23T10:46:51Z EMAPA:37858 FMA:7182 VSAO:0000214 appendage complex appendage-girdle complex appendage/girdle complex girdle plus limb or fin uberon limb UBERON:0010707 appendage girdle complex An organism subdivision that includes both an appendage and its associated girdle region. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). https://github.com/obophenotype/uberon/wiki/Appendages-and-the-appendicular-skeleton https://orcid.org/0000-0002-6601-2165 Anatomical group that consists of the soft and skeletal tissues of the appendicular region of the body and the appendage proper.[VSAO] 2012-08-14 VSAO:0000214 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO] 2012-09-06 VSAO:0000214 VSAO Curator note that the FMA uses the term 'limb' to refer to the entire appendage complex (free limb plus girdle region) FMA EMAPA:37858 MA:th appendage complex https://orcid.org/0000-0002-6601-2165 appendage-girdle complex https://orcid.org/0000-0002-6601-2165 appendage/girdle complex VSAO:0000214 girdle plus limb or fin https://orcid.org/0000-0002-6601-2165 limb FMA:7182 Appendage girdle complex that when present, encompasses the pelvic appendicular skeleton and the pelvic girdle. Appendage girdle complex that when present, encompasses the pelvic appendage and the pelvic girdle.[VSAO] note that the FMA uses the terms 'upper limb' and 'lower limb' to refer to the entire appendage complex (free limb plus girdle region). Note the MA class 'hindlimb' may also belong here EMAPA:37863 FMA:7184 SCTID:416631005 VSAO:0000215 pelvic appendage/girdle complex pelvic girdle plus pelvic limb or fin pelvic girdle plus posterior limb or fin uberon lower limb lower limb and pelvic girdle lower limb and pelvis UBERON:0010709 pelvic complex Appendage girdle complex that when present, encompasses the pelvic appendicular skeleton and the pelvic girdle. VSAO:0000215 Appendage girdle complex that when present, encompasses the pelvic appendage and the pelvic girdle.[VSAO] 2012-08-14 VSAO:0000215 VSAO VSAO:MAH note that the FMA uses the terms 'upper limb' and 'lower limb' to refer to the entire appendage complex (free limb plus girdle region). Note the MA class 'hindlimb' may also belong here FMA EMAPA:37863 MA:th pelvic appendage/girdle complex VSAO:0000215 pelvic girdle plus pelvic limb or fin https://orcid.org/0000-0002-6601-2165 pelvic girdle plus posterior limb or fin https://orcid.org/0000-0002-6601-2165 lower limb FMA:7184 lower limb and pelvic girdle https://orcid.org/0000-0002-6601-2165 lower limb and pelvis https://orcid.org/0000-0002-6601-2165 The subdivision of the skeleton of either the pectoral or pelvic girdle. Skeletal subdivision that is part of the appendage girdle region.[VSAO] relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: part_of subdivision of skeleton (UBERON:0010912)[VSAO] relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: proximally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO] AAO:0010686 VSAO:0000302 skeleton of girdle uberon UBERON:0010719 girdle skeleton The subdivision of the skeleton of either the pectoral or pelvic girdle. https://orcid.org/0000-0002-6601-2165 Skeletal subdivision that is part of the appendage girdle region.[VSAO] 2012-08-14 VSAO:0000302 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: part_of subdivision of skeleton (UBERON:0010912)[VSAO] 2012-08-14 VSAO:0000302 VSAO relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: proximally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO] 2012-08-14 VSAO:0000302 VSAO A bone that is part of an appendage girdle complex (i.e. any bone in a limb, fin or girdle). EMAPA:35494 MA:0000688 uberon bone of extended limb/fin region limb bone UBERON:0010740 bone of appendage girdle complex UBERONREF:0000003 A bone that is part of an appendage girdle complex (i.e. any bone in a limb, fin or girdle). UBERONREF:0000003 https://orcid.org/0000-0002-6601-2165 bone of extended limb/fin region UBERONREF:0000003 https://orcid.org/0000-0002-6601-2165 limb bone MA:0000688 UBERONREF:0000003 A bone that is part of a pelvic complex. Examples: pubis, ischium, fot phalanx, any tarsal bone, any bone of the pelvic fin or girdle. the MA class called 'hindlimb bone' belongs here, as it includes bones in the pelvic girdle EMAPA:32633 EMAPA:35934 MA:0000660 uberon hindlimb bone UBERON:0010742 bone of pelvic complex MA A bone that is part of a pelvic complex. Examples: pubis, ischium, fot phalanx, any tarsal bone, any bone of the pelvic fin or girdle. UBERONREF:0000003 https://orcid.org/0000-0002-6601-2165 the MA class called 'hindlimb bone' belongs here, as it includes bones in the pelvic girdle MA hindlimb bone MA:0000660 UBERONREF:0000003 Muscles of the pelvic girdle, hindlimb or pelvic fin. Muscles of the pelvic girdle, thigh, leg (crus), and foot (pes).[AAO] AAO:0000218 EMAPA:32634 FMA:9622 MA:0000663 pelvic girdle and hind limb muscles pelvic girdle or hind limb muscle pelvic girdle or posterior limb muscle uberon lower limb muscle muscle of lower limb muscle of pelvic girdle and leg UBERON:0010890 pelvic complex muscle prolog Muscles of the pelvic girdle, hindlimb or pelvic fin. https://orcid.org/0000-0002-6601-2165 Muscles of the pelvic girdle, thigh, leg (crus), and foot (pes).[AAO] 2012-06-20 AAO:0000218 AAO AAO:EJS pelvic girdle and hind limb muscles AAO:0000218 pelvic girdle or hind limb muscle https://orcid.org/0000-0002-6601-2165 pelvic girdle or posterior limb muscle https://orcid.org/0000-0002-6601-2165 lower limb muscle FMA:9622 muscle of lower limb FMA:9622 Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO] FMA:23879 SCTID:129140006 VSAO:0000042 skeletal subdivision uberon subdivision of skeleton (in vivo) UBERON:0010912 subdivision of skeleton cjm UBERONREF:0000003 VSAO Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. UBERONREF:0000003 https://orcid.org/0000-0002-6601-2165 Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO] 2012-08-14 VSAO:0000042 incorrect VSAO VSAO:curator skeletal subdivision VSAO:0000042 subdivision of skeleton (in vivo) FMA:23879 Skeletal element that forms around the notochord and is part of the vertebral column. we include a distinct subclass for bony vertebra In contrast to lampreys and jawed vertebrates, hagfishes were thought to lack vertebrae. Now, long overlooked vertebral rudiments have been analysed in hagfish, suggesting that vertebrae existed in the last common ancestor of all vertebrates.[well established][VHOG] vertebral Typically an endochondral element, in salamanders there is an argument that vertebral development is perichondral and not preformed in cartilage UBERON:0015005 vertebra skeletal element VHOG:0001143 VSAO:0000184 vertebra element vertebra endochondral element vertebral endochondral element uberon UBERON:0010913 vertebral element VSAO https://github.com/obophenotype/uberon/issues/82 VSAO cjm Skeletal element that forms around the notochord and is part of the vertebral column. GO_REF:0000034 VSAO:0000184 http://dx.plos.org/10.1371/journal.pone.0051070 https://github.com/obophenotype/uberon/issues/294 In contrast to lampreys and jawed vertebrates, hagfishes were thought to lack vertebrae. Now, long overlooked vertebral rudiments have been analysed in hagfish, suggesting that vertebrae existed in the last common ancestor of all vertebrates.[well established][VHOG] 2012-09-17 VHOG:0001143 VHOG DOI:10.1016/j.cub.2011.07.014 Janvier P, Comparative anatomy: all vertebrates do have vertebrae. Current Biology (2011) http://bgee.unil.ch/ vertebra skeletal element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern vertebra element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern vertebra endochondral element https://github.com/obophenotype/uberon/issues/82 vertebral endochondral element https://github.com/obophenotype/uberon/issues/82 Any muscle organ that is part of either the head or the neck. NCIT:C32716 UMLS:C0448281 muscle of head or neck uberon muscle of head and neck UBERON:0010959 craniocervical muscle prolog Any muscle organ that is part of either the head or the neck. http://orcid.org/0000-0002-6601-2165 UMLS:C0448281 ncithesaurus:Head_and_Neck_Muscle A cartilage element that is part of a splanchnocranium. EFO:0003689 TAO:0001460 ZFA:0001460 pharyngeal arch cartilages splanchnocranium cartilage uberon UBERON:0011004 pharyngeal arch cartilage ZFA ZFA A cartilage element that is part of a splanchnocranium. OBOL:automatic pharyngeal arch cartilages ZFA:0001460 splanchnocranium cartilage ZFA:0001460 A skeleton of pelvic girdle that is part of a right pelvic girdle region. FMA:87593 uberon UBERON:0011090 skeleton of right pelvic girdle A skeleton of pelvic girdle that is part of a right pelvic girdle region. OBOL:automatic A skeleton of pelvic girdle that is part of a left pelvic girdle region. FMA:87594 uberon UBERON:0011091 skeleton of left pelvic girdle A skeleton of pelvic girdle that is part of a left pelvic girdle region. OBOL:automatic A pelvic girdle region that is in the right side of a multicellular organism. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern FMA:16582 right pelvic girdle uberon UBERON:0011092 right pelvic girdle region A pelvic girdle region that is in the right side of a multicellular organism. OBOL:automatic right pelvic girdle FMA:16582 A pelvic girdle region that is in the left side of a multicellular organism. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern FMA:16583 left pelvic girdle uberon UBERON:0011093 left pelvic girdle region A pelvic girdle region that is in the left side of a multicellular organism. OBOL:automatic left pelvic girdle FMA:16583 The cartilaginous form of a vertebral element, a skeletal element that forms around the notochord and is part of the vertebral column. This class is a superclass of individual vertebral cartilage condensations. Note that EHDAA2 represents these as condensation groups EMAPA:32669 VHOG:0000584 vertebral cartilage condensation uberon UBERON:0011094 vertebra cartilage element The cartilaginous form of a vertebral element, a skeletal element that forms around the notochord and is part of the vertebral column. GO_REF:0000034 VSAO:0000184 http://dx.plos.org/10.1371/journal.pone.0051070 http://orcid.org/0000-0002-6601-2165 vertebra-like cartilage in hagfish are homologous to gnathostome vertebrae. mesenchymal cells express Pax1/9 and Twist PMC3157150 This class is a superclass of individual vertebral cartilage condensations. Note that EHDAA2 represents these as condensation groups EHDAA2 vertebral cartilage condensation VHOG:0000584 The pre-cartilaginous form of a vertebral element, a skeletal element that forms around the notochord and is part of the vertebral column. EMAPA:32671 VHOG:0000582 vertebral pre-cartilage condensation uberon UBERON:0011095 vertebra pre-cartilage condensation The pre-cartilaginous form of a vertebral element, a skeletal element that forms around the notochord and is part of the vertebral column. GO_REF:0000034 VSAO:0000184 http://dx.plos.org/10.1371/journal.pone.0051070 http://orcid.org/0000-0002-6601-2165 vertebral pre-cartilage condensation VHOG:0000582 A synovial joint that is part of a pelvic girdle region. FMA:35173 NCIT:C32890 UMLS:C0827002 joint of pelvic girdle pelvic girdle joint uberon UBERON:0011107 synovial joint of pelvic girdle A synovial joint that is part of a pelvic girdle region. OBOL:automatic UMLS:C0827002 ncithesaurus:Joint_of_the_Pelvic_Girdle pelvic girdle joint FMA:35173 A skeletal joint that connects a laryngeal cartilage. FMA:55100 joint of larynx laryngeal articulation uberon UBERON:0011120 laryngeal joint FMA A skeletal joint that connects a laryngeal cartilage. OBOL:automatic joint of larynx FMA:55100 laryngeal articulation FMA:55100 Joint in which the articulating bones or cartilages are connected by ligaments or fibrocartilage without an intervening synovial cavity. Examples: sagittal suture, inferior tibiofibular syndesmosis, costochondral joint, pubic symphysis. FMA:7491 solid joint uberon UBERON:0011134 nonsynovial joint FMA Joint in which the articulating bones or cartilages are connected by ligaments or fibrocartilage without an intervening synovial cavity. Examples: sagittal suture, inferior tibiofibular syndesmosis, costochondral joint, pubic symphysis. FMA:7491 solid joint FMA:7491 Subdivision of the skeletal system which consists of the axial skeleton plus associated joints. FMA:7483 uberon UBERON:0011137 axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton FMA Subdivision of the skeletal system which consists of the axial skeleton plus associated joints. https://orcid.org/0000-0002-6601-2165 Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. axial skeletal system FMA:302077 post-cranial axial skeletal system uberon UBERON:0011138 postcranial axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton FMA cjm Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. https://github.com/obophenotype/uberon/issues/44 https://orcid.org/0000-0002-6601-2165 axial skeletal system https://github.com/obophenotype/uberon/wiki/The-axial-skeleton Subdivision of skull that consists of the facial bones. EHDAA2:0002206 EHDAA:8361 EMAPA:18022 FMA:53673 MA:0000318 Wikipedia:Facial_skeleton facial skeleton uberon facial bone ossa facialia ossa faciei viscerocranium UBERON:0011156 facial skeleton http://upload.wikimedia.org/wikipedia/commons/7/77/Illu_facial_bones.jpg FMA FMA Subdivision of skull that consists of the facial bones. MP:0005274 Wikipedia:Facial_skeleton http://www.bartleby.com/107/37.html https://orcid.org/0000-0002-6601-2165 facial skeleton FMA:53673 facial bone MA:0000318 ossa facialia Wikipedia:Facial_skeleton ossa faciei Wikipedia:Facial_skeleton viscerocranium MA:0000318 The skull can be divided into two: the neurocranium and the facial skeleton FMA:54964 skull subdivision subdivision of skull uberon UBERON:0011158 primary subdivision of skull FMA The skull can be divided into two: the neurocranium and the facial skeleton http://orcid.org/0000-0002-6601-2165 skull subdivision FMA:54964 subdivision of skull FMA:54964 uberon UBERON:0011159 primary subdivision of cranial skeletal system FMA A bone that is part of a neurocranium [Automatically generated definition]. EMAPA:35238 MA:0001478 SCTID:120229002 chondrocranium bone uberon UBERON:0011164 neurocranium bone A bone that is part of a neurocranium [Automatically generated definition]. OBOL:automatic chondrocranium bone MA:0001478 A lamina propria that is part of a large intestine. FMA:15654 NCIT:C49298 UMLS:C1708644 lamina propria of mucosa of large intestine large intestinal lamina propria large intestine lamina propria uberon UBERON:0011189 lamina propria of large intestine FMA A lamina propria that is part of a large intestine. OBOL:automatic UMLS:C1708644 ncithesaurus:Large_Intestinal_Lamina_Propria lamina propria of mucosa of large intestine FMA:15654 large intestine lamina propria FMA:15654 A muscle layer that is part of a large intestine. FMA:14971 NCIT:C32927 UMLS:C0734205 muscular coat of large intestine muscular layer of large intestine muscularis externa of large intestine tunica muscularis intestini crassi uberon UBERON:0011198 muscle layer of large intestine FMA A muscle layer that is part of a large intestine. OBOL:automatic UMLS:C0734205 ncithesaurus:Large_Intestinal_Muscular_Coat muscular coat of large intestine FMA:14971 muscular layer of large intestine FMA:14971 muscularis externa of large intestine FMA:14971 tunica muscularis intestini crassi FMA:TA A multi cell part structure that is part of a central nervous system. FMA:83143 cell part cluster of neuraxis neuraxis layer uberon UBERON:0011215 central nervous system cell part cluster A multi cell part structure that is part of a central nervous system. OBOL:automatic cell part cluster of neuraxis FMA:83143 neuraxis layer FMA:83143 A subdivision of an anatomical system. FBbt:00007330 FMA:67509 SCTID:91690000 uberon UBERON:0011216 organ system subdivision FBbt FBbt A subdivision of an anatomical system. http://orcid.org/0000-0002-6601-2165 Muscles within the eye (bulbus oculi).[AAO] AAO:0010038 EMAPA:18808 FMA:49150 intrinsic muscle of eyeball intrinsic ocular muscle uberon UBERON:0011222 intra-ocular muscle EMAPA Muscles within the eye (bulbus oculi).[AAO] 2012-06-20 AAO:0010038 AAO AAO:EJS intrinsic ocular muscle EMAPA:18808 Synovial sac which surrounds parts of one or more tendons. Examples: synovial tendon sheath of manual digit 2, radial bursa. synovium BTO:0001823 FMA:40878 Wikipedia:Synovial_sheath uberon UBERON:0011233 Alternate def: A synovial sheath is a layer of a tendon sheath containing tendons in the hand and foot. They lie internal to the fibrous tendon sheaths. An example is the common synovial sheath for the flexor tendons. [Wikipedia:Synovial_sheath] synovial membrane of synovial tendon sheath Synovial sac which surrounds parts of one or more tendons. Examples: synovial tendon sheath of manual digit 2, radial bursa. FMA:45087 Wikipedia:Synovial_sheath synovium BTO:0001823 FMA:40877 uberon UBERON:0011234 fibrous membrane of synovial tendon sheath Subdivision of the skeletal system which consists of the appendicular skeleton plus associated joints. Skeletal system which consists of the appendicular skeleton plus associated joints.[VSAO] FMA:7484 VHOG:0001666 VSAO:0000306 uberon UBERON:0011249 appendicular skeletal system https://github.com/obophenotype/uberon/wiki/Appendages-and-the-appendicular-skeleton Subdivision of the skeletal system which consists of the appendicular skeleton plus associated joints. https://orcid.org/0000-0002-6601-2165 Skeletal system which consists of the appendicular skeleton plus associated joints.[VSAO] 2012-08-14 VSAO:0000306 VSAO https://orcid.org/0000-0002-6601-2165 The part of the trunk that is in the dorsum[cjm]. In humans, the subdivision of trunk which is demarcated from the trunk proper by the external surface of the posterolateral part of the rib cage, the anterior surface of the thoracic vertebral column and the posterior axillary lines, the external surface of the posterior abdominal wall; together with the trunk proper, it constitutes the trunk[FMA] EMAPA:35162 FMA:25056 MA:0000020 Wikipedia:Human_back back of trunk dorsal part of trunk dorsum of trunk trunk back uberon UBERON:0011270 dorsal trunk FMA FMA The part of the trunk that is in the dorsum[cjm]. UBERONREF:0000006 Wikipedia:Human_back back of trunk FMA:25056 dorsum of trunk FMA:25056 trunk back FMA:25056 compare with 'stratum basale of epidermis'. This class is the source for many adult structures - see WP2062. See also: 'enveloping layer of ectoderm' EHDAA2:0001845 uberon basal cell layer of skin outer epithelium of body UBERON:0011272 embryonic skin basal layer EHDAA2 EHDAA2 EHDAA2 outer epithelium of body Wikipathways:WP2062 A portion of gray matter that is part of a telencephalon. UBERON:0024186 BIRNLEX:1067 FMA:83911 predominantly gray regional part of telencephalon uberon UBERON:0011300 gray matter of telencephalon A portion of gray matter that is part of a telencephalon. OBOL:automatic predominantly gray regional part of telencephalon BIRNLEX:1067 A blood vasculature that is part of a head. Blood vessel part of cranial vasculature.[TAO] TAO:0005297 ZFA:0005297 cranial blood vessel set of blood vessels of head uberon cranial blood vessels UBERON:0011362 cranial blood vasculature A blood vasculature that is part of a head. OBOL:automatic Blood vessel part of cranial vasculature.[TAO] 2012-08-14 TAO:0005297 TAO ZFIN:curator cranial blood vessel ZFA:0005297 cranial blood vessels TAO:0005297 FMA:54364 SCTID:432899004 cavity of digestive tract cavity of gastrointestinal tract gastrointestinal tract lumen lumen of gastrointestinal tract uberon UBERON:0011565 lumen of gastrointestinal system gastrointestinal tract lumen FMA:54364 lumen of gastrointestinal tract FMA:54364 An anatomical cavity that is part of a esophagus. EMAPA:18380 FMA:9398 SCTID:322648002 cavity of eosophagus cavity of esophagus eosophageal cavity eosophageal lumen eosophagus lumen esophageal cavity esophageal lumen esophagus lumen uberon UBERON:0011566 lumen of esophagus FMA An anatomical cavity that is part of a esophagus. OBOL:automatic cavity of esophagus FMA:9398 esophageal cavity FMA:9398 esophageal lumen FMA:9398 esophagus lumen FMA:9398 The collection of all skeletal elements in an individual limb or fin. Skeletal subdivision that is part of the paired limb/fin.[VSAO] VSAO:0000301 limb/fin skeleton skeletal parts of limb/fin skeleton of limb/fin uberon UBERON:0011582 paired limb/fin skeleton ISBN:9780878932504 The collection of all skeletal elements in an individual limb or fin. https://orcid.org/0000-0002-6601-2165 Skeletal subdivision that is part of the paired limb/fin.[VSAO] 2012-08-14 VSAO:0000301 VSAO GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 limb/fin skeleton VSAO:0000301 Anatomical structure that is an aggregation of similar cells from which cartilages and bones form, and from which chondrogenesis and osteogenesis are initiated during repair and/or regeneration. (Hall and Miyake 1995). consider obsoleting, coordinate with VSAO VSAO:0000006 XAO:0004021 uberon UBERON:0011585 cell condensation VSAO Anatomical structure that is an aggregation of similar cells from which cartilages and bones form, and from which chondrogenesis and osteogenesis are initiated during repair and/or regeneration. (Hall and Miyake 1995). GO_REF:0000034 PSPUB:0000170 VSAO:0000006 http://dx.plos.org/10.1371/journal.pone.0051070 A subdivision of the head that corresponds to the jaw skeleton, containing both soft tissue, skeleton and teeth (when present). The jaw region is divided into upper and lower regions. EMAPA:32905 NCIT:C114916 uberon UBERON:0011595 jaw region http://eol.org/collections/11578 EMAPA FMA-abduced ZFA-abduced A subdivision of the head that corresponds to the jaw skeleton, containing both soft tissue, skeleton and teeth (when present). The jaw region is divided into upper and lower regions. http://orcid.org/0000-0002-6601-2165 EHDAA2:0001020 lower jaw future lip uberon UBERON:0011596 future lower lip EHDAA2 Wikipedia:Mandibular_prominence lower jaw future lip EHDAA2:0001020 An epithelium that develops_from a ectoderm and is part of a oral epithelium. EHDAA2:0004137 uberon UBERON:0011642 oral epithelium from ectoderm EHDAA2 EHDAA2 An epithelium that develops_from a ectoderm and is part of a oral epithelium. OBOL:automatic AAO:0000247 EFO:0003511 TAO:0000236 XAO:0003269 ZFA:0000236 mandibular muscle mandibular muscles uberon UBERON:0011648 jaw muscle mandibular muscle TAO:0000236 mandibular muscles TAO:0000236 A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column. Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem axial subdivision of organism uberon body segment main body segment UBERON:0011676 subdivision of organism along main body axis A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column. https://orcid.org/0000-0002-6601-2165 A vertebra in the trunk region. For tetrapods, includes lumbar and thoracic vertebrae. Excludes caudal/coccygeal vertebra, which are located posteriorly. In tetrapods this includes thoracic, lumbar and sacral vertebrae, and excludes the cervical vertebrae, which are located anteriorly. thoracolumbar vertebra uberon presacral vertebra UBERON:0011677 trunk vertebra true A vertebra in the trunk region. For tetrapods, includes lumbar and thoracic vertebrae. Excludes caudal/coccygeal vertebra, which are located posteriorly. In tetrapods this includes thoracic, lumbar and sacral vertebrae, and excludes the cervical vertebrae, which are located anteriorly. UBERONREF:0000006 presacral vertebra http://orcid.org/0000-0002-6601-2165 A cardiovascular system that is part of a conceptus. EHDAA2:0000216 FMA:305965 NCIT:C34148 conceptus cardiovascular system uberon embryonic circulatory system fetal circulatory system UBERON:0011695 embryonic cardiovascular system A cardiovascular system that is part of a conceptus. OBOL:automatic The left nerve is longer than the right, because it crosses under the arch of the aorta at the ligamentum arteriosum.[WP] EMAPA:25350 FMA:14469 MA:0001107 SCTID:280300006 left recurrent laryngeal branch left recurrent laryngeal nerve vagus X nerve left recurrent laryngeal branch uberon UBERON:0011766 left recurrent laryngeal nerve https://upload.wikimedia.org/wikipedia/commons/6/64/Recurrent_laryngeal_nerve.svg left recurrent laryngeal branch EMAPA:25350 left recurrent laryngeal nerve FMA:14469 vagus X nerve left recurrent laryngeal branch MA:0001107 EMAPA:17275 FMA:14468 MA:0001108 SCTID:280299003 right recurrent laryngeal branch right recurrent laryngeal nerve vagus X nerve right recurrent laryngeal branch uberon UBERON:0011767 right recurrent laryngeal nerve right recurrent laryngeal branch EMAPA:17275 right recurrent laryngeal nerve FMA:14468 vagus X nerve right recurrent laryngeal branch MA:0001108 An anatomical space that is part of a bone of lower jaw. AAO:0000273 uberon UBERON:0011772 lower jaw opening An anatomical space that is part of a bone of lower jaw. OBOL:automatic A cranial nerve nucleus that is associated with a vagus nerve. FMA:54573 SCTID:362467005 nucleus of Xth nerve nucleus of vagal X nerve nucleus of vagal nerve nucleus of vagus nerve tenth cranial nerve nucleus vagal X nucleus vagal nucleus vagus nucleus uberon nodosal nucleus UBERON:0011775 vagus nerve nucleus A cranial nerve nucleus that is associated with a vagus nerve. OBOL:automatic nucleus of vagus nerve FMA:54573 tenth cranial nerve nucleus FMA:54573 vagal X nucleus http://orcid.org/0000-0002-6601-2165 vagal nucleus http://orcid.org/0000-0002-6601-2165 vagus nucleus http://orcid.org/0000-0002-6601-2165 nodosal nucleus http://orcid.org/0000-0002-6601-2165 A neural nucleus that is part of the spinal cord. FMA:77011 spinal cord nucleus uberon UBERON:0011777 nucleus of spinal cord A neural nucleus that is part of the spinal cord. http://orcid.org/0000-0002-6601-2165 spinal cord nucleus FMA:77011 A nerve that is part of a head. uberon cephalic nerve head nerve UBERON:0011779 nerve of head region A nerve that is part of a head. OBOL:automatic Ectodermal placode that does not develop into a component of the nervous system. uberon UBERON:0011814 non-neurogenic ectodermal placode cjm Ectodermal placode that does not develop into a component of the nervous system. PMID:11523831 http://orcid.org/0000-0002-6601-2165 An anatomical junction that divides and overlaps with and atrium and a ventricle in the heart. EHDAA2:0004149 FMA:85125 uberon AV region AV segment atrial ventricular junction atrioventricular junction atrioventricular segment UBERON:0011820 atrioventricular region An anatomical junction that divides and overlaps with and atrium and a ventricle in the heart. http://orcid.org/0000-0002-6601-2165 AV region PMID:21234997 AV segment PMID:21234997 atrial ventricular junction GO:0003294 atrioventricular junction FMA:85125 GO:0003294 atrioventricular segment PMID:21234997 Connective tissue, which consists of a population of connective tissue cells, the intercellular matrix of which contains an irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, mucoid tissue, connective tissue of peritoneum, connective tissue of fibrous pericardium. FMA:20107 uberon UBERON:0011821 irregular connective tissue FMA Connective tissue, which consists of a population of connective tissue cells, the intercellular matrix of which contains an irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, mucoid tissue, connective tissue of peritoneum, connective tissue of fibrous pericardium. FMA:20107 Irregular connective tissue is an irregular connective tissue, the intercellular matrix of which contains a dense irregular network of collagen and elastic fiber bundles. Examples: connective tissue of peritoneum, connective tissue of fibrous pericardium. Tissue characterized by a thick, random arrangement of collagen and elastin fibers with very few cells. The majority of the cells are fibroblasts, but mast cells and macrophages may also be seen. It is found in the dermis, periosteum, perichondrium, capsules of organs and sheaths of nerves and muscles[NCIT] FMA:20109 NCIT:C32882 UMLS:C0738366 Wikipedia:Dense_irregular_connective_tissue irregular dense connective tissue typus irregularis (textus connectivus collagenosus compactus) uberon UBERON:0011822 dense irregular connective tissue FMA Irregular connective tissue is an irregular connective tissue, the intercellular matrix of which contains a dense irregular network of collagen and elastic fiber bundles. Examples: connective tissue of peritoneum, connective tissue of fibrous pericardium. FMA:20109 Wikipedia:Dense_irregular_connective_tissue Tissue characterized by a thick, random arrangement of collagen and elastin fibers with very few cells. The majority of the cells are fibroblasts, but mast cells and macrophages may also be seen. It is found in the dermis, periosteum, perichondrium, capsules of organs and sheaths of nerves and muscles[NCIT] 2012-08-29 ncithesaurus:Irregular_Dense_Connective_Tissue NCIT UMLS:C0738366 ncithesaurus:Irregular_Dense_Connective_Tissue typus irregularis (textus connectivus collagenosus compactus) FMA:20109 Dense connective tissue is mainly composed of collagen type I. Crowded between the collagen fibers are rows of fibroblasts, fiber-forming cells, that manufacture the fibers. Dense connective tissue forms strong, rope-like structures such as tendons and ligaments. Tendons attach skeletal muscles to bones; ligaments connect bones to bones at joints. Ligaments are more stretchy and contain more elastic fibers than tendons. Dense connective tissue also make up the lower layers of the skin (dermis), where it is arranged in sheets our OWL definition states that this is differentiated from other connective tissue types by virtue of the fact that the collage fiber component predominates, as opposed to cells and fluid. Connective tissue in which the fibrous component predominates. The cells, ground substance, and tissue fluid represent a minor component[NCIT] AAO:0000121 NCIT:C32450 UMLS:C1511770 Wikipedia:Dense_connective_tissue uberon UBERON:0011823 dense connective tissue Dense connective tissue is mainly composed of collagen type I. Crowded between the collagen fibers are rows of fibroblasts, fiber-forming cells, that manufacture the fibers. Dense connective tissue forms strong, rope-like structures such as tendons and ligaments. Tendons attach skeletal muscles to bones; ligaments connect bones to bones at joints. Ligaments are more stretchy and contain more elastic fibers than tendons. Dense connective tissue also make up the lower layers of the skin (dermis), where it is arranged in sheets Wikipedia:Dense_connective_tissue Connective tissue in which the fibrous component predominates. The cells, ground substance, and tissue fluid represent a minor component[NCIT] 2012-08-29 ncithesaurus:Dense_Connective_Tissue NCIT UMLS:C1511770 ncithesaurus:Dense_Connective_Tissue FMA:75634 SCTID:363130003 uberon UBERON:0011824 fibrous connective tissue FMA Irregular connective tissue, the intercellular matrix of which contains a sparse irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, neuroglial tissue, mucoid tissue. FMA:19783 NCIT:C33007 UMLS:C1253917 Wikipedia:Loose_connective_tissue textus connectivus collagenosus laxus textus connectivus laxus uberon UBERON:0011825 loose connective tissue FMA Irregular connective tissue, the intercellular matrix of which contains a sparse irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, neuroglial tissue, mucoid tissue. FMA:19783 UMLS:C1253917 ncithesaurus:Loose_Connective_Tissue textus connectivus collagenosus laxus FMA:19783 FMA:TA textus connectivus laxus FMA:19783 FMA:TA An acinus that is part of a exocrine gland. exocrine gland acinus uberon UBERON:0011858 acinus of exocrine gland An acinus that is part of a exocrine gland. OBOL:automatic the FMA class specifically refers to ureter FMA:63212 MESH:D024022 NCIT:C32339 NIF_Subcellular:sao7547390221 uberon UBERON:0011860 collection of collagen fibrils ZFA the FMA class specifically refers to ureter FMA The connective tissue bundles in the extracellular matrix of aorta tissue that are composed of collagen, and play a role in tissue strength and elasticity uberon UBERON:0011861 aorta collagen fibril The connective tissue bundles in the extracellular matrix of aorta tissue that are composed of collagen, and play a role in tissue strength and elasticity MP:0011640 The connective tissue bundles in the extracellular matrix of pulmonary tissue that are composed of collagen, and play a role in tissue strength and elasticity uberon UBERON:0011862 pulmonary collagen fibril The connective tissue bundles in the extracellular matrix of pulmonary tissue that are composed of collagen, and play a role in tissue strength and elasticity MP:0011641 The connective tissue bundles in the extracellular matrix of bone tissue that are composed of collagen, and play a role in tissue strength and elasticity uberon UBERON:0011863 bone collagen fibril The connective tissue bundles in the extracellular matrix of bone tissue that are composed of collagen, and play a role in tissue strength and elasticity MP:0011642 The connective tissue bundles in the extracellular matrix of tendon tissue that are composed of collagen, and play a role in tissue strength and elasticity uberon UBERON:0011864 tendon collagen fibril The connective tissue bundles in the extracellular matrix of tendon tissue that are composed of collagen, and play a role in tissue strength and elasticity MP:0011643 The connective tissue bundles in the extracellular matrix of corneal stroma that are composed of collagen, and play a role in tissue strength and elasticity uberon UBERON:0011865 corneal stroma collagen fibril The connective tissue bundles in the extracellular matrix of corneal stroma that are composed of collagen, and play a role in tissue strength and elasticity MP:0011650 A muscle layer that is part of a wall of esophagus. In the upper esophagus, part of the externa is skeletal muscle, rather than smooth muscle FMA:62998 muscle coat of esophagus muscular coat of oesophagus muscular layer of oesophagus tela muscularis (oesophagus) tunica muscularis esophagi tunica muscularis oesophageae uberon UBERON:0011878 muscle layer of esophagus upper part Wikipedia:Muscular_layer A muscle layer that is part of a wall of esophagus. OBOL:automatic In the upper esophagus, part of the externa is skeletal muscle, rather than smooth muscle WP muscle coat of esophagus FMA:62998 muscular coat of oesophagus FMA:62998 muscular layer of oesophagus FMA:62998 tela muscularis (oesophagus) FMA:62998 FMA:TA tunica muscularis esophagi tunica muscularis oesophageae FMA:TA Front (ventral) portion of the vascular, pigmentary, or middle coat of the eye, including the ciliary body and the iris. EMAPA:37417 SCTID:280656002 Haller tunica vascula anterior part of uveal tract anterior uveal tract anterior vascular layer of the eyeball anterior vascular tunic of the eye tunica vasculosa bulbosa ventral uveal tract uberon ciliary body and iris vasculosa oculi UBERON:0011892 anterior uvea ZFA MP lexical Front (ventral) portion of the vascular, pigmentary, or middle coat of the eye, including the ciliary body and the iris. MP:0005194 EMAPA:37417 MA:th Haller tunica vascula MP:0005194 tunica vasculosa bulbosa MP:0005194 vasculosa oculi MP:0005194 Epimysium is a layer of connective tissue which ensheaths the entire muscle. It is composed of dense irregular connective tissue. It is continuous with fascia and other connective tissue wrappings of muscle including the endomysium, and perimysium. It is also continuous with tendons where it becomes thicker and collagenous. The Epimysium also protects muscles from friction against other muscles and bones FMA:9726 NCIT:C32527 UMLS:C0504096 Wikipedia:Epimysium fascia of muscle organ uberon epimysia UBERON:0011899 epimysium FMA FMA Epimysium is a layer of connective tissue which ensheaths the entire muscle. It is composed of dense irregular connective tissue. It is continuous with fascia and other connective tissue wrappings of muscle including the endomysium, and perimysium. It is also continuous with tendons where it becomes thicker and collagenous. Wikipedia:Epimysium UMLS:C0504096 ncithesaurus:Epimysium fascia of muscle organ FMA:9726 epimysia Wikipedia:Epimysium A region of the stomach that is lined with glandular epithelium. as currently defined, this would include the cardiac antrum; however, the intent may be to exclude the cardiac glands and in mice for this to be part of the region distal to the margo plicatus EMAPA:17623 MA:0001613 NCIT:C77661 SCTID:27633001 UMLS:C0227197 uberon glandular stomach UBERON:0011953 stomach glandular region A region of the stomach that is lined with glandular epithelium. http://orcid.org/0000-0002-6601-2165 UMLS:C0227197 ncithesaurus:Glandular_Stomach The aggregate of the coelemic cavity lumen plus the membranes that line the lumen. EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining. coelomic EHDAA2:0004731 Wikipedia:Coelom enterocoelom haemocoelom schizocoelom uberon coelem coelomic cavity UBERON:0011997 coelom EHDAA2 The aggregate of the coelemic cavity lumen plus the membranes that line the lumen. UBERON:cjm Wikipedia:Body_cavity Wikipedia:Coelom Wikipedia:Acoelomorpha enterocoelom NCBITaxon:33511 coelomic cavity EHDAA2:0004731 The cavity within a myotome The central cavity within the mesoderm is the paired primary or embryonic coelom. Parts of the embryonic coelom often become enclosed in the mesoderm, forming a myocoel within the epimere, a nephrocoel within the mesomere, and simple coelom (body cavity) within the lateral plate mesoderm.[well established][VHOG] EMAPA:31134 VHOG:0001283 uberon UBERON:0012054 myocoele The cavity within a myotome http://medical-dictionary.thefreedictionary.com/myocoele The central cavity within the mesoderm is the paired primary or embryonic coelom. Parts of the embryonic coelom often become enclosed in the mesoderm, forming a myocoel within the epimere, a nephrocoel within the mesomere, and simple coelom (body cavity) within the lateral plate mesoderm.[well established][VHOG] 2012-09-17 VHOG:0001283 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.166 and Figure 5.6 http://bgee.unil.ch/ Bone that forms as a replacement of another structural tissue. Bone that forms as a replacement of another structural tissue.[TAO] This class was introduced to be consistent with the ZFA hierarchy. The corresponding TAO term was obsoleted, and never introduced into VSAO. Note that VSAO does have replacement element. AAO:0010768 TAO:0001637 ZFA:0001628 replacement bones uberon UBERON:0012075 replacement bone ZFA ZFA Bone that forms as a replacement of another structural tissue. ZFA:0001628 Bone that forms as a replacement of another structural tissue.[TAO] 2012-08-14 TAO:0001637 TAO TAO:wd This class was introduced to be consistent with the ZFA hierarchy. The corresponding TAO term was obsoleted, and never introduced into VSAO. Note that VSAO does have replacement element. ZFA replacement bones ZFA:0001628 Anatomical system that consists of the integumental system plus all mucosae and submucosae. uberon dermatological system UBERON:0012125 dermatological-muscosal system Anatomical system that consists of the integumental system plus all mucosae and submucosae. https://github.com/obophenotype/uberon/issues/53 dermatological system OBI:MC A primordium that has the potential to develop into a stomach. EFO:0002580 NCIT:C34305 UMLS:C1514976 uberon stomach endoderm UBERON:0012172 stomach primordium A primordium that has the potential to develop into a stomach. OBOL:automatic UMLS:C1514976 ncithesaurus:Stomach_Primordium stomach endoderm EFO:0002580 A zone of skin that is part of a craniocervical region. EMAPA:37276 MA:0000574 NCIT:C12294 UMLS:C1522650 uberon UBERON:0012180 head or neck skin A zone of skin that is part of a craniocervical region. OBOL:automatic EMAPA:37276 MA:th UMLS:C1522650 ncithesaurus:Skin_of_the_Scalp_and_Neck The veins that run parallel to the phrenic arteries which include the two superior and two inferior phrenic veins. EMAPA:37180 MA:0002194 NCIT:C53062 UMLS:C1709532 uberon UBERON:0012193 phrenic vein The veins that run parallel to the phrenic arteries which include the two superior and two inferior phrenic veins. ncithesaurus:Phrenic_Vein EMAPA:37180 MA:th UMLS:C1709532 ncithesaurus:Phrenic_Vein An artery that originates from the abdominal aorta SCTID:281470000 abdominal artery artery of abdomen uberon UBERON:0012254 abdominal aorta artery An artery that originates from the abdominal aorta Wikipedia:Abdominal_aorta#Branches https://orcid.org/0000-0002-6601-2165 An epithelium that consists of columnar epithelial cells. Columnar epithelia are epithelial cells whose heights are at least four times their width. Columnar epithelia are divided into simple (or unilayered), and the rarer stratified (or multi-layered).[WP, modified] Wikipedia:Columnar_epithelium uberon UBERON:0012274 columnar epithelium An epithelium that consists of columnar epithelial cells. Columnar epithelia are epithelial cells whose heights are at least four times their width. Columnar epithelia are divided into simple (or unilayered), and the rarer stratified (or multi-layered).[WP, modified] Wikipedia:Columnar_epithelium Epithelium that derives from the mesoderm. [Automatically generated definition]. FMA:86452 mesoderm-derived epithelium mesoepithelium uberon UBERON:0012275 meso-epithelium Epithelium that derives from the mesoderm. [Automatically generated definition]. OBOL:automatic One of five swellings formed during the development of the face FMA:293103 SCTID:89066004 uberon embryonic facial process facial primordium primordium of face UBERON:0012314 embryonic facial prominence One of five swellings formed during the development of the face http://www.indiana.edu/~anat550/hnanim/face/face.html An artery of the neck EMAPA:37075 NCIT:C52850 UMLS:C1707349 uberon UBERON:0012320 cervical artery An artery of the neck https://orcid.org/0000-0002-6601-2165 EMAPA:37075 MA:th UMLS:C1707349 ncithesaurus:Cervical_Artery The deep cervical artery (Profunda cervicalis) is an artery of the neck. FMA:10659 SCTID:244223002 Wikipedia:Deep_cervical_artery uberon profunda cervicalis UBERON:0012321 deep cervical artery FMA The deep cervical artery (Profunda cervicalis) is an artery of the neck. Wikipedia:Deep_cervical_artery profunda cervicalis Wikipedia:Deep_cervical_artery A bone element that is part of a jaw region. Do not manually classify under here - bones are automatically classified EMAPA:35453 MA:0003130 SCTID:369003004 jaw bone uberon UBERON:0012360 bone of jaw A bone element that is part of a jaw region. OBOL:automatic EHDAA2:0004588 uberon UBERON:0012361 internal anal region EHDAA2 A muscle layer that is part of an intestine. FMA:15697 intestinal muscularis propria muscularis externa of intestine uberon smooth muscle of intestine UBERON:0012367 muscle layer of intestine FMA A muscle layer that is part of an intestine. OBOL:automatic intestinal muscularis propria FMA:15697 muscularis externa of intestine FMA:15697 A layer of tissue between the muscularis and serosa. FMA:45636 NCIT:C94494 SCTID:2255006 UMLS:C0225334 Wikipedia:Subserosa uberon UBERON:0012375 Contains nerves, blood vessels, lymphatics and lymph nodes subserosa A layer of tissue between the muscularis and serosa. Wikipedia:Subserosa UMLS:C0225334 ncithesaurus:Subserosa EMAPA:37567 MA:0001802 uberon UBERON:0012416 respiratory system arterial smooth muscle EMAPA:37567 MA:th A smooth muscle tissue that is part of a respiratory system venous blood vessel. EMAPA:37586 MA:0001812 uberon UBERON:0012418 respiratory system venous smooth muscle A smooth muscle tissue that is part of a respiratory system venous blood vessel. OBOL:automatic EMAPA:37586 MA:th Blood-forming tissue, consisting of reticular fibers and cells. Bone marrow in humans, kidney interstitium in Danio, within a stroma of reticuloendothelial tissue CALOHA:TS-2142 FMA:14073 NCIT:C13051 UMLS:C0229619 haemopoietic tissue hematopoietic tissue hemopoietic tissue textus haemopoieticus bone marrow tissue uberon UBERON:0012429 hematopoietic tissue FMA defitional Blood-forming tissue, consisting of reticular fibers and cells. http://encyclopedia2.thefreedictionary.com/hematopoietic+tissue UMLS:C0229619 ncithesaurus:Hematopoietic_Tissue haemopoietic tissue FMA:14073 hematopoietic tissue FMA:14073 hemopoietic tissue FMA:14073 textus haemopoieticus FMA:14073 bone marrow tissue NCBITaxon:9606 The sclera and cornea form the fibrous tunic of the bulb of the eye; the sclera is opaque, and constitutes the posterior five-sixths of the tunic; the cornea is transparent, and forms the anterior sixth. tunica fibrosa FMA:58102 SCTID:361318005 Wikipedia:Fibrous_tunic_of_eyeball fibrous layer of eyeball uberon corneosclera fibrous tunic UBERON:0012430 tunica fibrosa of eyeball FMA The sclera and cornea form the fibrous tunic of the bulb of the eye; the sclera is opaque, and constitutes the posterior five-sixths of the tunic; the cornea is transparent, and forms the anterior sixth. Wikipedia:Fibrous_tunic_of_eyeball DOI:10.1177/0192623311409597 fibrous layer of eyeball FMA:58102 corneosclera Wikipedia:Fibrous_tunic_of_eyeball fibrous tunic Wikipedia:Fibrous_tunic_of_eyeball A anatomical space that is enclosed by a cloaca. the ZFA class belongs here as it is an anatomical space. See https://sourceforge.net/p/obo/zebrafish-anatomy-zfa-term-requests/102/ TAO:0000330 ZFA:0000330 cloaca lumen cloacal chamber uberon UBERON:0012463 cloacal lumen cjm A anatomical space that is enclosed by a cloaca. OBOL:automatic the ZFA class belongs here as it is an anatomical space. See https://sourceforge.net/p/obo/zebrafish-anatomy-zfa-term-requests/102/ ZFA cloaca lumen ZFA:0000330 cloacal chamber ZFA:0000330 The opening of the cloacal chamber to the outside of the organism. Birds maintain a single cloacal opening throughout their lives. cloacal opening uberon cloacal orifice vent UBERON:0012464 cloacal vent The opening of the cloacal chamber to the outside of the organism. Birds maintain a single cloacal opening throughout their lives. http://orcid.org/0000-0002-6601-2165 A anatomical space that is enclosed by a terminal part of digestive tract. includes the cloacal lumen, in species where this is present uberon UBERON:0012465 lumen of terminal part of digestive tract A anatomical space that is enclosed by a terminal part of digestive tract. OBOL:automatic EHDAA2:0000472 EMAPA:16054 VHOG:0000767 uberon extraembryonic cavities UBERON:0012466 extraembryonic cavity extraembryonic cavities EHDAA2:0000472 An anatomical space with no opening to another space or to the exterior. AEO:0000222 closed anatomical space uberon UBERON:0012467 enclosed anatomical space An anatomical space with no opening to another space or to the exterior. AEO:0000222 EHDAA2:0004589 uberon UBERON:0012469 external anal region EHDAA2 The collection of all skeletal elements in a pelvic complex - i.e. the combination of free limb or fin plus pelvic girdle. FMA:24140 uberon bones of lower limb lower limb skeleton ossa membri inferioris pelvic complex skeleton set of bones of lower limb skeleton of posterior limb/fin and girdle UBERON:0012476 skeleton of pelvic complex FMA The collection of all skeletal elements in a pelvic complex - i.e. the combination of free limb or fin plus pelvic girdle. https://orcid.org/0000-0002-6601-2165 bones of lower limb FMA:24140 lower limb skeleton FMA:24140 ossa membri inferioris FMA:TA pelvic complex skeleton https://orcid.org/0000-0002-6601-2165 set of bones of lower limb FMA:24140 skeleton of posterior limb/fin and girdle https://orcid.org/0000-0002-6601-2165 The posterior region of the neck, including the suboccipital region. nuchal nape BTO:0000957 FMA:24189 SCTID:182326009 SCTID:304036007 back of neck nape of neck neck back nucha nuchal region posterior cervical region posterior neck region posterior part of neck regio cervicalis posterior uberon hindneck UBERON:0012477 dorsal part of neck FMA FMA FMA The posterior region of the neck, including the suboccipital region. MP:0012723 nape BTO:0000957 back of neck FMA:24189 neck back FMA:24189 nucha FMA:24189 nuchal region FMA:24189 posterior cervical region FMA:24189 posterior neck region FMA:24189 posterior part of neck FMA:24189 regio cervicalis posterior FMA:TA A gland that is part of a cloaca. uberon UBERON:0012478 cloacal gland A gland that is part of a cloaca. OBOL:automatic A mucosa that is part of a cloaca [Automatically generated definition]. UBERON:0003349 cloaca mucosa cloaca mucosa of organ cloaca mucous membrane cloaca organ mucosa cloacal mucous membrane mucosa of cloaca mucosa of organ of cloaca mucous membrane of cloaca organ mucosa of cloaca uberon UBERON:0012480 cloacal mucosa A mucosa that is part of a cloaca [Automatically generated definition]. OBOL:automatic An epithelium that is part of a cloaca. cloacal epithelium (cle) (syn: cloacal endoderm) (TS17-TS20): the cloacal epithelium is derived from endoderm and lines the cloacal cavity. It is marked by Shh and Cdh1 and lines the cloacal lumen. The cloacal epithelium gives rise to the urogenital sinus epithelium, hindgut epithelium and the urethral plate epithelium. EMAPA:27577 EMAPA:36070 ZFA:0005783 uberon cloacal endoderm UBERON:0012481 cloacal epithelium An epithelium that is part of a cloaca. http://orcid.org/0000-0002-6601-2165 cloacal epithelium (cle) (syn: cloacal endoderm) (TS17-TS20): the cloacal epithelium is derived from endoderm and lines the cloacal cavity. It is marked by Shh and Cdh1 and lines the cloacal lumen. The cloacal epithelium gives rise to the urogenital sinus epithelium, hindgut epithelium and the urethral plate epithelium. EMAPA:27577 cloacal endoderm EMAPA:27577 A submucosa that is part of a cloaca [Automatically generated definition]. cloaca submucosa cloacal submucosa uberon UBERON:0012482 submucosa of cloaca A submucosa that is part of a cloaca [Automatically generated definition]. OBOL:automatic A serous membrane that is part of a cloaca [Automatically generated definition]. cloaca serosa cloaca serous membrane cloacal serosa serous membrane of cloaca visceral peritoneum of cloaca uberon UBERON:0012483 serosa of cloaca A serous membrane that is part of a cloaca [Automatically generated definition]. OBOL:automatic A muscular coat that is part of a cloaca. muscularis externa of cloaca uberon smooth muscle of cloaca UBERON:0012486 muscle layer of cloaca A muscular coat that is part of a cloaca. OBOL:automatic A muscular coat that is part of a colon. EMAPA:27383 FMA:14986 MA:0003198 SCTID:362158003 colonic muscularis propria muscular coat of colon muscular layer of colon muscularis externa of colon tunica muscularis coli uberon colon muscularis UBERON:0012489 muscle layer of colon A muscular coat that is part of a colon. OBOL:automatic colonic muscularis propria FMA:14986 muscular coat of colon FMA:14986 muscular layer of colon FMA:14986 muscularis externa of colon FMA:14986 tunica muscularis coli FMA:TA colon muscularis MA:0003198 A muscular coat that is part of a anal canal. FMA:15708 SCTID:362171000 anal canal muscularis propria anal muscularis propria muscular coat of anal canal muscular layer of anal canal muscularis externa of anal canal muscularis propria of anal canal uberon UBERON:0012490 muscle layer of anal canal A muscular coat that is part of a anal canal. OBOL:automatic anal muscularis propria FMA:15708 muscularis propria of anal canal FMA:15708 A adventitia that is part of a esophagus. FMA:63006 SCTID:85950006 adventitia of oesophagus adventitious layer of esophagus esophageal adventitia esophagus adventitia tunica adventitia (esophagus) tunica adventitia oesophageae uberon UBERON:0012504 adventitia of esophagus A adventitia that is part of a esophagus. OBOL:automatic adventitia of oesophagus FMA:63006 adventitious layer of esophagus FMA:63006 esophageal adventitia FMA:63006 esophagus adventitia FMA:63006 tunica adventitia (esophagus) FMA:63006 tunica adventitia oesophageae FMA:TA A vein that is part of a abdomen. TODO mirror representation of abdominal aorta this class groups all veins that are in the abdomen. The term 'abdominal vein' may have specific meanings in different contexts. The lateral abdominal veins are present in fishes but usually merged or absent in tetrapods; in amphibians, the L&R abdominal veins merge into the ventral abdominal vein SCTID:281473003 abdominal vein uberon UBERON:0013126 vein of abdomen A vein that is part of a abdomen. OBOL:automatic A vein that drains a lip. SCTID:367664002 labial vein of face lip vein vena labialis uberon labial vein UBERON:0013136 vein of lip FMA A vein that drains a lip. OBOL:automatic lip vein OBOL:automatic vena labialis Any vein within the general circulation that transports blood back to the right atrium of the heart. FMA:66644 NCIT:C33719 SCTID:244389004 UMLS:C0447117 systemic venous tree organ part uberon UBERON:0013140 systemic vein Any vein within the general circulation that transports blood back to the right atrium of the heart. ncithesaurus:Systemic_Vein UMLS:C0447117 ncithesaurus:Systemic_Vein systemic venous tree organ part FMA:66644 A gland that is part of a foregut-midgut junction. EHDAA2:0000574 EMAPA:17065 gland of foregut-midgut junction uberon UBERON:0013158 foregut-midgut junction gland A gland that is part of a foregut-midgut junction. OBOL:automatic gland of foregut-midgut junction EMAPA:17065 The secretory unit of a serous gland. The acinar portion is composed of serous secreting cells. FMA:86279 acinus of serous gland uberon UBERON:0013232 serous acinus The secretory unit of a serous gland. The acinar portion is composed of serous secreting cells. http://orcid.org/0000-0002-6601-2165 http://www.siumed.edu/~dking2/intro/glands.htm Anatomical cavity that is the lumen of the skull and contains the brain. EMAPA:37497 FMA:9644 MA:0003061 NCIT:C77638 SCTID:264452006 UMLS:C0230041 Wikipedia:Cranial_cavity http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=2806 cavitas cranii uberon intracranial cavity intracranial space UBERON:0013411 cranial cavity http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg Wikipedia Anatomical cavity that is the lumen of the skull and contains the brain. UBERON:cjm EMAPA:37497 MA:th UMLS:C0230041 ncithesaurus:Cranial_Cavity cavitas cranii FMA:9644 FMA:TA intracranial cavity Wikipedia:Cranial_cavity intracranial space Wikipedia:Cranial_cavity A blood vessel endothelium that is part of a lung [Automatically generated definition]. BTO:0004128 CALOHA:TS-0573 uberon respiratory endothelium UBERON:0013479 lung endothelium A blood vessel endothelium that is part of a lung [Automatically generated definition]. OBOL:automatic respiratory endothelium BTO:0004128 A caudal vertebra endochondral element that is composed primarily of cartilage tissue. UBERON:0013517 EHDAA2:0000260 EMAPA:18044 coccygeal vertebra cartilage element coccygeal vertebral cartilage condensation group tail vertebral cartilage condensation uberon UBERON:0013503 caudal vertebra cartilage element A caudal vertebra endochondral element that is composed primarily of cartilage tissue. OBOL:automatic coccygeal vertebra cartilage element http://orcid.org/0000-0002-6601-2165 coccygeal vertebral cartilage condensation group EHDAA2:0000260 tail vertebral cartilage condensation EMAPA:18044 A caudal vertebra endochondral element that is composed primarily of a pre-cartilage condensation. UBERON:0013518 EMAPA:18045 coccygeal vertebra pre-cartilage condensation tail vertebral pre-cartilage condensation uberon UBERON:0013504 caudal vertebra pre-cartilage condensation A caudal vertebra endochondral element that is composed primarily of a pre-cartilage condensation. OBOL:automatic coccygeal vertebra pre-cartilage condensation http://orcid.org/0000-0002-6601-2165 tail vertebral pre-cartilage condensation EMAPA:18045 A cervical vertebra endochondral element that is composed primarily of cartilage tissue. EHDAA2:0000240 cervical vertebral cartilage condensation group uberon UBERON:0013505 cervical vertebra cartilage element A cervical vertebra endochondral element that is composed primarily of cartilage tissue. OBOL:automatic cervical vertebral cartilage condensation group EHDAA2:0000240 A cervical vertebra endochondral element that is composed primarily of a pre-cartilage condensation. uberon UBERON:0013506 cervical vertebra pre-cartilage condensation A cervical vertebra endochondral element that is composed primarily of a pre-cartilage condensation. OBOL:automatic A thoracic vertebra endochondral element that is composed primarily of cartilage tissue. EHDAA2:0002014 thoracic vertebral cartilage condensation group uberon UBERON:0013507 thoracic vertebra cartilage element A thoracic vertebra endochondral element that is composed primarily of cartilage tissue. OBOL:automatic thoracic vertebral cartilage condensation group EHDAA2:0002014 A thoracic vertebra endochondral element that is composed primarily of a pre-cartilage condensation. uberon UBERON:0013508 thoracic vertebra pre-cartilage condensation A thoracic vertebra endochondral element that is composed primarily of a pre-cartilage condensation. OBOL:automatic The space that surrounds an organism. external to organism outside of body uberon UBERON:0013514 space surrounding organism The space that surrounds an organism. https://orcid.org/0000-0002-6601-2165 uberon UBERON:0013522 subdivision of tube The anatomical space that is enclosed by a stomach. Organ cavity which is bound by the internal surface of the wall of stomach. Examples: There is only one cavity of stomach[FMA:14585]. EMAPA:18395 FMA:14585 cavity of stomach uberon gastric cavity UBERON:0013525 stomach lumen FMA The anatomical space that is enclosed by a stomach. http://orcid.org/0000-0002-6601-2165 Organ cavity which is bound by the internal surface of the wall of stomach. Examples: There is only one cavity of stomach[FMA:14585]. FMA:14585 cavity of stomach FMA:14585 gastric cavity FMA:14585 Anatomical space that is an opening in a bone of the skull. FMA:53165 SCTID:276742007 Wikipedia:Foramina_of_the_skull foramen of skull cranial conduit cranial foramen uberon foramina of the skull UBERON:0013685 foramen of skull Anatomical space that is an opening in a bone of the skull. TAO:curator http://orcid.org/0000-0002-6601-2165 foramen of skull Wikipedia:Foramina_of_the_skull cranial conduit FMA:53165 foramina of the skull Wikipedia:Foramina_of_the_skull 2 2 An anatomical space which is the lumen of some anatomical conduit and connects two or more spaces together[FMA,modified]. FMA:9338 foramen space uberon UBERON:0013686 anatomical conduit space FMA An anatomical space which is the lumen of some anatomical conduit and connects two or more spaces together[FMA,modified]. FMA:9338 http://orcid.org/0000-0002-6601-2165 Vascular endothelium found in blood vessels of the blood-brain-barrier. BTO:0001852 BTO:0003248 CALOHA:TS-0092 uberon cerebromicrovascular endothelium UBERON:0013694 brain endothelium Vascular endothelium found in blood vessels of the blood-brain-barrier. CALOHA:TS-0092 cerebromicrovascular endothelium CALOHA:TS-0092 Vascular endothelium found in colon blood vessels. CALOHA:TS-0162 uberon colon endothelial cell colon endothelial cells colonic endothelial cell colonic endothelium colorectal endothelial cell colorectal endothelium UBERON:0013695 colon endothelium Vascular endothelium found in colon blood vessels. CALOHA:TS-0162 colon endothelial cell CALOHA:TS-0162 colon endothelial cells CALOHA:TS-0162 colonic endothelial cell CALOHA:TS-0162 colonic endothelium CALOHA:TS-0162 colorectal endothelial cell CALOHA:TS-0162 colorectal endothelium CALOHA:TS-0162 Musculature of the head and neck, spine, and ribs. EHDAA2:0000159 EMAPA:18166 uberon UBERON:0013700 axial musculature Musculature of the head and neck, spine, and ribs. HP:0003327 A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages. uberon UBERON:0013701 main body axis A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages. https://orcid.org/0000-0002-6601-2165 The region of the organism associated with the visceral organs. Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]. AEO:0000103 BTO:0001489 EMAPA:36031 FMA:231424 uberon body whole body UBERON:0013702 body proper AEO The region of the organism associated with the visceral organs. AEO:0000103 Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]. FMA:231424 body AEO:0000103 whole body BTO:0001489 A tubular passage that extends from the primitive pit into the head process during the early stages of embryonic development in mammals. It perforates the splanchnopleure layer so that the yolk sac and the amnion are connected temporarily. FMA:293127 NCIT:C34230 UMLS:C1518428 uberon chordal canal UBERON:0013704 notochordal canal A tubular passage that extends from the primitive pit into the head process during the early stages of embryonic development in mammals. It perforates the splanchnopleure layer so that the yolk sac and the amnion are connected temporarily. http://medical-dictionary.thefreedictionary.com/notochordal+canal UMLS:C1518428 ncithesaurus:Notochordal_Canal Fluid contained within the notochordal canal notochord fluid portion of notochordal fluid uberon UBERON:0013727 Distinct feature of coelocanths notochordal fluid Fluid contained within the notochordal canal http://animaldiversity.org/accounts/Latimeria_chalumnae/ http://orcid.org/0000-0002-6601-2165 A organ component layer that is part of a integumental system. SCTID:314820002 layer of skin skin layer uberon UBERON:0013754 integumentary system layer A organ component layer that is part of a integumental system. OBOL:automatic A blood that is part of a artery. FMA:83066 arterial blood blood in artery portion of arterial blood uberon UBERON:0013755 arterial blood A blood that is part of a artery. OBOL:automatic arterial blood FMA:83066 blood in artery FMA:83066 portion of arterial blood FMA:83066 A blood that is part of a vein. FMA:83067 blood in vein portion of venous blood venous blood uberon UBERON:0013756 venous blood A blood that is part of a vein. OBOL:automatic blood in vein FMA:83067 portion of venous blood FMA:83067 venous blood FMA:83067 A blood that is part of a capillary. FMA:263901 NCIT:C32212 blood in capillary portion of blood in capillary portion of capillary blood uberon UBERON:0013757 capillary blood A blood that is part of a capillary. OBOL:automatic portion of blood in capillary FMA:263901 Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements. EMAPA:37843 SCTID:272627002 digestive organ digestive system organ uberon UBERON:0013765 digestive system element Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements. http://orcid.org/0000-0002-6601-2165 EMAPA:37843 MA:th Great vessels is a term used to refer collectively to the large vessels that bring blood to and from the heart. great vessel EMAPA:36460 SCTID:304066000 Wikipedia:Great_vessels great vessel of thorax uberon UBERON:0013768 Groupings may vary - typically pulmonary vessels and aorta and vena cavae great vessel of heart Great vessels is a term used to refer collectively to the large vessels that bring blood to and from the heart. Wikipedia:Great_vessels Embryonic structure that gives rise to the telencephalon. EHDAA2:0004424 EMAPA:36024 TAO:0000571 ZFA:0000571 presumptive telencephalon uberon UBERON:0014371 paired anteriolateral division of the embryonic prosencephalon plus the lamina terminalis from which the olfactory lobes, cerebral cortex, and subcortical nuclei are derived[MP] future telencephalon definitional Embryonic structure that gives rise to the telencephalon. ZFA:0000571 ZFA:curator presumptive telencephalon ZFA:0000571 Mesenchyme that develops_from the neural crest[Automatically generated definition]. EMAPA:32735 FMA:293883 mesenchyme from neural crest neural crest derived mesenchyme neural crest mesenchyme uberon UBERON:0014387 mesenchyme derived from neural crest Mesenchyme that develops_from the neural crest[Automatically generated definition]. OBOL:automatic https://github.com/obophenotype/uberon/issues/248 Muscle that is part of the respiratory system. this class may be merged with 'respiratory system muscle'; check intercostals uberon UBERON:0014398 respiratory muscle Muscle that is part of the respiratory system. http://orcid.org/0000-0002-6601-2165 A anatomical space that is enclosed by a sinusoid. FMA:63133 lumen of sinusoid sinusoid lumen uberon UBERON:0014399 sinusoidal space A anatomical space that is enclosed by a sinusoid. OBOL:automatic lumen of sinusoid FMA:63133 sinusoid lumen FMA:63133 Subcutaneous adipose tissue that is located in the peritoneal cavity. Adipose tissue located inside the peritoneal cavity, packed in between internal organs and torso. An excess of visceral fat is known as central obesity, or belly fat, the pot belly or beer belly effect, in which the abdomen protrudes excessively[BTO:0004041]. BTO:0004041 CALOHA:TS-2405 uberon abdominal fat intra-abdominal adipose tissue intra-abdominal fat organ fat visceral adipose tissue visceral fat UBERON:0014454 visceral abdominal adipose tissue Subcutaneous adipose tissue that is located in the peritoneal cavity. CALOHA:paula MGI:csmith http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/259 Adipose tissue located inside the peritoneal cavity, packed in between internal organs and torso. An excess of visceral fat is known as central obesity, or belly fat, the pot belly or beer belly effect, in which the abdomen protrudes excessively[BTO:0004041]. BTO:0004041 abdominal fat BTO:0004041 intra-abdominal fat BTO:0004041 organ fat BTO:0004041 visceral adipose tissue BTO:0004041 visceral fat BTO:0004041 Subcutaneous adipose tissue that is located in the abdominal region. CALOHA:TS-2406 abdominal subcutaneous adipose tissue subcutaneous abdominal fat subcutaneous fat of abdominal region uberon UBERON:0014455 subcutaneous abdominal adipose tissue Subcutaneous adipose tissue that is located in the abdominal region. CALOHA:paula MGI:csmith http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/259 Subdivision of skeletal system that consists of all skeletal elements in the thoracic region of the trunk. In most vertebrates this is the rib cage and sternum. EHDAA2:0002013 FMA:77169 Wikipedia:Thoracic_skeleton skeleton of thorax thoracic part of axial skeleton thoracic skeleton uberon UBERON:0014477 thoracic skeleton Subdivision of skeletal system that consists of all skeletal elements in the thoracic region of the trunk. In most vertebrates this is the rib cage and sternum. Wikipedia:Rib_cage https://orcid.org/0000-0002-6601-2165 thoracic skeleton EHDAA2:0002013 A gray matter of spinal cord that is part of a cervical spinal cord. BIRNLEX:1521 SCTID:362438009 UMLS:C0228610 cervical spinal cord gray matter uberon UBERON:0014613 cervical spinal cord gray matter A gray matter of spinal cord that is part of a cervical spinal cord. OBOL:automatic UMLS:C0228610 BIRNLEX:1521 cervical spinal cord gray matter BIRNLEX:1521 A gray matter of spinal cord that is part of a thoracic spinal cord. BIRNLEX:980 SCTID:362441000 UMLS:C0228627 thoracic spinal cord gray matter uberon UBERON:0014636 thoracic spinal cord gray matter A gray matter of spinal cord that is part of a thoracic spinal cord. OBOL:automatic UMLS:C0228627 BIRNLEX:980 thoracic spinal cord gray matter BIRNLEX:980 A unilaminar epithelium that develops_from a ectoderm and is part of a anal region. EHDAA2:0004019 EMAPA:25040 uberon UBERON:0014703 anal membrane ectodermal component A unilaminar epithelium that develops_from a ectoderm and is part of a anal region. OBOL:automatic A anatomical space that is enclosed by a pleuroperitoneal canal. EHDAA2:0004736 EMAPA:25034 pleuro-peritoneal canal cavity uberon UBERON:0014704 pleuroperitoneal canal lumen EHDAA2 A anatomical space that is enclosed by a pleuroperitoneal canal. OBOL:automatic pleuro-peritoneal canal cavity EMAPA:25034 The domain of the diaphragm that is located dorsally and attaches to the vertebrae and surrounds the esophagus and aorta. EHDAA2:0000597 EMAPA:17703 SCTID:244668003 VHOG:0001546 Wikipedia:Crus_of_diaphragm crural diaphragm uberon crura of the diaphragm crus of the diaphragm diaphragm crura diaphragmatic crura UBERON:0014765 Classification notes: May be considered an external sphincter[PMID:8224664] crus of diaphragm PMID:23586979 PMID:23586979 The domain of the diaphragm that is located dorsally and attaches to the vertebrae and surrounds the esophagus and aorta. PMID:23586979 crural diaphragm PMID:23586979 crura of the diaphragm Wikipedia:Crus_of_diaphragm crus of the diaphragm Wikipedia:Crus_of_diaphragm diaphragm crura diaphragmatic crura Wikipedia:Crus_of_diaphragm A crus of diaphragm that is in_the_right_side_of a diaphragm. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern FMA:58286 SCTID:362690009 crus dextrum (Diaphragma) crus dextrum diaphragmatis external sphincter of esophagus right crus of diaphragm right crus of lumbar part of diaphragm uberon UBERON:0014766 right crus of diaphragm A crus of diaphragm that is in_the_right_side_of a diaphragm. OBOL:automatic crus dextrum (Diaphragma) FMA:58286 FMA:TA crus dextrum diaphragmatis FMA:58286 FMA:TA external sphincter of esophagus FMA:58286 right crus of diaphragm FMA:58286 right crus of lumbar part of diaphragm FMA:58286 A crus of diaphragm that is in_the_left_side_of a diaphragm. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern FMA:58287 SCTID:244937004 crus sinistrum (Diaphragma) crus sinistrum diaphragmatis left crus of diaphragm left crus of lumbar part of diaphragm uberon UBERON:0014767 left crus of diaphragm A crus of diaphragm that is in_the_left_side_of a diaphragm. OBOL:automatic crus sinistrum (Diaphragma) FMA:58287 FMA:TA crus sinistrum diaphragmatis FMA:58287 FMA:TA left crus of diaphragm FMA:58287 left crus of lumbar part of diaphragm FMA:58287 A neuromere that is part of the presumptive forebrain forebrain segment segment of forebrain FMA:61996 forebrain neuromere uberon future prosencephalon UBERON:0014775 prosomere A neuromere that is part of the presumptive forebrain http://orcid.org/0000-0002-6601-2165 A neuromere that is part of the presumptive midbrain mesomere midbrain segment segment of midbrain EHDAA2:0004352 FMA:61997 mesomere of nervous system neuromere of mesomere group uberon future mesencephalon mesomere group UBERON:0014776 midbrain neuromere A neuromere that is part of the presumptive midbrain http://orcid.org/0000-0002-6601-2165 mesomere group EHDAA2:0004352 A neuromere that is part of the presumptive spinal cord TAO:0001332 ZFA:0001332 spinal cord metameric segment spinal neuromeres uberon spinal cord segment UBERON:0014777 spinal neuromere A neuromere that is part of the presumptive spinal cord http://orcid.org/0000-0002-6601-2165 spinal neuromeres TAO:0001332 spinal cord segment TAO:0001332 Any muscle organ that is part of a cloaca. uberon UBERON:0014783 cloacal muscle Any muscle organ that is part of a cloaca. OBOL:automatic Any collection of muscles that is part of a pelvic complex. The pelvic complex comprises the pelvic girdle and the associated limb or fin. currently defined by location rather than attachment EMAPA:37864 FMA:71297 muscles of lower limb musculature of lower limb musculi membri inferioris uberon UBERON:0014792 musculature of pelvic complex Any collection of muscles that is part of a pelvic complex. The pelvic complex comprises the pelvic girdle and the associated limb or fin. OBOL:automatic EMAPA:37864 MA:th muscles of lower limb FMA:71297 musculature of lower limb FMA:71297 musculi membri inferioris FMA:TA Any muscle organ that is part of a pelvic appendage (hindlimb or pelvic fin). uberon UBERON:0014795 pelvic appendage muscle prolog Any muscle organ that is part of a pelvic appendage (hindlimb or pelvic fin). OBOL:automatic A muscle organ that consists of skeletal muscle tissue ensheathed in epimysium, that develops from myotome and that is innervated by some somatic motor neuron. Skeletal muscles are typically attached (via a tendon) to a bone but there are exceptions (e.g. intrinsic tongue muscles). skeletal muscle AAO:0011099 BTO:0001103 CALOHA:TS-0933 EFO:0000888 EHDAA:5035 EHDAA:5043 EHDAA:5978 EHDAA:5984 EMAPA:35988 EV:0100377 GAID:141 MA:0003148 MAT:0000302 MESH:D018482 MIAA:0000302 OpenCyc:Mx4rv2kf-5wpEbGdrcN5Y29ycA TAO:0005277 VHOG:0000319 XAO:0000174 ZFA:0005277 uberon UBERON:0014892 skeletal muscle organ A muscle organ that consists of skeletal muscle tissue ensheathed in epimysium, that develops from myotome and that is innervated by some somatic motor neuron. Skeletal muscles are typically attached (via a tendon) to a bone but there are exceptions (e.g. intrinsic tongue muscles). GOC:dos A portion of tissue that will develop into vasculature. EFO:0003708 TAO:0005076 ZFA:0005076 uberon UBERON:0014903 primordial vasculature A portion of tissue that will develop into vasculature. ZFA:0005076 ZFA:curator these layers primarily refer to the mammalian future neocortex uberon UBERON:0014950 layer of developing cerebral cortex EMAPA A vertebral endochondral element in the cervical region of the vertebral column. cervical vertebra skeletal element cervical vertebra element uberon UBERON:0015007 cervical vertebra endochondral element A vertebral endochondral element in the cervical region of the vertebral column. http://orcid.org/0000-0002-6601-2165 cervical vertebra skeletal element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern cervical vertebra element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern A vertebral endochondral element in the thoracic region of the vertebral column. thoracic vertebra skeletal element thoracic vertebra element uberon UBERON:0015008 thoracic vertebra endochondral element A vertebral endochondral element in the thoracic region of the vertebral column. http://orcid.org/0000-0002-6601-2165 thoracic vertebra skeletal element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern thoracic vertebra element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern consider merging into myocardial compact layer FMA:83105 perimysial connective tissue of subepicardium subepicardial connective tissue uberon UBERON:0015128 subepicardial layer of epicardium FMA perimysial connective tissue of subepicardium FMA:83105 subepicardial connective tissue FMA:83105 Visceral intrapericardial fat contiguous with the myocardial surface. FMA:9871 SCTID:42267001 epicardial adipose tissue pericardial adipose tissue uberon UBERON:0015129 epicardial fat Visceral intrapericardial fat contiguous with the myocardial surface. DOI:10.5935/abc.20130138 A gland that is typically found in or near the orbital region, in or around either the medial or lateral canthi, and is typically associated with secretions onto the eyeball or associated ducts. Includes the Harderian, nictitans and lacrimal glands. the only orbital gland found in anuran amphibians is either the Harderian or the lacrimal; if it is a lacrimal, then a progressive lateral migration of the lacrimal glands must occur through the amniotes[PMID:7559104] the only orbital gland found in anuran amphibians is the Harderian[PMID:8843648] ocular gland uberon orbital gland UBERON:0015152 gland of ocular region inferred A gland that is typically found in or near the orbital region, in or around either the medial or lateral canthi, and is typically associated with secretions onto the eyeball or associated ducts. Includes the Harderian, nictitans and lacrimal glands. http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/614 An eye consisting of multiple light-sensing organs uberon UBERON:0015165 multi-unit eye An eye consisting of multiple light-sensing organs PMID:21062451 http://orcid.org/0000-0002-6601-2165 present on tentacular crown PMID:21062451 present on mantle edge in arcacean Bivalvia PMID:21062451 The eyes (optic cushions) on the oral surface of Asteroida (Echinodermata), close to the base of the terminal tentacles, are also composed of a number of simple ocelli - as many as 80-200 in certain species PMID:21062451 A region of somite adjacent to presomitic mesoderm. TAO:0001462 XAO:0004074 ZFA:0001462 uberon inter-somited border intersomitic boundary intersomitic fissure intersomitic junction segmental border somite boundary UBERON:0015178 somite border A region of somite adjacent to presomitic mesoderm. http://orcid.org/0000-0002-6601-2165 intersomitic junction XAO:0004074 somite boundary ZFA:0001462 Epithelium located in the intersomitic region. XAO:0004077 intersomitic epithelium intersomitic membrane uberon UBERON:0015179 somite boundary epithelium Epithelium located in the intersomitic region. XAO:0004077 XAO:EJS intersomitic epithelium XAO:0004077 intersomitic membrane XAO:0004077 Any structure that is placed on one side of the left-right axis of a bilaterian. This class is primarily to implement taxon constraints. It may be removed in the future. uberon UBERON:0015212 lateral structure Any structure that is placed on one side of the left-right axis of a bilaterian. http://orcid.org/0000-0002-6601-2165 A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile. heart SPD:0000130 cardiac pump heart or heart like organ circulatory vessel uberon cardiac structure UBERON:0015228 circulatory organ A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile. http://orcid.org/0000-0002-6601-2165 A basement membrane of epithelium that is part of a respiratory system. EMAPA:37570 MA:0001815 uberon UBERON:0015329 respiratory system basement membrane MA A basement membrane of epithelium that is part of a respiratory system. OBOL:automatic EMAPA:37570 MA:th EMAPA:37597 MA:0002449 heart/pericardium uberon UBERON:0015410 heart plus pericardium MA EMAPA:37597 MA:th heart/pericardium MA:0002449 A epithelium that is part of a anal canal. EMAPA:18835 FMA:17511 anal canal epithelium epithelium of anal canal uberon UBERON:0015716 anal canal epithelium A epithelium that is part of a anal canal. OBOL:automatic anal canal epithelium FMA:17511 epithelium of anal canal FMA:17511 FMA:62798 portion of heterogeneous tissue uberon UBERON:0015757 heterogeneous tissue FMA portion of heterogeneous tissue FMA:62798 A smooth muscle tissue that is part of a hypodermis. FMA:77862 muscle layer in fatty layer of subcutaneous tissue stratum musculosum panniculi adiposi telae subcutaneae uberon UBERON:0015783 smooth muscle layer in fatty layer of subcutaneous tissue A smooth muscle tissue that is part of a hypodermis. OBOL:automatic muscle layer in fatty layer of subcutaneous tissue FMA:77862 stratum musculosum panniculi adiposi telae subcutaneae FMA:77862 FMA:TA A epithelium that is part of a camera-type eye. EMAPA:35957 MA:0003162 uberon UBERON:0015808 eye epithelium A epithelium that is part of a camera-type eye. OBOL:automatic A epithelium that is part of a foregut. EMAPA:32922 MA:0003204 uberon UBERON:0015833 foregut epithelium A epithelium that is part of a foregut. OBOL:automatic A capillary that is part of a lung. FMA:14121 capillary of lung uberon UBERON:0016405 pulmonary capillary A capillary that is part of a lung. OBOL:automatic capillary of lung FMA:14121 A hole in the diaphragm through which the esophagus passes FMA:58289 esophageal hiatus of diaphragm oesophageal aperture oesophageal hiatus uberon UBERON:0016458 esophageal hiatus A hole in the diaphragm through which the esophagus passes HP:0002036 esophageal hiatus of diaphragm FMA:58289 oesophageal aperture FMA:58289 oesophageal hiatus FMA:58289 is the sensory system for the sense of hearing. Auditory system is general anatomical term in FMA EMAPA:36002 FMA:7192 MA:0002443 NCIT:C12889 NLXANAT:090817 OpenCyc:Mx4rvViwtJwpEbGdrcN5Y29ycA UMLS:C0587901 Wikipedia:Auditory_system http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=2888 uberon UBERON:0016490 auditory system is the sensory system for the sense of hearing. NLXANAT:090817 Auditory system is general anatomical term in FMA FMA UMLS:C0587901 ncithesaurus:Auditory_System Luminal space of the right ventricle of the heart. EMAPA:26047 FMA:9291 right ventricle lumen right ventricular cavity uberon UBERON:0016509 cavity of right ventricle Luminal space of the right ventricle of the heart. http://orcid.org/0000-0002-6601-2165 right ventricle lumen EMAPA:26047 right ventricular cavity FMA:FMA luminal space of the left atrium of the heart. EMAPA:26011 FMA:9465 left atrial cavity left atrium lumen uberon UBERON:0016513 cavity of left atrium luminal space of the left atrium of the heart. http://orcid.org/0000-0002-6601-2165 left atrial cavity FMA:FMA left atrium lumen EMAPA:26011 luminal space of the left ventricle of the heart. EMAPA:26038 FMA:9466 left ventricular cavity uberon UBERON:0016514 cavity of left ventricle luminal space of the left ventricle of the heart. http://orcid.org/0000-0002-6601-2165 left ventricular cavity FMA:FMA luminal space of the right atrium of the heart. EMAPA:26020 FMA:11359 right atrial cavity uberon UBERON:0016522 cavity of right atrium luminal space of the right atrium of the heart. http://orcid.org/0000-0002-6601-2165 right atrial cavity FMA:FMA The external part of the developing pharynx that is made of ectoderm. During vertebrate development, pockets form in pharyngeal ectoderm between the pharyngeal arches. UBERON:2001379 TAO:0001379 ZFA:0001379 uberon UBERON:0016545 pharyngeal ectoderm The external part of the developing pharynx that is made of ectoderm. During vertebrate development, pockets form in pharyngeal ectoderm between the pharyngeal arches. PMID:23020903 http://orcid.org/0000-0002-6601-2165 A layer of of the central nervous system that is part of gray matter. grey matter layer FMA:83142 CNS gray matter layer CNS grey matter layer gray matter layer of neuraxis grey matter layer of neuraxis uberon UBERON:0016548 central nervous system gray matter layer A layer of of the central nervous system that is part of gray matter. http://orcid.org/0000-0002-6601-2165 gray matter layer of neuraxis FMA:83142 An roughly circular indentation in a surface. AEO:0000204 uberon UBERON:0016566 pit An roughly circular indentation in a surface. AEO:0000204 AEO:JB FMA:68861 Wikipedia:Rexed_laminae http://neurolex.org/wiki/Category:Rexed_spinal_cord_parcellation_scheme_region rexed lamina uberon UBERON:0016570 lamina of gray matter of spinal cord rexed lamina FMA:68861 The dorsal region of the optic cup that gives rise to the dorsal part of the retina. dorsal optic cup dorsal region of optic cup uberon UBERON:0016854 dorsal part of optic cup The dorsal region of the optic cup that gives rise to the dorsal part of the retina. http://orcid.org/0000-0002-6601-2165 dorsal optic cup http://orcid.org/0000-0002-6601-2165 dorsal region of optic cup http://orcid.org/0000-0002-6601-2165 Primordium that develops into the central nervous system UBERON:3000469 future CNS presumptive central nervous system uberon UBERON:0016879 future central nervous system Primordium that develops into the central nervous system http://orcid.org/0000-0002-6601-2165 Primordium that develops into the nervous system UBERON:3000477 AAO:0000477 presumptive nervous system uberon UBERON:0016880 future nervous system Primordium that develops into the nervous system http://orcid.org/0000-0002-6601-2165 presumptive nervous system AAO:0000477 Epithelium lining the distalmost portion of the digestive tract. BTO:0005445 WBbt:0005800 rectum epithelium uberon UBERON:0016885 epithelium of terminal part of digestive tract Epithelium lining the distalmost portion of the digestive tract. http://orcid.org/0000-0002-6601-2165 rectum epithelium BTO:0005445 Any muscle tissue of the distalmost portion of the digestive tract. rectum muscle rectum muscle structure uberon UBERON:0016886 muscle tissue of terminal part of digestive tract Any muscle tissue of the distalmost portion of the digestive tract. http://orcid.org/0000-0002-6601-2165 The part of the conceptus that may be lost before birth or will be discarded at birth, or when the embryo becomes an independent organism. AEO:0000195 EHDAA2:0000003 EMAPA:16042 extra-embryonic component extraembryonic component uberon UBERON:0016887 entire extraembryonic component AEO AEO The part of the conceptus that may be lost before birth or will be discarded at birth, or when the embryo becomes an independent organism. AEO:0000195 AEO:JB extraembryonic component AEO:0000195 An embryonic anatomical entity that will turn into one or more other anatomical entities, perhaps with other anatomical entities, later in development. AEO:0000132 uberon UBERON:0016888 transitional anatomical structure AEO An embryonic anatomical entity that will turn into one or more other anatomical entities, perhaps with other anatomical entities, later in development. AEO:0000132 AEO:JB The zone of the skin that surrounds a lip and is colored red due to thin epithelium and presence of eleidin vermilion border FMA:59824 SCTID:362086008 vermilion border of lip vermilion of lip uberon vermillion UBERON:0016915 vermilion The zone of the skin that surrounds a lip and is colored red due to thin epithelium and presence of eleidin http://orcid.org/0000-0002-6601-2165 vermillion A vermilion that is part of a lower lip. FMA:59828 SCTID:245800000 vermilion border of lower lip vermilion of lower lip uberon UBERON:0016919 lower vermilion A vermilion that is part of a lower lip. OBOL:automatic vermilion of lower lip FMA:59828 A mesenchyme-derived anatomical entity undergoing a transtion to become another structure. AEO:0001016 uberon UBERON:0017650 developing mesenchymal structure A mesenchyme-derived anatomical entity undergoing a transtion to become another structure. AEO:0001016 AEO:JB A viscus that is part of a abdomen. FMA:32413 FMA:67355 abdominal viscera abdominal viscera set set of abdominal viscera uberon UBERON:0017672 abdominal viscera A viscus that is part of a abdomen. OBOL:automatic abdominal viscera FMA:32413 abdominal viscera set FMA:32413 set of abdominal viscera FMA:32413 A muscle layer that is part of the rectum FMA:15035 muscular coat of rectum muscularis externa of rectum rectal muscularis propria tunica muscularis (rectum) tunica muscularis recti uberon UBERON:0018111 muscle layer of rectum A muscle layer that is part of the rectum http://orcid.org/0000-0002-6601-2165 muscular coat of rectum FMA:15035 muscularis externa of rectum FMA:15035 rectal muscularis propria FMA:15035 tunica muscularis (rectum) FMA:15035 tunica muscularis recti FMA:TA Any portion of smooth muscle tissue that is part of the rectum rectal smooth muscle tissue rectum smooth muscle smooth muscle of rectum uberon UBERON:0018112 rectum smooth muscle tissue Any portion of smooth muscle tissue that is part of the rectum http://orcid.org/0000-0002-6601-2165 FMA:83521 uberon UBERON:0018135 fibrocollagenous connective tissue Any vertebra endochondral element that is part of the caudal region of the vertebral column (tail or coccyx). UBERON:0015006 caudal vertebra element tail vertebra element coccygeal vertebra element coccyx vertebra element uberon UBERON:0018142 caudal vertebra endochondral element Any vertebra endochondral element that is part of the caudal region of the vertebral column (tail or coccyx). http://orcid.org/0000-0002-6601-2165 A zone of skin that is part of a lower lip. FMA:24767 SCTID:281630002 lower lip skin uberon UBERON:0018150 skin of lower lip A zone of skin that is part of a lower lip. OBOL:automatic lower lip skin FMA:24767 A boundary delimiting a rhombomere. rhombomere junction uberon UBERON:0018239 rhombomere boundary A boundary delimiting a rhombomere. GO:0021654 Added for consistency with MA EMAPA and EHDAA2. See https://github.com/obophenotype/mouse-anatomy-ontology/issues/104 EHDAA2:0001842 EMAPA:35578 MA:0000165 uberon UBERON:0018254 skeletal musculature MA Any portion of submucosa that lines the digestive tract. uberon UBERON:0018257 submucosa of digestive tract Any portion of submucosa that lines the digestive tract. http://orcid.org/0000-0002-6601-2165 Any organ component layer that consists of muscle tissue. NCITA class may refer to smooth muscle only FMA:45634 NCIT:C75444 UMLS:C0225358 uberon UBERON:0018260 layer of muscle tissue Any organ component layer that consists of muscle tissue. http://orcid.org/0000-0002-6601-2165 NCITA class may refer to smooth muscle only NCIT A muscular coat that is part of a digestive tract. responsible for gut movement, such as peristalsis tunica muscularis of digestive tract uberon muscular layer of digestive tract muscularis externa of digestive tract tunica externa of digestive tract UBERON:0018261 muscular coat of digestive tract A muscular coat that is part of a digestive tract. OBOL:automatic Foramen that allows the passge of the glossopharyngeal nerve (cranial nerve IX). UBERONTEMP:9ca0bda7-9111-4f59-bc72-5d47bc3d7d61 uberon UBERON:0018321 foramen for glossopharyngeal nerve Foramen that allows the passge of the glossopharyngeal nerve (cranial nerve IX). PHENOSCAPE:alex The anatomical space within the intestine. see notes in inclusivity in class 'intestine' FMA:14586 TADS:0000495 WBbt:0005791 ZFA:0005807 intestinal lumen intestine lumen uberon gut lumen UBERON:0018543 lumen of intestine The anatomical space within the intestine. http://orcid.org/0000-0002-6601-2165 intestinal lumen FMA:14586 intestine lumen ZFA:0005807 gut lumen ZFA:0005807 Muscle innervated by the trigeminal nerve (Cranial Nerve V). MFMO:0000072 muscle innervated by the trigeminal nerve muscles innervated by the trigeminal nerve uberon UBERON:0018544 trigeminal nerve muscle Muscle innervated by the trigeminal nerve (Cranial Nerve V). MFMO:0000072 muscles innervated by the trigeminal nerve MFMO:0000072 FMA:83450 ventricular cardiac muscle tissue ventricular heart muscle uberon ventricular muscle UBERON:0018649 cardiac muscle tissue of ventricle ventricular cardiac muscle tissue http://orcid.org/0000-0002-6601-2165 ventricular heart muscle http://orcid.org/0000-0002-6601-2165 ventricular muscle http://orcid.org/0000-0002-6601-2165 An interconnected tubular multi-tissue structure that contains fluid that is actively transported around the heart. FMA:73747 ZFA:0005811 cardiac vasculature uberon UBERON:0018674 heart vasculature An interconnected tubular multi-tissue structure that contains fluid that is actively transported around the heart. ZFA:0005811 ZFA:CVS cardiac vasculature FMA:73747 uberon UBERON:0018692 dorsal side of post-anal tail BTO:0002439 genital mucosa uberon UBERON:0019042 reproductive system mucosa genital mucosa BTO:0002439 Adipose tissue which is located throughout skeletal muscle and is responsible for the marbling seen in certain cuts of beef. In humans, excess accumulation of intramuscular fat is associated with insulin resistance and type 2 diabetes. BTO:0004043 uberon intramuscular fat UBERON:0019143 intramuscular adipose tissue Adipose tissue which is located throughout skeletal muscle and is responsible for the marbling seen in certain cuts of beef. In humans, excess accumulation of intramuscular fat is associated with insulin resistance and type 2 diabetes. BTO:0004043 intramuscular fat BTO:0004043 BTO:0004626 uberon carotid endothelium carotid epithelium UBERON:0019189 carotid artery endothelium carotid endothelium BTO:0004626 Any region of epithelium that is part of a skin region. BTO:0004382 uberon UBERON:0019204 skin epithelium Any region of epithelium that is part of a skin region. http://orcid.org/0000-0002-6601-2165 The part of the eye that consists of both the retina and the optic choroid SCTID:110701000 chorioretina choroid and retina retinachoroid retinachoroidal region uberon UBERON:0019207 chorioretinal region The part of the eye that consists of both the retina and the optic choroid UBERON:drseb http://orcid.org/0000-0002-6601-2165 DHBA:10654 FMA:268630 gray matter of the hindbrain uberon UBERON:0019263 gray matter of hindbrain gray matter of the hindbrain DHBA:HGM DHBA:10157 FMA:268608 uberon UBERON:0019264 gray matter of forebrain DHBA:10649 FMA:83913 uberon UBERON:0019267 gray matter of midbrain FMA:83912 uberon UBERON:0019269 gray matter of diencephalon EMAPA:35952 MA:0003174 uberon UBERON:0019304 sensory organ epithelium An exocrine gland that is part of a integumental system. integumental exocrine gland integumental system exocrine gland uberon UBERON:0019319 exocrine gland of integumental system An exocrine gland that is part of a integumental system. GOC:dos http://orcid.org/0000-0002-6601-2165 integumental exocrine gland http://orcid.org/0000-0002-6601-2165 integumental system exocrine gland http://orcid.org/0000-0002-6601-2165 The spinal accessory nucleus lies within the cervical spinal cord (C1-C5) in the ventral horn. The nucleus ambiguus is classically said to provide the 'cranial component' of the accessory nerve. However, the very existence of this cranial component has been recently questioned and seen as contributing exclusively to the vagus nerve. The terminology continues to be used in describing both human anatomy, and that of other animals. EMAPA:37067 FMA:83965 MA:0001033 Wikipedia:Spinal_accessory_nucleus http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=2003 accessory neural nucleus uberon accessory nucleus of anterior column of spinal cord nucleus accessorius columnae anterioris medullae spinalis nucleus nervi accessorii nucleus of accessory nerve nucleus of the accessory nerve nucleus of the spinal accessory nerve spinal accessory nucleus UBERON:0020358 See also: Wikipedia:Spinal_accessory_nucleus accessory XI nerve nucleus FMA The spinal accessory nucleus lies within the cervical spinal cord (C1-C5) in the ventral horn. The nucleus ambiguus is classically said to provide the 'cranial component' of the accessory nerve. However, the very existence of this cranial component has been recently questioned and seen as contributing exclusively to the vagus nerve. The terminology continues to be used in describing both human anatomy, and that of other animals. Wikipedia:Spinal_accessory_nucleus EMAPA:37067 MA:th accessory neural nucleus FMA:83965 accessory nucleus of anterior column of spinal cord NeuroNames:2003 nucleus accessorius columnae anterioris medullae spinalis NeuroNames:2003 nucleus nervi accessorii NeuroNames:2003 nucleus of accessory nerve NeuroNames:2003 nucleus of the accessory nerve NeuroNames:2003 nucleus of the spinal accessory nerve NeuroNames:2003 spinal accessory nucleus http://orcid.org/0000-0002-6601-2165 FMA:58315 uberon surface of region of wall of eyeball UBERON:0022288 surface of eyeball surface of region of wall of eyeball FMA:58315 A portion of organism substance that is secreted by a reproductive gland. uberon genital fluid genital secretion reproductive system fluid reproductive system fluid/secretion reproductive system secretion UBERON:0022293 reproductive gland secretion A portion of organism substance that is secreted by a reproductive gland. UBERON:cjm Single layer of a laminar structure, identified by different density, arrangement or size of cells and processes arranged in flattened layers or lamina[CUMBO]. this is currently used to group some cellular layers that may not strictly conform to the CARO definition of cell-part layer. Consider genericisizing and introducing subtypes for cellular layer, fibrous layer and cell soma layer lamina layer NLX:149357 uberon UBERON:0022303 nervous system cell part layer Single layer of a laminar structure, identified by different density, arrangement or size of cells and processes arranged in flattened layers or lamina[CUMBO]. NLX:149357 lamina CUMBO:CUMBO layer CUMBO:CUMBO Serous membrane layer that is adjacent to and lines an organ. FMA:15860 visceral wall of serous membrane uberon UBERON:0022350 visceral serous membrane Serous membrane layer that is adjacent to and lines an organ. http://orcid.org/0000-0002-6601-2165 visceral wall of serous membrane FMA:15860 Serous membrane layer that lines to a body cavity. cavity lining FMA:15859 MA:0002448 parietal wall of serous membrane uberon UBERON:0022351 parietal serous membrane Serous membrane layer that lines to a body cavity. http://orcid.org/0000-0002-6601-2165 cavity lining MA:0002448 parietal wall of serous membrane FMA:15859 A specific region of the foregut into the area in which the lung will develop. SCTID:34922002 lung field uberon UBERON:0022361 lung field A specific region of the foregut into the area in which the lung will develop. GOC:dph GOC:mtg_lung An embryonic or larval epithelium that is committed to form part of the nervous system. neurepithelium AEO:0001008 BTO:0000314 EHDAA2_RETIRED:0004654 FMA:64807 embryonic neuroepithelium neuroepithelium uberon UBERON:0034705 developing neuroepithelium An embryonic or larval epithelium that is committed to form part of the nervous system. AEO:0001008 AEO:JB neurepithelium BTO:0000314 embryonic neuroepithelium http://orcid.org/0000-0002-6601-2165 neuroepithelium AEO:0001008 An epithelium that is undergoing proliferation to provide large numbers of neuronal cells. AEO:0001009 uberon UBERON:0034706 proliferating neuroepithelium AEO An epithelium that is undergoing proliferation to provide large numbers of neuronal cells. AEO:0001009 A neuroepithelium some of whose cells are undergoing terminal differentiation to become neuronal cells. AEO:0001010 uberon UBERON:0034707 differentiating neuroepithelium AEO A neuroepithelium some of whose cells are undergoing terminal differentiation to become neuronal cells. AEO:0001010 DHBA:12694 EMAPA:32916 marginal zone of hindbrain uberon MZH UBERON:0034709 hindbrain marginal layer marginal zone of hindbrain DHBA:12694 MZH DHBA:12694 EHDAA2:0001267 EMAPA:17585 spinal cord lateral wall ventricular layer uberon UBERON:0034710 spinal cord ventricular layer EHDAA2 spinal cord lateral wall ventricular layer EHDAA2:0001267 The layer of the developing cerebral cortex that is formed from the first cohort of neurons to migrate out of the cortical ventricular zone; split by the second wave into marginal zone and subplate. EMAPA:35261 uberon UBERON:0034711 cortical preplate The layer of the developing cerebral cortex that is formed from the first cohort of neurons to migrate out of the cortical ventricular zone; split by the second wave into marginal zone and subplate. PMID:12626695 Any of the cranial nerves, or their central nervous system analogs (the optic tract, the epiphyseal tract). These analogs are not true nerves, and are instead evaginated sensory afferents emanating from the brain uberon cranial nerve fiber bundle cranial nerve fiber tract cranial nerve or tract neuron projection bundle from brain UBERON:0034713 cranial neuron projection bundle Any of the cranial nerves, or their central nervous system analogs (the optic tract, the epiphyseal tract). These analogs are not true nerves, and are instead evaginated sensory afferents emanating from the brain ISBN:0471888893 http://orcid.org/0000-0002-6601-2165 cranial nerve fiber bundle http://orcid.org/0000-0002-6601-2165 cranial nerve fiber tract http://orcid.org/0000-0002-6601-2165 cranial nerve or tract http://orcid.org/0000-0002-6601-2165 neuron projection bundle from brain http://orcid.org/0000-0002-6601-2165 A taste bud that is located external to the digestive tube, on the head or body, as found in species such as goldfish. uberon UBERON:0034717 integumental taste bud A taste bud that is located external to the digestive tube, on the head or body, as found in species such as goldfish. PMID:11921337 http://orcid.org/0000-0002-6601-2165 A taste bud that is located on a lip. uberon UBERON:0034719 lip taste bud A taste bud that is located on a lip. PMID:11921337 http://orcid.org/0000-0002-6601-2165 A taste bud that is located on the skin of the head. uberon UBERON:0034720 head taste bud A taste bud that is located on the skin of the head. http://orcid.org/0000-0002-6601-2165 A taste bud that is located in the pharynx. uberon UBERON:0034721 pharyngeal taste bud A taste bud that is located in the pharynx. http://orcid.org/0000-0002-6601-2165 A taste bud that is located in the esophagus. uberon UBERON:0034724 esophageal taste bud A taste bud that is located in the esophagus. http://orcid.org/0000-0002-6601-2165 A taste bud that is located on the skin of the trunk. uberon UBERON:0034726 trunk taste bud A taste bud that is located on the skin of the trunk. http://orcid.org/0000-0002-6601-2165 The autonomic nerve is a small nerve which carries postganglionic sympathetic and parasympathetic neurons from the zygomaticotemporal nerve; a branch of the maxillary nerve, to the lacrimal nerve; a branch of the ophthalmic nerve. These neurons derive from the superior cervical ganglion and the pterygopalatine ganglion respectively. They will travel to the lacrimal gland via the lacrimal nerve. Parasympathetic will induce lacrimation and vice versa. EMAPA:37957 FMA:5866 MESH:D017776 SCTID:276145003 Wikipedia:Autonomic_nerve nervus visceralis visceral nerve uberon UBERON:0034728 autonomic nerve The autonomic nerve is a small nerve which carries postganglionic sympathetic and parasympathetic neurons from the zygomaticotemporal nerve; a branch of the maxillary nerve, to the lacrimal nerve; a branch of the ophthalmic nerve. These neurons derive from the superior cervical ganglion and the pterygopalatine ganglion respectively. They will travel to the lacrimal gland via the lacrimal nerve. Parasympathetic will induce lacrimation and vice versa. Wikipedia:Autonomic_nerve EMAPA:37957 MA:th nervus visceralis FMA:5866 visceral nerve FMA:5866 EMAPA:37958 SCTID:181098007 uberon UBERON:0034729 sympathetic nerve EMAPA:37958 MA:th FMA:79770 NCIT:C41168 uberon UBERON:0034769 lymphomyeloid tissue FMA Any substance in the body or expelled from the body that is in a gaseous state. FMA:84580 gas in anatomical space portion of gas in anatomical space uberon UBERON:0034873 bodily gas Any substance in the body or expelled from the body that is in a gaseous state. http://orcid.org/0000-0002-6601-2165 portion of gas in anatomical space FMA:84580 Any portion of gas located in a part of the respiratory system that is composed primarily of air. FMA:84581 respiratory air respiratory system air uberon UBERON:0034874 air in respiratory system Any portion of gas located in a part of the respiratory system that is composed primarily of air. http://orcid.org/0000-0002-6601-2165 respiratory air FMA:84581 the area of axial mesoderm that develops into the prechordal plate prechordal mesenchyme uberon UBERON:0034878 prechordal mesoderm the area of axial mesoderm that develops into the prechordal plate MGI:anna Endocardium that is part of the left atrium. Endocardium of atrium which is continuous with the tunica intima of the trunk of pulmonary vein. FMA:7286 SCTID:190064008 VHOG:0001226 endocardium of left atrium left atrial endocardium uberon left atrium endocardial tissue UBERON:0034903 left atrium endocardium Endocardium that is part of the left atrium. http://orcid.org/0000-0002-6601-2165 Endocardium of atrium which is continuous with the tunica intima of the trunk of pulmonary vein. FMA:7286 endocardium of left atrium FMA:7286 left atrium endocardial tissue VHOG:0001226 lumen of gland uberon UBERON:0034905 gland lumen An multicellular anatomical structure that has subparts of multiple organs as a part. CARO:0020001 uberon anatomical cluster UBERON:0034921 multi organ part structure CARO An multicellular anatomical structure that has subparts of multiple organs as a part. CARO:0020001 anatomical cluster CARO:0020001 A cluster of cells, largely surrounded by a morphological boundary. CARO:0020002 FMA:62807 uberon UBERON:0034922 cell cluster CARO A cluster of cells, largely surrounded by a morphological boundary. CARO:0020002 A collection of anatomical structures that are alike in terms of their morphology or developmental origin. resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected uberon UBERON:0034925 anatomical collection A collection of anatomical structures that are alike in terms of their morphology or developmental origin. http://orcid.org/0000-0002-6601-2165 A region or zone on the surface of an organism that encompasses skin and any adnexa, down through muscles and bounded by underlying skeletal support structures. uberon UBERON:0034929 external soft tissue zone A region or zone on the surface of an organism that encompasses skin and any adnexa, down through muscles and bounded by underlying skeletal support structures. http://orcid.org/0000-0002-6601-2165 Any organ component layer that consists of smooth muscle tissue. uberon UBERON:0034933 layer of smooth muscle tissue Any organ component layer that consists of smooth muscle tissue. http://orcid.org/0000-0002-6601-2165 FMA:55268 organ sector organ zonal region organ zone uberon organ region with floating fiat boundary UBERON:0034944 zone of organ organ sector FMA:55268 organ zone FMA:55268 organ region with floating fiat boundary FMA:55268 Any gaseous product of an excretory process. uberon UBERON:0034945 excreted gas Any gaseous product of an excretory process. http://orcid.org/0000-0002-6601-2165 Any excreted gas that is produced by the digestive tract. FMA:78440 flatulence flatus intestinal gas uberon UBERON:0034946 In mammals, mostly produced as a byproduct of bacterial fermentation in the gastrointestinal (GI) tract, especially the colon, and excreted through the rectum gas excreted from digestive tract Any excreted gas that is produced by the digestive tract. http://orcid.org/0000-0002-6601-2165 flatulence FMA:78440 flatus Wikipedia:Flatulence Any portion of gas located in a part of the respiratory system. respiratory gas respiratory system gas uberon UBERON:0034947 gas in respiratory system Any portion of gas located in a part of the respiratory system. http://orcid.org/0000-0002-6601-2165 NCIT:C25787 UMLS:C1512086 uberon duct epithelium ductal epithelium UBERON:0034969 epithelial layer of duct DHBA:12682 EMAPA:32917 hindbrain mantle layer uberon UBERON:0034994 hindbrain cortical intermediate zone hindbrain mantle layer EMAPA:32917 Mesenchyme that is part of a developing jaw [Automatically generated definition]. EMAPA:32907 EMAPA:35454 uberon UBERON:0034995 jaw mesenchyme Mesenchyme that is part of a developing jaw [Automatically generated definition]. OBOL:automatic EMAPA:32904 MA:0003220 uberon UBERON:0035037 jaw epithelium SCTID:277967008 hemorrhoidal artery uberon UBERON:0035039 rectal artery A post-anal tail that attaches outside the tail. uberon UBERON:0035091 extrinsic post-anal tail muscle A post-anal tail that attaches outside the tail. http://orcid.org/0000-0002-6601-2165 Any material entity that is located in the digestive tract. This includes undigested food and liquid as well as unexcreted waste products. It also includes other entities such as ingested stones used to aid digestion. Any microbial cells or cell populations are also included. Note that we treat any material entity that is ingested as an anatomical structure by defintion, although this may be expanding the CARO usage somewhat digestive tract contents uberon ingested material entity UBERON:0035118 material entity in digestive tract Any material entity that is located in the digestive tract. This includes undigested food and liquid as well as unexcreted waste products. It also includes other entities such as ingested stones used to aid digestion. Any microbial cells or cell populations are also included. https://github.com/EnvironmentOntology/envo/issues/110 digestive tract contents Anatomical surface, which is the external surface of the whole body. Examples: There is only one body surface. FMA:61695 NCIT:C29667 SCTID:261060002 UMLS:C0489451 surface of body uberon UBERON:0035159 entire surface of organism Anatomical surface, which is the external surface of the whole body. Examples: There is only one body surface. FMA:61695 surface of body FMA:61695 FMA:70506 NCIT:C32837 SCTID:360629008 UMLS:C1182571 internal carotid arterial subdivision subdivision of internal carotid artery uberon UBERON:0035237 branch of internal carotid artery internal carotid arterial subdivision FMA:70506 subdivision of internal carotid artery FMA:70506 FMA:70505 NCIT:C32552 SCTID:244216003 UMLS:C0447038 external carotid arterial subdivision subdivision of external carotid artery uberon UBERON:0035398 branch of external carotid artery external carotid arterial subdivision FMA:70505 subdivision of external carotid artery FMA:70505 Any of several arteries that arise from the aorta and supply blood to the esophagus. FMA:4149 NCIT:C32535 SCTID:56548006 UMLS:C0226294 aortic esophageal artery oesophageal artery uberon UBERON:0035539 esophageal artery FMA FMA Any of several arteries that arise from the aorta and supply blood to the esophagus. ncithesaurus:Esophageal_Artery aortic esophageal artery FMA:4149 oesophageal artery FMA:4149 FMA:51797 SCTID:149683007 ciliary vein uberon UBERON:0035546 uveal vein ciliary vein FMA:51797 SCTID:77852007 uberon UBERON:0035548 colic artery The part of the circulatory system that lies within the subcutaneous tissue layers close to the surface of the skin. FMA:225275 superficial part of circulatory system superficial vasculature dermis vasculature hypodermis vasculature uberon skin vasculature subcutaneous vasculature vasculature of skin UBERON:0035549 vasculature of integument The part of the circulatory system that lies within the subcutaneous tissue layers close to the surface of the skin. http://orcid.org/0000-0002-6601-2165 vasculature of skin FMA:225275 Any of the veins carrying deoxygenated blood from the subcutaneous tissue layers. FMA:76719 NCIT:C33666 SCTID:341382008 UMLS:C0226513 Wikipedia:Superficial_vein uberon superfical vein superficial veins superficial vessels UBERON:0035550 superficial vein Any of the veins carrying deoxygenated blood from the subcutaneous tissue layers. ncithesaurus:Superficial_Vein superfical vein Wikipedia:Superficial_vein superficial veins Wikipedia:Superficial_vein superficial vessels Wikipedia:Superficial_vein The part of the circulatory system that lies deep beneath the subcutaneous tissue layers away from the surface of the skin. deep part of circulatory system uberon UBERON:0035551 deep vasculature The part of the circulatory system that lies deep beneath the subcutaneous tissue layers away from the surface of the skin. http://orcid.org/0000-0002-6601-2165 A blood vessel carrying deoxygenated blood far beneath the skin usually accompanying an artery. FMA:76718 NCIT:C32444 SCTID:341484008 UMLS:C0226514 Wikipedia:Deep_vein uberon deep veins deep vessels UBERON:0035552 deep vein A blood vessel carrying deoxygenated blood far beneath the skin usually accompanying an artery. ncithesaurus:Deep_Vein deep veins Wikipedia:Deep_vein deep vessels Wikipedia:Deep_vein Any chamber of the left side of the heart FMA:7166 SCTID:362008007 uberon UBERON:0035553 left cardiac chamber Any chamber of the left side of the heart http://orcid.org/0000-0002-6601-2165 Any chamber of the right side of the heart FMA:7165 SCTID:362007002 uberon UBERON:0035554 right cardiac chamber Any chamber of the right side of the heart http://orcid.org/0000-0002-6601-2165 The parts of the orbital region that are outside of the the eyeball, including the lacrimal apparatus, the extraocular muscles and the eyelids, eyelashes, eyebrows and the conjunctiva FMA:76554 NCIT:C32574 SCTID:120612006 UMLS:C0229243 Wikipedia:Accessory_visual_structures adnexa oculi uberon accessory parts of orbital region accessory visual structures accessory visual structures set adnexal parts of orbital region appendage of eye appendages of the eye eye adnexa set of accessory visual structures structurae oculi accessoriae UBERON:0035639 ocular adnexa The parts of the orbital region that are outside of the the eyeball, including the lacrimal apparatus, the extraocular muscles and the eyelids, eyelashes, eyebrows and the conjunctiva HPO:pr UBERON:cjm http://medical-dictionary.thefreedictionary.com/ocular+adnexa https://github.com/obophenotype/uberon/issues/1132 adnexa oculi http://medical-dictionary.thefreedictionary.com/ocular+adnexa accessory visual structures FMA:76554 accessory visual structures Wikipedia:Accessory_visual_structures accessory visual structures set FMA:76554 appendage of eye http://medical-dictionary.thefreedictionary.com/ocular+adnexa appendages of the eye http://medical-dictionary.thefreedictionary.com/ocular+adnexa set of accessory visual structures FMA:76554 structurae oculi accessoriae Wikipedia:Accessory_visual_structures Any nerve that innervates the larynx. MESH:A08.800.050.050.925.450 SCTID:307013006 uberon UBERON:0035642 laryngeal nerve Any nerve that innervates the larynx. UBERON:cjm EHDAA2:0004181 FMA:9464 cardiac chamber cavity heart cavity heart lumen uberon UBERON:0035763 cavity of cardiac chamber FMA cardiac chamber cavity FMA:9464 heart cavity FMA:9464 heart lumen EHDAA2:0004181 The primordial mouth region of the developing head. FMA:293105 primitive mouth primordial mouth uberon UBERON:0035804 future mouth The primordial mouth region of the developing head. MP:0003119 primitive mouth FMA:293105 A muscle layer that is part of the sigmoid colon FMA:15028 muscularis externa of sigmoid colon muscularis propria of sigmoid colon sigmoid colon muscularis propria uberon sigmoideum muscularis tunica muscularis colon sigmoideum UBERON:0035805 muscle layer of sigmoid colon A muscle layer that is part of the sigmoid colon https://github.com/obophenotype/uberon/issues/1162 muscularis externa of sigmoid colon FMA:15028 FMA:12241 SCTID:304404008 uberon UBERON:0035809 serous cavity The sum of epicardial and paracardial fat deposits. SCTID:42267001 ZFA:0005765 uberon UBERON:0035814 pericardial fat The sum of epicardial and paracardial fat deposits. DOI:10.5935/abc.20130138 Fat deposits in the mediastinum outside the parietal pericardium . intrathoracic fat uberon UBERON:0035815 paracardial fat Fat deposits in the mediastinum outside the parietal pericardium . DOI:10.5935/abc.20130138 intrathoracic fat DOI:10.5935/abc.20130138 Any fat deposit surrounding a visceral organ. uberon UBERON:0035818 visceral fat Any fat deposit surrounding a visceral organ. UBERON:cjm The part of the ventral body cavity that is within the abdominal segment of the trunk, which encompasses the abdomen proper plus pelvic cavity. FMA:12267 Wikipedia:Abdominopelvic_cavity cavitas abdominis et pelvis uberon UBERON:0035819 abdominopelvic cavity The part of the ventral body cavity that is within the abdominal segment of the trunk, which encompasses the abdomen proper plus pelvic cavity. UBERON:cjm cavitas abdominis et pelvis FMA:TA A serous sac that is the aggregate of the peritoneum and the peritoneal cavity, located in the abdominal cavity. EMAPA:16137 FMA:9908 MA:0000054 uberon peritoneal component UBERON:0035820 peritoneal sac A serous sac that is the aggregate of the peritoneum and the peritoneal cavity, located in the abdominal cavity. https://github.com/obophenotype/uberon/issues/86 peritoneal component EMAPA:16137 The domain of the diaphragm that is a thin domed sheet of muscle composed of a radial array of myofibers extending laterally from the ribs and medially to a central tendon. FMA:58277 SCTID:368048007 costal part of diaphragm pars costalis diaphragmatis uberon UBERON:0035831 costal diaphragm PMID:23586979 PMID:23586979 The domain of the diaphragm that is a thin domed sheet of muscle composed of a radial array of myofibers extending laterally from the ribs and medially to a central tendon. PMID:23586979 costal part of diaphragm FMA:58277 pars costalis diaphragmatis FMA:TA BTO:0004378 EMAPA:37987 FMA:67473 blood vessel wall uberon vascular wall UBERON:0035965 wall of blood vessel EMAPA:37987 MA:th blood vessel wall FMA:67473 vascular wall BTO:0004378 EHDAA2:0004070 uberon UBERON:0036072 respiratory primordium epithelium EHDAA2 EHDAA2:0004071 respiratory primordium associated mesenchyme uberon UBERON:0036073 respiratory primordium mesenchyme EHDAA2 respiratory primordium associated mesenchyme EHDAA2:0004071 An region of the mesoderm that includes anterior lateral mesoderm of the first heart field plus contiguous pharyngeal mesoderm that gives rise to second-heart-field-derived regions of the heart and branchiomeric muscles. uberon UBERON:0036146 cardiopharyngeal field An region of the mesoderm that includes anterior lateral mesoderm of the first heart field plus contiguous pharyngeal mesoderm that gives rise to second-heart-field-derived regions of the heart and branchiomeric muscles. BGEE:ann http://www.nature.com/nature/journal/v520/n7548/full/nature14435.html#bx1 FMA:83520 uberon UBERON:0036186 fibroelastic connective tissue An anatomical junction that is between the sigmoid colon and rectum. NCIT:C54188 SCTID:245429006 uberon rectosigmoid region UBERON:0036214 rectosigmoid junction An anatomical junction that is between the sigmoid colon and rectum. NCIT:C54188 https://github.com/obophenotype/uberon/issues/1319 https://www.cdc.gov/cancer/npcr/pdf/abstracting/colon.pdf rectosigmoid region NCIT:C54188 Material anatomical entity that forms the outermost boundary of an anatomical structure. AAO:0010270 AEO:0000154 ZFA:0005594 uberon UBERON:0036215 anatomical surface region Material anatomical entity that forms the outermost boundary of an anatomical structure. https://github.com/obophenotype/uberon/issues/1324 A bodily fluid that is located in the coelom. he coelomic fluid serves several functions; it acts as a hydroskeleton, it allows free movement and growth of internal organs, it serves for transport of gases, nutrients and waste products between different parts of the body, it allows storage of sperm and eggs during maturation and it acts as a reservoir for waste [Wikipedia:Coelom#Coelomic_fluid] BTO:0001708 uberon UBERON:0036217 coelomic fluid A bodily fluid that is located in the coelom. PMID:10874572 https://github.com/obophenotype/uberon/issues/1326 Any gland that is part os the respiratory system. uberon UBERON:0036225 respiratory system gland Any gland that is part os the respiratory system. UBERON:cjm A notochord that has persisted beyond the embryonic stage. uberon UBERON:0036242 post-embryonic notochord A notochord that has persisted beyond the embryonic stage. UBERON:cjm A transudate found in the serous sac. serous fluid FMA:20932 serous sac fluid uberon UBERON:0036244 secretion of serous membrane A transudate found in the serous sac. FMA:20932 serous fluid FMA:20932 FMA:53133 cranial orifice skull orifice uberon UBERON:0036253 orifice of skull cranial orifice FMA:53133 skull orifice FMA:53133 The zygomaticotemporal nerve or zygomaticotemporal branch (temporal branch) is derived from the maxillary branch of the trigeminal nerve (Cranial nerve V). It runs along the lateral wall of the orbit in a groove in the zygomatic bone, receives a branch of communication from the lacrimal, and passes through zygomaticotemporal foramen in the zygomatic bone to enter the temporal fossa. It ascends between the bone, and substance of the Temporalis muscle, pierces the temporal fascia about 2.5 cm. above the zygomatic arch, and is distributed to the skin of the side of the forehead, and communicates with the facial nerve and with the auriculotemporal branch of the mandibular nerve. As it pierces the temporal fascia, it gives off a slender twig, which runs between the two layers of the fascia to the lateral angle of the orbit. FMA:52972 SCTID:280243001 Wikipedia:Zygomaticotemporal_nerve ramus zygomaticotemporalis (Nervus zygomaticus) ramus zygomaticotemporalis nervus zygomatici zygomaticotemporal branch of zygomatic nerve uberon zygomaticotemporal zygomaticotemporal branch UBERON:0036264 zygomaticotemporal nerve The zygomaticotemporal nerve or zygomaticotemporal branch (temporal branch) is derived from the maxillary branch of the trigeminal nerve (Cranial nerve V). It runs along the lateral wall of the orbit in a groove in the zygomatic bone, receives a branch of communication from the lacrimal, and passes through zygomaticotemporal foramen in the zygomatic bone to enter the temporal fossa. It ascends between the bone, and substance of the Temporalis muscle, pierces the temporal fascia about 2.5 cm. above the zygomatic arch, and is distributed to the skin of the side of the forehead, and communicates with the facial nerve and with the auriculotemporal branch of the mandibular nerve. As it pierces the temporal fascia, it gives off a slender twig, which runs between the two layers of the fascia to the lateral angle of the orbit. Wikipedia:Zygomaticotemporal_nerve ramus zygomaticotemporalis (Nervus zygomaticus) FMA:52972 ramus zygomaticotemporalis nervus zygomatici FMA:TA zygomaticotemporal branch of zygomatic nerve FMA:52972 zygomaticotemporal Wikipedia:Zygomaticotemporal_nerve zygomaticotemporal branch Wikipedia:Zygomaticotemporal_nerve SCTID:13152008 uberon UBERON:0036268 pelvic vein Wall of ventricle which is continuous with the wall of aorta. FMA:9556 left ventricular wall uberon UBERON:0036285 wall of left ventricle FMA FMA Wall of ventricle which is continuous with the wall of aorta. FMA:9556 left ventricular wall FMA:9556 Wall of ventricle which is continuous with the wall of pulmonary trunk. FMA:9533 right ventricular wall uberon UBERON:0036286 wall of right ventricle FMA FMA Wall of ventricle which is continuous with the wall of pulmonary trunk. FMA:9533 right ventricular wall FMA:9533 FMA:9560 uberon UBERON:0036288 anterior wall of left ventricle FMA Region of wall of right ventricle which is continuous with the lateral and septal walls of right ventricle. FMA:9553 uberon UBERON:0036289 anterior wall of right ventricle Region of wall of right ventricle which is continuous with the lateral and septal walls of right ventricle. FMA:9553 FMA:87177 uberon UBERON:0036290 myocardium of anterior wall of left ventricle FMA:260877 uberon UBERON:0036291 myocardium of anterior wall of right ventricle A mucosa that is part of a lip region [Automatically generated definition]. NCIT:C12226 labial mucosa uberon UBERON:0036294 mucosa of lip A mucosa that is part of a lip region [Automatically generated definition]. OBOL:automatic labial mucosa UBERON:cjm uberon UBERON:0036302 vasculature of central nervous system plus retina FMA:259905 uberon UBERON:0036303 vasculature of central nervous system FMA:15089 brachiocephalic arterial wall uberon UBERON:0036351 wall of brachiocephalic artery FMA FMA brachiocephalic arterial wall FMA:15089 FMA:15704 anal canal wall uberon UBERON:0036362 wall of anal canal FMA anal canal wall FMA:15704 FMA:18211 pulmonary arterial wall uberon UBERON:0036422 wall of pulmonary artery FMA FMA pulmonary arterial wall FMA:18211 FMA:231590 uberon UBERON:0036553 wall of synovial tendon sheath FMA FMA FMA:58098 eyeball wall uberon UBERON:0036925 wall of eyeball FMA FMA eyeball wall FMA:58098 FMA:66284 common carotid arterial wall uberon UBERON:0037094 wall of common carotid artery FMA FMA common carotid arterial wall FMA:66284 wall of organ which has as its parts the endocardium, myocardium , epicardium, and the cardiac septum, surrounded by the pericardial sac proper and is continuous with the walls of the systemic and pulmonary arterial and venous trees. FMA:7274 cardiac wall uberon UBERON:0037144 wall of heart FMA FMA FMA FMA wall of organ which has as its parts the endocardium, myocardium , epicardium, and the cardiac septum, surrounded by the pericardial sac proper and is continuous with the walls of the systemic and pulmonary arterial and venous trees. FMA:7274 cardiac wall FMA:7274 A zone of skin that is part of the face. eriks 2012-02-05T05:23:01Z EMAPA:36657 FMA:24758 NCIT:C33561 SCTID:361703006 UMLS:C0222084 face skin uberon facial skin UBERON:1000021 skin of face A zone of skin that is part of the face. UBERON:EJS https://github.com/obophenotype/uberon/issues/34 UMLS:C0222084 ncithesaurus:Skin_of_the_Face face skin EMAPA:36657 FMA:24758 An anatomical junction between two parts of the digestive tract. 2021-02-05T11:19:31Z uberon UBERON:1100000 digestive tract junction An anatomical junction between two parts of the digestive tract. ORCID:0000-0002-7073-9172 EFO:0003612 TAO:0001053 ZFA:0001053 PICA primitive internal carotid artery uberon UBERON:2001053 future internal carotid artery EHDAA2 PICA TAO:0001053 primitive internal carotid artery ZFA:0001053 This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon teleost_anatomy_curators ZFA:0001073 uberon UBERON:2001073 axial vasculature Cartilage which is part of the axial skeleton. This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon teleost_anatomy_curators ZFA:0001457 uberon UBERON:2001457 postcranial axial cartilage Cartilage which is part of the axial skeleton. ZFIN:curator Pharyngeal arch cartilage that is the median cartilage of the ventral hyoid arch, generally lying between the paired ventral hypohyals. This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon teleost_anatomy_curators uberon UBERON:2001544 sublingual cartilage Pharyngeal arch cartilage that is the median cartilage of the ventral hyoid arch, generally lying between the paired ventral hypohyals. TAO:wd Capillary that has pores in the endothelial cells (60-80 nm in diameter) that are spanned by a diaphragm of radially oriented fibrils and allow small molecules and limited amounts of protein to diffuse the ZFA class from which this was derived is not explicitly classified as a capillary - need to verify for taxon histology differences Blood vessel endothelium that has pores that allow passage small molecules and proteins[ZFA]. fenestrated blood vessel endothelium FMA:63196 NCIT:C32595 TAO:0005260 UMLS:C1179615 Wikipedia:Capillary#Types ZFA:0005260 fenestrated capillary vessel uberon UBERON:2005260 fenestrated capillary FMA ZFA Capillary that has pores in the endothelial cells (60-80 nm in diameter) that are spanned by a diaphragm of radially oriented fibrils and allow small molecules and limited amounts of protein to diffuse Wikipedia:Capillary#Types Wikipedia:Fenestra_(histology) fenestrated blood vessel endothelium ZFA:0005260 UMLS:C1179615 ncithesaurus:Fenestrated_Capillary fenestrated capillary vessel FMA:63196 Non neural ectoderm that surrounds the presumptive neural plate and gives rise to neurogenic placodes. This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon teleost_anatomy_curators ZFA:0007013 uberon UBERON:2007013 preplacodal ectoderm Non neural ectoderm that surrounds the presumptive neural plate and gives rise to neurogenic placodes. ZFIN:curator Structures of the dermis, epidermis, glands and pigment cells recognizable on the external surfaces of the integument. This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon amphibian_anatomy_curators uberon UBERON:3000961 Not clear how this differs from parent class. See https://github.com/obophenotype/uberon/issues/1305 external integument structure Structures of the dermis, epidermis, glands and pigment cells recognizable on the external surfaces of the integument. AAO:EJS Dermal, epidermal, glandular and pigment structures of the external head integument. This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon amphibian_anatomy_curators uberon UBERON:3000972 head external integument structure Dermal, epidermal, glandular and pigment structures of the external head integument. AAO:EJS Dermal, epidermal, glandular and pigment structures of the body integument. This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon amphibian_anatomy_curators uberon UBERON:3000977 body external integument structure Dermal, epidermal, glandular and pigment structures of the body integument. AAO:EJS Dermal, epidermal, glandular and pigment structures of the tail integument. This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon amphibian_anatomy_curators uberon UBERON:3000982 tail external integument structure Dermal, epidermal, glandular and pigment structures of the tail integument. AAO:EJS Blood vessels in respiratory skin. Modified from the original AAO source amphibian_anatomy_curators uberon UBERON:3010200 vasculature of respiratory integument Blood vessels in respiratory skin. AAO:EJS Skeletal tissue that is mineralized. mineralized tissue VSAO:0000013 XAO:0004039 uberon UBERON:4000013 mineralized skeletal tissue Skeletal tissue that is mineralized. XAO:0004039 XAO:EJS mineralized tissue VSAO:0000013 Extracellular matrix that is mineralized. This class was sourced from an external ontology (vertebrate_skeletal_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon vertebrate_skeletal_anatomy_curators uberon UBERON:4000020 mineralized extracellular matrix Extracellular matrix that is mineralized. PSPUB:0000170 Bone tissue mineralized with hydroxyapatite. vertebrate_skeletal_anatomy_curators uberon UBERON:4000115 mineralized bone tissue Bone tissue mineralized with hydroxyapatite. PSPUB:0000170 An anatomical surface that is part of a bone. bone surface uberon UBERON:4200230 surface of bone surface of bone An anatomical surface that is part of a bone. PHENOSCAPE Left part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. http://orcid.org/0000-0001-5208-3432 uberon UBERON:8000006 left side of back Left part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. https://microbiomedb.org/ Right part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. http://orcid.org/0000-0001-5208-3432 uberon UBERON:8000007 right side of back Right part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. https://microbiomedb.org/ A venule that is located in the anorectum. http://orcid.org/0000-0002-2825-0621 anorectum venule uberon UBERON:8410008 venule of anorectum A venule that is located in the anorectum. http://orcid.org/0000-0003-3440-1876 An arteriole that is located in the anorectum. http://orcid.org/0000-0002-2825-0621 anorectum arteriole uberon UBERON:8410009 arteriole of anorectum An arteriole that is located in the anorectum. http://orcid.org/0000-0003-3440-1876 An arteriole located in the colon. http://orcid.org/0000-0002-2825-0621 uberon UBERON:8410015 arteriole of colon An arteriole located in the colon. http://orcid.org/0000-0003-3440-1876 http://orcid.org/0000-0003-4183-8865/ An anatomical junction between two parts of the intestine. http://orcid.org/0000-0002-2825-0621 junction of intestine uberon UBERON:8410024 intestinal junction An anatomical junction between two parts of the intestine. ORCID:0000-0002-7073-9172 A venule located in the colon. http://orcid.org/0000-0002-2825-0621 uberon UBERON:8410048 venule of colon A venule located in the colon. https://orcid.org/0000-0003-3440-1876 https://orcid.org/0000-0003-4183-8865 A subdivision of the digestive tract in humans that includes the rectum, the anal canal and the anus. The anatomy, pathology and medical community considers the anus to be part of the large intestine, and supports the use of 'anorectum' to include rectum, anal canal and anus. Although a few resources seem to only include the distal part of the rectum in 'anorectum', this UBERON grouping term is meant to refer more broadly to the whole of rectum. Homo sapiens anorectal http://orcid.org/0000-0002-2825-0621 anorectal canal uberon UBERON:8410050 anorectum A subdivision of the digestive tract in humans that includes the rectum, the anal canal and the anus. DOI:10.1007/978-3-319-26938-2_8 DOI:10.1148/rg.2015150037 PMID:29742860 http://orcid.org/0000-0002-6826-8770 http://orcid.org/0000-0003-3440-1876 A capillary that is part of the anorectum. http://orcid.org/0000-0002-2825-0621 blood vessel capillary of anorectum uberon UBERON:8410056 capillary of anorectum A capillary that is part of the anorectum. http://orcid.org/0000-0003-3440-1876 A capillary that is part of the colon. http://orcid.org/0000-0002-2825-0621 blood vessel capillary of colon uberon UBERON:8410057 capillary of colon A capillary that is part of the colon. http://orcid.org/0000-0003-3440-1876 2 2 1 2 FMA-abduced-lr definitional https://github.com/obophenotype/uberon/wiki/The-neural-crest only in species that have a stomach FMA https://github.com/obophenotype/uberon/wiki/The-neural-crest FMA cjm AAO https://github.com/geneontology/go-ontology/issues/16143 Mammals conservatively place at deuterostome, excluding acoelomates EHDAA2 true MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z infer input from direct reg GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity' enabling an MF enables its parts true GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' involved in BP This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps" If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this. inferring direct reg edge from input to regulatory subfunction inferring direct neg reg edge from input to regulatory subfunction inferring direct positive reg edge from input to regulatory subfunction effector input is compound function input Input of effector is input of its parent MF if effector directly regulates X, its parent MF directly regulates X if effector directly positively regulates X, its parent MF directly positively regulates X if effector directly negatively regulates X, its parent MF directly negatively regulates X 'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties). 'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).