An ontology for respresenting spatial concepts, anatomical axes, gradients, regions, planes, sides and surfaces. These concepts can be used at multiple biological scales and in a diversity of taxa, including plants, animals and fungi. The BSPO is used to provide a source of anatomical location descriptors for logically defining anatomical entity classes in anatomy ontologies. Biological Spatial Ontology * BSPO:$sequence(7,0,999999999)$ spatial based on FBql 2021-10-13 definition The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition definition term replaced by Use on obsolete terms, relating the term to another term that can be used as a substitute Person:Alan Ruttenberg Person:Alan Ruttenberg Add as annotation triples in the granting ontology 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 synonym typically used in the context of human anatomy synonym typically used in the context of vertebrate anatomy namespace-id-rule synonym_type_property database_cross_reference has_exact_synonym has_narrow_synonym has_obo_format_version has_obo_namespace has_related_synonym has_scope has_synonym_type shorthand http://www.w3.org/2000/01/rdf-schema#seeAlso spatial seeAlso true seeAlso see also is part of 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) this day is part of this year (occurrent parthood) 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. 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/ 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 BFO:0000050 spatial part_of part_of part of part of http://www.obofoundry.org/ro/#OBO_REL:part_of has part 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) this year has part this day (occurrent parthood) 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. 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/ 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 BFO:0000051 spatial has_part has_part has part has part preceded by 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 preceded by 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. precedes BSPO:0000095 spatial anatomical_relation anatomical_relation anatomical relation true 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:0000096 rostral_to spatial 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 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 spatial 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 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:0000098 spatial 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 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:0000099 caudal to spatial 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 caudal to x proximal to y iff x is closer to the point of attachment with the body than y. BSPO:0000100 spatial proximal_to proximal_to The elbow is proximal to the hand, but distal to the shoulder. proximal to x proximal to y iff x is closer to the point of attachment with the body than y. BSPO:cjm RO:0002221 BSPO:0000101 spatial obsolete_surrounds obsolete_surrounds obsolete surrounds true 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:0000102 spatial 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 BSPO:0000103 spatial vicinity_of vicinity_of vicinity of Crosses at an angle that is 90 degrees, or close to 90 degrees. In any non-linear organism, the main axes are rarely perpendicular when taken through the organism as a whole. BSPO:0000104 spatial approximately_perpendicular_to approximately_perpendicular_to approximately perpendicular to Crosses at an angle that is 90 degrees, or close to 90 degrees. In any non-linear organism, the main axes are rarely perpendicular when taken through the organism as a whole. BSPO:cjm On the same side as. For example, the left arm is ipsilateral to the left leg. BSPO:0000105 spatial ipsilateral_to ipsilateral_to ipsilateral to On the same side as. For example, the left arm is ipsilateral to the left leg. BSPO:cjm On the opposite side from. For example, the left arm is contralateral to the right arm (and the right leg). BSPO:0000106 spatial contralateral_to contralateral_to contralateral to On the opposite side from. For example, the left arm is contralateral to the right arm (and the right leg). BSPO:cjm Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines. BSPO:0000107 spatial 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 spatial superficial_to superficial_to superficial to Near the outer surface of the organism. Thus, skin is superficial to the muscle layer. BSPO:cjm RO:0002219 BSPO:0000109 spatial obsolete_surrounded_by obsolete_surrounded_by obsolete surrounded_by true Closer to the left side of the organism. Example: The dorsal fin is right of the left pectoral fin, but is left of the right eye. On the type level: X left of Y <=> every instance x of X is left of some instance y of Y, and there exists some organism o such that x part of o and y part of o. BSPO:0000110 spatial left_of left_of left of Closer to the left side of the organism. Example: The dorsal fin is right of the left pectoral fin, but is left of the right eye. On the type level: X left of Y <=> every instance x of X is left of some instance y of Y, and there exists some organism o such that x part of o and y part of o. BSPO:cjm Closer to the right side of the organism. Example: The dorsal fin is right of the left pectoral fin, but is left of the right eye. On the type level: X left of Y <=> every instance x of X is right of some instance y of Y, and there exists some organism o such that x part of o and y part of o. BSPO:0000111 spatial right_of right_of right of Closer to the right side of the organism. Example: The dorsal fin is right of the left pectoral fin, but is left of the right eye. On the type level: X left of Y <=> every instance x of X is right of some instance y of Y, and there exists some organism o such that x part of o and y part of o. BSPO:cjm Direcly opposite to. i.e. on the opposite side through the axis. BSPO:0000113 spatial opposite_to opposite_to opposite to Direcly opposite to. i.e. on the opposite side through the axis. BSPO:cjm X lateral to y if x is further from the midsagittal plane than y. Jennifer Girón 2021-04-21T01:01:01Z lateral to Jennifer Girón 2021-04-21T01:01:01Z X medial to y if x is closer to the midsagittal plane than y. medial to X in left side of Y <=> if Y is subdivided into two left and right portions, X is part of the left portion. BSPO:0000120 spatial 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 right side of Y <=> if Y is subdivided into two left and right portions, X is part of the right portion. BSPO:0000121 spatial 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 posterior side of Y <=> if Y is subdivided into two anterior and posterior portions, X is part of the posterior portion. BSPO:0000122 spatial 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 anterior side of Y <=> if Y is subdivided into two anterior and posterior portions, X is part of the anterior portion. BSPO:0000123 spatial 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 in proximal side of y <=> if y is subdivided into two proximal and distal portions, y is part of the proximal portion. BSPO:0000124 spatial in_proximal_side_of in_proximal_side_of in proximal side of 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 in distal side of y <=> if y is subdivided into two proximal and distal portions, y is part of the distal portion. BSPO:0000125 spatial in_distal_side_of in_distal_side_of in distal side of 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 BSPO:0000126 spatial 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 superficial part of Y <=> if Y is subdivided into two superficial and deep portions, X is part of the superficial portion. BSPO:0001100 spatial in_superficial_part_of in_superficial_part_of in superficial part of X superficial part of Y <=> if Y is subdivided into two superficial and deep portions, X is part of the superficial portion. BSPO:cjm X superficial part of Y <=> if Y is subdivided into two superficial and deep portions, X is part of the deep portion. BSPO:0001101 spatial in_deep_part_of in_deep_part_of in deep part of X superficial part of Y <=> if Y is subdivided into two superficial and deep portions, X is part of the deep portion. BSPO:cjm X proximalmost part of Y <=> X is in proximal side of Y and X is adjacent to the proximal boundary of Y BSPO:0001106 spatial 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 immediately deep to y iff x deep_to y and x is contiguous with y. BSPO:0001107 spatial immediately_deep_to immediately_deep_to immediately deep to 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 BSPO:0001108 spatial 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 BSPO:0001113 spatial preaxialmost_part_of preaxialmost_part_of preaxialmost part of x preaxial to y iff x is further along the preaxial-postaxial axis than y, towards the postaxial side. BSPO:0001114 spatial posterior to (developmentally) postaxial_to postaxial_to postaxial to x preaxial to y iff x is further along the preaxial-postaxial axis than y, towards the postaxial side. http://medical-dictionary.thefreedictionary.com/postaxial posterior to (developmentally) MA:th BSPO:0001115 spatial postaxialmost_part_of postaxialmost_part_of postaxialmost part of X intersects median plane of iff X crosses the midine plane of Y. BSPO:0005001 spatial intersects_midsagittal_plane_of intersects_midsagittal_plane_of intersects midsagittal plane of BSPO:0015001 spatial finishes_axis finishes_axis A directional axis can be divided by a plane. Following Allen Interval Algebra terminology we say that the side on which the axis initiates starts the axis, with the other side finishing the axis. If s finishes axis x, and x has end point p, then x overlaps p finishes axis BSPO:0015002 spatial follows_axis follows_axis follows axis BSPO:0015003 spatial has_axis has_axis has axis A relation between an axis and a part of an organism, in which the part defines the initial point of the axis. BSPO:0015004 spatial has_end_point has_end_point Axes can be defined in a given species by subtyping the relevant axis type and stating a end and end point has end point A relation between an axis and a part of an organism, in which the part defines the initial point of the axis. BSPO:cjm crossing at right angles BSPO:0015005 spatial orthogonal_to orthogonal_to orthogonal to crossing at right angles BSPO:cjm Intersects at two points. BSPO:0015006 spatial passes_through passes_through passes through Intersects at two points. BSPO:cjm BSPO:0015007 spatial starts_axis starts_axis A directional axis can be divided by a plane. Following Allen Interval Algebra terminology we say that the side on which the axis initiates starts the axis, with the other side finishing the axis. . If s starts axis x, and x has start point p, then x overlaps p starts axis BSPO:0015008 spatial surface_of surface_of placeholder. used for relation between anatomical surface and an anatomical side. surface of x immediately anterior to y iff x anterior to y and x is contiguous with y. BSPO:0015009 spatial immediately_anterior_to immediately_anterior_to immediately anterior to x immediately anterior to y iff x anterior to y and x is contiguous with y. BSPO:curators x immediately distal to y iff x distal to y and x is contiguous with y. BSPO:0015010 spatial immediately_distal_to immediately_distal_to immediately distal to x immediately distal to y iff x distal to y and x is contiguous with y. BSPO:curators x immediately dorsal to y iff x dorsal to y and x is contiguous with y. BSPO:0015011 spatial immediately_dorsal_to immediately_dorsal_to immediately dorsal to x immediately dorsal to y iff x dorsal to y and x is contiguous with y. BSPO:curators x immediately posterior to y iff x posterior_to y and x is contiguous with y. BSPO:0015012 spatial immediately_posterior_to immediately_posterior_to immediately posterior to x immediately posterior to y iff x posterior_to y and x is contiguous with y. BSPO:curators x immediately proximal to y iff x proximal to y and x is contiguous with y. BSPO:0015013 spatial immediately_proximal_to immediately_proximal_to immediately proximal to x immediately proximal to y iff x proximal to y and x is contiguous with y. BSPO:curators x immediately superficial to y iff x superficial to y and x is contiguous with y. BSPO:0015014 spatial 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 immediately ventral to y iff x ventral to y and x is contiguous with y. BSPO:0015015 spatial immediately_ventral_to immediately_ventral_to immediately ventral to x immediately ventral to y iff x ventral to y and x is contiguous with y. BSPO:curators x immediately left of y iff x left_of y and x is contiguous with y. BSPO:0015016 spatial immediately_left_of immediately_left_of immediately left of x immediately left of y iff x left_of y and x is contiguous with y. BSPO:curators x immediately right of y iff x right of y and x is contiguous with y. BSPO:0015017 spatial immediately_right_of immediately_right_of immediately right of x immediately right of y iff x right of 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 spatial 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 X ventral side of Y <=> if Y is subdivided into two dorsal and ventral portions, X is part of the ventral portion. BSPO:0015102 spatial in_ventral_side_of in_ventral_side_of in ventral side of X ventral side of Y <=> if Y is subdivided into two dorsal and ventral portions, X is part of the ventral portion. BSPO:cjm nearer to the oral opening of the organism, on the oral-aboral axis. BSPO:0015201 spatial oral_to oral_to oral to nearer to the oral opening of the organism, on the oral-aboral axis. BSPO:cjm nearer to the aboral opening of the organism, on the oral-aboral axis. BSPO:0015202 spatial aboral_to aboral_to aboral to nearer to the aboral opening of the organism, on the oral-aboral axis. BSPO:cjm x preaxial to y iff x is further along the preaxial-postaxial axis than y, towards the front. BSPO:1000000 spatial anterior to (developmentally) lateral (radial) to medial (tibial) to preaxial_to preaxial_to preaxial to x preaxial to y iff x is further along the preaxial-postaxial axis than y, towards the front. http://medical-dictionary.thefreedictionary.com/preaxial anterior to (developmentally) MA:th 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 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 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 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 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 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 '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 David Osumi-Sutherland X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after David Osumi-Sutherland starts_at_end_of X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by David Osumi-Sutherland ends_at_start_of meets X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes 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. http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) RO:0002131 spatial overlaps overlaps "(forall (x y) (iff (overlaps x y) (exists (z) (and (part of z x) (part of z y)))))" CLIF [] overlaps overlaps true x overlaps y iff they have some part in common. BSPO:cjm A is spatially_disjoint_from B if and only if they have no parts in common There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. Chris Mungall Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy BFO_0000051 exactly 0 (BFO_0000050 some ?Y) spatially disjoint from https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern 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. has component 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 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) 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) 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)". 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 capable of part of true A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. The epidermis layer of a vertebrate is adjacent to the dermis. The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies. The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used. x adjacent to y if and only if x and y share a boundary. This relation acts as a join point with BSPO Chris Mungall RO:0002220 spatial adjacent_to adjacent_to adjacent to adjacent to A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. 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 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 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 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 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 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 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 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 inverse of has input Chris Mungall input of 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 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) Chris Mungall is kinase activity 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 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 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 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 A relation between an axis and a part of an organism, in which the part defines the initial point of the axis. :has_start_point spatial has_start_point has_start_point Axes can be defined in a given species by subtyping the relevant axis type and stating a start and end point. has start point A relation between an axis and a part of an organism, in which the part defines the initial point of the axis. BSPO:cjm x is parallel t y iff x and y are lines or planes which when extended indefinitely do not cross. spatial parallel_to parallel to x is parallel t y iff x and y are lines or planes which when extended indefinitely do not cross. BSPO:curators 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 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 immaterial entity The side of an organism that is left of the sagittal plane. left spatial BSPO:0000000 left side The side of an organism that is left of the sagittal plane. BSPO:cjm upper spatial BSPO:0000001 Consider merging with superior side. upper side lower spatial BSPO:0000002 Consider merging with inferior side. lower side BSPO:0000021 spatial BSPO:00000021 was made obsolete because the ID had too many digits deep-superficial gradient (obsolete) true deep spatial BSPO:0000003 deep side superficial spatial BSPO:0000004 superficial side A 2D surface of an anatomical continuant. FMA:24137 surface spatial BSPO:0000005 to be merged into CARO anatomical surface A 2D surface of an anatomical continuant. BSPO:cjm Fiat anatomical region extending a short distance from the boundary of an object inwards. edge margin spatial BSPO:0000006 anatomical margin Fiat anatomical region extending a short distance from the boundary of an object inwards. BSPO:cjm The side of an organism that is right of the sagittal plane. right spatial BSPO:0000007 right side The side of an organism that is right of the sagittal plane. BSPO:cjm BSPO:wd Sagittal plane that divides a bilateral body into unequal left and right parts. parasagittal section spatial BSPO:0000008 parasagittal plane Sagittal plane that divides a bilateral body into unequal left and right parts. BSPO:mah Sagittal plane that divides bilateral body into equal left and right parts. FMA:74563 median sagittal plane midline plane midsagittal section spatial median plane BSPO:0000009 only in bilaterally symmetrical organisms midsagittal plane Sagittal plane that divides bilateral body into equal left and right parts. BSPO:mah median sagittal plane FMA:74563 A straight line through space, intersecting an anatomical entity. http://upload.wikimedia.org/wikipedia/commons/3/34/Anatomical_Directions_and_Axes.JPG spatial BSPO:0000010 Axis directions are defined in terms of axes. anatomical axis A straight line through space, intersecting an anatomical entity. BSPO:cjm An anatomical axis determined by gravity. spatial superior-inferior axis BSPO:0000011 upper-lower axis An anatomical axis determined by gravity. BSPO:cjm An axis that extends from an internal position to a more external position in the body or body part. spatial BSPO:0000012 Muscles are frequently categorized as 'deep', 'intermediate', and 'superficial'. deep-superficial axis An axis that extends from an internal position to a more external position in the body or body part. BSPO:PM An axis that extends through an organism from head end to opposite end of body or tail. A-P axis AP axis anteroposterior axis cephalocaudal axis craniocaudal axis rostral/caudal rostrocaudal axis spatial longitudinal axis BSPO:0000013 In sponges, AP is used to indicate the direction of movement [in larval stage] (as it is in other metazoans that move, e.g., the basal bilaterians). [PM] anterior-posterior axis An axis that extends through an organism from head end to opposite end of body or tail. BSPO:cjm cephalocaudal axis http://en.wikipedia.org/wiki/Anatomical_terms_of_location craniocaudal axis rostral/caudal rostrocaudal axis An axis that extends through an organism or organism part from the part of the organism or organism part attached to a substrate (basal) to the furthest from the attachment (apical). Note that the apical-basal axis is often used for organismal parts where there is attachment via a basal lamina or other structure. apical/basal spatial longitudinal axis BSPO:0000014 apical-basal axis relative to substrate An axis that extends through an organism or organism part from the part of the organism or organism part attached to a substrate (basal) to the furthest from the attachment (apical). Note that the apical-basal axis is often used for organismal parts where there is attachment via a basal lamina or other structure. BSPO:mah An axis that extends from the point of attachment of a structure (proximal) to the point furthest away from the plane of attachment (distal). proximal/distal proximodistal spatial BSPO:0000015 In some communities, proximal and distal are used when specifying the position of parts of elements that are contained within the body, such as gill arches or vertebral spines. In these cases, use of the classes medial-lateral axis or medial-external axis are more appropriate. proximal-distal axis An axis that extends from the point of attachment of a structure (proximal) to the point furthest away from the plane of attachment (distal). BSPO:curators http://en.wikipedia.org/wiki/Anatomical_terms_of_location An axis that is approximately perpendicular to the anterior-posterior axis and that extends through the horizontal plane of the body. D-V axis DV axis dorsoventral axis anterior-posterior axis spatial BSPO:0000016 dorsal-ventral axis An axis that is approximately perpendicular to the anterior-posterior axis and that extends through the horizontal plane of the body. BSPO:curators anterior-posterior axis An axis that bisects an organism from left to right sides of body, through a sagittal plane. L-R axis LR axis R-L axis RL axis dextro-sinister axis left to right axis right to left axis right-left axis spatial BSPO:0000017 left-right axis An axis that bisects an organism from left to right sides of body, through a sagittal plane. BSPO:cjm Anatomical plane that divides body into anterior and posterior parts. FMA:12247 axial plane axial section transverse section spatial cross-section BSPO:0000018 transverse plane Anatomical plane that divides body into anterior and posterior parts. BSPO:mah Anatomical plane that divides bilateral body into dorsal and ventral parts. FMA:52810 frontal plane horizontal anatomical plane horizontal section spatial coronal section frontal section BSPO:0000019 horizontal plane Anatomical plane that divides bilateral body into dorsal and ventral parts. BSPO:mah horizontal anatomical plane FMA:52810 Anatomical gradient that is distributed along the upper-lower axis. spatial BSPO:0000020 upper-lower gradient Anatomical gradient that is distributed along the upper-lower axis. BSPO:wd Anatomical gradient that is distributed along the deep-superficial axis. spatial BSPO:0000021 deep-superficial gradient Anatomical gradient that is distributed along the deep-superficial axis. BSPO:wd The side that is higher relative to the substrate. superior spatial cranial BSPO:0000022 superior side The side that is higher relative to the substrate. BSPO:curators Anatomical gradient that is distributed along the apical-basal axis. spatial BSPO:0000023 apical-basal gradient Anatomical gradient that is distributed along the apical-basal axis. BSPO:wd Anatomical gradient that is distributed along the proximal-distal axis. spatial BSPO:0000024 proximal-distal gradient Anatomical gradient that is distributed along the proximal-distal axis. BSPO:wd The side that is lower relative to the substrate. inferior spatial caudal BSPO:0000025 inferior side The side that is lower relative to the substrate. BSPO:curators Anatomical region that overlaps the anterior and dorsal regions of a body or body part. Melissa Haendel 2009-06-15T01:01:38Z anterodorsal region spatial BSPO:0000026 antero-dorsal region Anatomical region that overlaps the anterior and dorsal regions of a body or body part. BSPO:wd Anatomical region that overlaps the anterior and ventral regions of a body or body part. Melissa Haendel 2009-06-15T01:04:59Z anteroventral region spatial BSPO:0000027 antero-ventral region Anatomical region that overlaps the anterior and ventral regions of a body or body part. BSPO:wd Anatomical region that overlaps the posterior and lateral regions of the body or body part. Melissa Haendel 2009-06-15T01:06:01Z posterolateral region spatial BSPO:0000028 postero-lateral region Anatomical region that overlaps the posterior and lateral regions of the body or body part. BSPO:wd Anatomical region that overlaps the anterior and lateral regions of a body or body part. Melissa Haendel 2009-06-15T01:07:18Z anterolateral region spatial BSPO:0000029 antero-lateral region Anatomical region that overlaps the anterior and lateral regions of a body or body part. BSPO:wd Anatomical region that overlaps the posterior and dorsal regions of the body or body part. Melissa Haendel 2009-06-15T01:08:13Z posterodorsal region spatial BSPO:0000030 postero-dorsal region Anatomical region that overlaps the posterior and dorsal regions of the body or body part. BSPO:wd spatial BSPO:0000031 upper region spatial BSPO:0000032 lower region Anatomical region located deep within an organism or structure. spatial BSPO:0000033 deep region Anatomical region located deep within an organism or structure. BSPO:wd Anatomical region superficially located on the body or body part. spatial BSPO:0000034 superficial region Anatomical region superficially located on the body or body part. BSPO:wd Anatomical region that overlaps the posterior and ventral regions of a body or body part. Melissa Haendel 2009-06-15T01:08:38Z posteroventral region spatial BSPO:0000035 postero-ventral region Anatomical region that overlaps the posterior and ventral regions of a body or body part. BSPO:wd Melissa Haendel 2009-06-16T08:49:03Z anterior-most anteriormost spatial BSPO:0000036 anterior-most region Melissa Haendel 2009-06-16T08:49:50Z posterior-most posteriormost spatial BSPO:0000037 posterior-most region Melissa Haendel 2009-06-16T08:50:26Z dorsal-most dorsalmost spatial BSPO:0000038 dorsal-most region Melissa Haendel 2009-06-16T08:51:07Z ventral-most ventralmost spatial BSPO:0000039 ventral-most region spatial BSPO:0000040 upper/lower compartment boundary spatial BSPO:0000041 deep/superficial compartment boundary Anatomical margin that is located on the antero-medial region of the body or body part. Melissa Haendel 2009-09-10T08:49:57Z anteromedial margin spatial BSPO:0000042 antero-medial margin Anatomical margin that is located on the antero-medial region of the body or body part. BSPO:wd spatial BSPO:0000043 apical/basal compartment boundary spatial BSPO:0000044 proximal/distal compartment boundary Anatomical margin that is located on the antero-lateral region of the body or body part. Melissa Haendel 2009-09-10T08:50:37Z anterolateral margin spatial BSPO:0000045 antero-lateral margin Anatomical margin that is located on the antero-lateral region of the body or body part. BSPO:wd Anatomical margin that is located on the postero-medial region of the body or body part. Melissa Haendel 2009-09-10T08:51:07Z posteromedial margin spatial BSPO:0000046 postero-medial margin Anatomical margin that is located on the postero-medial region of the body or body part. BSPO:wd Anatomical margin that is located on the postero-lateral region of the body or body part. Melissa Haendel 2009-09-10T08:51:42Z posterolateral margin spatial BSPO:0000047 postero-lateral margin Anatomical margin that is located on the postero-lateral region of the body or body part. BSPO:wd Anatomical margin that is located on the dorso-medial region of the body or body part. Melissa Haendel 2009-09-10T08:52:04Z dorso-medial margin spatial BSPO:0000048 dorso-medial margin Anatomical margin that is located on the dorso-medial region of the body or body part. BSPO:wd Anatomical margin that is located on the ventro-medial region of the body or body part. Melissa Haendel 2009-09-10T08:52:48Z ventromedial margin spatial BSPO:0000049 ventro-medial margin Anatomical margin that is located on the ventro-medial region of the body or body part. BSPO:wd Anatomical region that overlaps the anterior and medial regions of the body or body part. Melissa Haendel 2009-09-10T08:55:32Z anteromedial region spatial BSPO:0000050 antero-medial region Anatomical region that overlaps the anterior and medial regions of the body or body part. BSPO:wd Material anatomical entity defined by change in the value of some quantity per unit of distance across some spatial axis. FBql:00005254 spatial BSPO:0000051 anatomical gradient Material anatomical entity defined by change in the value of some quantity per unit of distance across some spatial axis. BSPO:cjm Anatomical gradient that is distributed along the anterior-posterior axis. FBcv:0000142 FBql:00005256 spatial BSPO:0000052 anterior-posterior gradient Anatomical gradient that is distributed along the anterior-posterior axis. BSPO:wd Anatomical gradient that is distributed along the dorsal-ventral axis. FBcv:0000143 FBql:00005255 spatial BSPO:0000053 dorsal-ventral gradient Anatomical gradient that is distributed along the dorsal-ventral axis. BSPO:wd An anatomical region bounded by a plane perpendicular to an axis through the middle. FBql:00005841 spatial BSPO:0000054 anatomical side An anatomical region bounded by a plane perpendicular to an axis through the middle. BSPO:cjm An anatomical region that is the entire part of an anatomical structure anterior to a transverse plane and bounded on one side by the same transverse plane. FBcv:0000053 FBql:00005848 anterior rostral spatial BSPO:0000055 anterior side An anatomical region that is the entire part of an anatomical structure anterior to a transverse plane and bounded on one side by the same transverse plane. BSPO:RW An anatomical region that is the entire part of an anatomical structure posterior to a transverse plane and bounded on one side by the same transverse plane. FBcv:0000065 FBql:00005849 posterior caudal spatial BSPO:0000056 posterior side An anatomical region that is the entire part of an anatomical structure posterior to a transverse plane and bounded on one side by the same transverse plane. BSPO:RW BSPO:wd caudal Anatomical side that is located on the apical end of an organism or structure. FBcv:0000054 FBql:00005854 apical spatial BSPO:0000057 apical side Anatomical side that is located on the apical end of an organism or structure. BSPO:wd Anatomical side that is located on the basal end of an organism or structure. FBcv:0000055 FBql:00005855 basal spatial BSPO:0000058 The part of the organism attached to a substrate. Axis of symmetry. basal side Anatomical side that is located on the basal end of an organism or structure. BSPO:wd Anatomical side that is centrally located on an organism or structure. FBcv:0000056 FBql:00015851 central spatial BSPO:0000059 central is not an axis direction central side Anatomical side that is centrally located on an organism or structure. BSPO:wd On the opposite side. FBcv:0000057 FBql:00005851 contralateral spatial BSPO:0000060 inherited from flybase cv. not clear how this would be used. Suggest we obsolete, and use the corresponding relation. contralateral side On the opposite side. BSPO:cjm FBcv:0000066 FBql:00005852 proximal spatial BSPO:0000061 proximal side Anatomical side that is distally located on an organism or structure. FBcv:0000058 FBql:00005853 distal spatial BSPO:0000062 distal side Anatomical side that is distally located on an organism or structure. BSPO:wd An anatomical region that is the entire part of an anatomical structure dorsal to a horizontal plane and bounded on one side by the same transverse plane. FBcv:0000059 FBql:00005842 dorsal spatial BSPO:0000063 dorsal side An anatomical region that is the entire part of an anatomical structure dorsal to a horizontal plane and bounded on one side by the same transverse plane. BSPO:wd Anatomical region that overlaps the posterior and medial regions of the body or body part. Melissa Haendel 2009-09-10T08:56:39Z posteromedial region spatial BSPO:0000064 postero-medial region Anatomical region that overlaps the posterior and medial regions of the body or body part. BSPO:wd On the same side FBcv:0000062 FBql:00005850 ipsilateral spatial BSPO:0000065 inherited from flybase cv. not clear how this would be used. Suggest we obsolete, and use the corresponding relation. ipsilateral side On the same side BSPO:cjm FBcv:0000063 FBql:00005844 lateral spatial BSPO:0000066 lateral side FBcv:0000064 FBql:00005847 medial spatial BSPO:0000067 a point in the centre of the organism (where the left-right axis intersects the midsagittal plane) medial side An anatomical region that is the entire part of an anatomical structure ventral to a horizontal plane and bounded on one side by the same horizontal plane. FBcv:0000070 FBql:00005843 ventral spatial BSPO:0000068 ventral side An anatomical region that is the entire part of an anatomical structure ventral to a horizontal plane and bounded on one side by the same horizontal plane. BSPO:RW BSPO:wd Anatomical region that overlaps the dorsal and medial regions of the body or body part. Melissa Haendel 2009-09-10T08:57:22Z dorsomedial region spatial BSPO:0000069 dorso-medial region Anatomical region that overlaps the dorsal and medial regions of the body or body part. BSPO:wd A 3D region in space without well-defined compartmental boundaries; for example, the dorsal region of an ectoderm. FBql:00005841 spatial BSPO:0000070 to be merged into CARO anatomical region A 3D region in space without well-defined compartmental boundaries; for example, the dorsal region of an ectoderm. BSPO:cjm Anatomical region anteriorly located on the body or body part. FBql:00005848 spatial BSPO:0000071 anterior region Anatomical region anteriorly located on the body or body part. BSPO:wd Anatomical region posteriorly located on the body or body part. FBql:00005849 spatial BSPO:0000072 posterior region Anatomical region posteriorly located on the body or body part. BSPO:wd Anatomical region located on the apical end on the body or body part. FBql:00005854 spatial BSPO:0000073 apical region Anatomical region located on the apical end on the body or body part. BSPO:wd Anatomical region located basally on the body or body part. FBql:00005855 spatial BSPO:0000074 basal region Anatomical region located basally on the body or body part. BSPO:wd Anatomical region centrally located on the body or body part. FBql:00015851 spatial BSPO:0000075 central region Anatomical region centrally located on the body or body part. BSPO:wd FBql:00005851 spatial BSPO:0000076 inherited from flybase cv. not clear how this would be used contralateral region Anatomical region proximally located on the body or body part. FBql:00005852 spatial BSPO:0000077 proximal region Anatomical region proximally located on the body or body part. BSPO:wd Anatomical region distally located on the body or body part. FBql:00005853 spatial BSPO:0000078 distal region Anatomical region distally located on the body or body part. BSPO:wd Anatomical region dorsally located on the body or body part. FBql:00005842 spatial BSPO:0000079 dorsal region Anatomical region dorsally located on the body or body part. BSPO:wd Anatomical region that overlaps the dorsal and lateral regions of a body or body part. FBql:00005845 dorsolateral region spatial BSPO:0000080 dorso-lateral region Anatomical region that overlaps the dorsal and lateral regions of a body or body part. BSPO:wd FBql:00005850 spatial BSPO:0000081 ipsilateral region Anatomical region laterally located on the body or body part. FBql:00005844 spatial BSPO:0000082 lateral region Anatomical region laterally located on the body or body part. BSPO:wd Anatomical region medially located on the body or body part. FBql:00005847 spatial BSPO:0000083 medial region Anatomical region medially located on the body or body part. BSPO:wd Anatomical region ventrally located on the body or body part. FBql:00005843 spatial BSPO:0000084 ventral region Anatomical region ventrally located on the body or body part. BSPO:wd Anatomical region that overlaps the ventral and lateral regions of a body or body part. FBql:00005846 ventrolateral region spatial BSPO:0000085 This is an example of a composition of two axis positions. ventro-lateral region Anatomical region that overlaps the ventral and lateral regions of a body or body part. BSPO:wd FBql:00005873 FMA:9647 spatial BSPO:0000086 to be merged into CARO anatomical compartment FBcv:0000031 FBql:00005874 spatial BSPO:0000087 anterior compartment FBcv:0000032 FBql:00005878 spatial BSPO:0000088 compartment boundary FBcv:0000035 FBql:00005876 spatial BSPO:0000089 dorsal compartment FBcv:0000036 FBql:00005875 spatial BSPO:0000090 posterior compartment FBcv:0000037 FBql:00005877 spatial BSPO:0000091 ventral compartment FBql:00005881 spatial BSPO:0000092 to be merged into CARO anatomical compartment boundary FBcv:0000033 FBql:00005880 spatial BSPO:0000093 anterior/posterior compartment boundary FBcv:0000034 FBql:00005879 spatial BSPO:0000094 dorsal/ventral compartment boundary The region corresponding to the ventral region of the entity, towards the midline. Melissa Haendel 2009-09-10T08:57:54Z medioventral region ventromedial region spatial BSPO:0000112 ventro-medial region The region corresponding to the ventral region of the entity, towards the midline. BSPO:wd Anatomical region peripherally located on the body or body part. spatial BSPO:0000127 peripheral region Anatomical region peripherally located on the body or body part. BSPO:wd spatial BSPO:0000128 axial region spatial BSPO:0000129 peripheral side spatial BSPO:0000130 axial side An anatomical axis that extends from the side of the anatomical entity that is closer to an axis (adaxial) to the side that is further from the same axis (abaxial). wasila.dahdul 2013-07-02T11:20:29Z AA axis spatial dorsal-ventral axis BSPO:0000195 adaxial-abaxial axis An anatomical axis that extends from the side of the anatomical entity that is closer to an axis (adaxial) to the side that is further from the same axis (abaxial). BSPO:RW An anatomical axis that extends from the center of the body outwards or externally. wasila.dahdul 2013-07-02T11:21:42Z spatial proximal-distal axis BSPO:0000196 The medial-external axis could apply to a sphere-shaped body. medial-external axis An anatomical axis that extends from the center of the body outwards or externally. BSPO:curators An anatomical axis that is perpendicular to an apical/basal axis or proximal/distal axis and extends from the center of an axis (shoot axis or root in the case of plants) to any point on the exterior of the axis. wasila.dahdul 2013-07-02T11:23:31Z M-R axis MR axis spatial BSPO:0000197 In plants, lateral growth (http://purl.obolibrary.org/obo/GO_0080190) run is along the medial/radial axis (from medial to radial) [RW]. Also applies to radially symmetrical animals such as sea urchins, cnidarians [PM] or applies to more-or-less cylindrical body parts in animals, like limbs. medial-radial axis An anatomical axis that is perpendicular to an apical/basal axis or proximal/distal axis and extends from the center of an axis (shoot axis or root in the case of plants) to any point on the exterior of the axis. BSPO:curators An axis that extends from the oral opening to the furthest point in an organism that is directly opposite. wasila.dahdul 2013-07-02T11:29:33Z spatial BSPO:0000198 oral-aboral axis An axis that extends from the oral opening to the furthest point in an organism that is directly opposite. BSPO:PM An axis that extends from the animal end of an egg or early embryo to the opposite, vegetal end. In animals with yolk-bearing eggs, the vegetal end is the yolk bearing pole. (pertains to animals only - both vertebrate and invertebrate embryos). wasila.dahdul 2013-07-02T11:30:13Z A-V axis AV axis animal/vegetal axis spatial BSPO:0000199 animal-vegetal axis An axis that extends from the animal end of an egg or early embryo to the opposite, vegetal end. In animals with yolk-bearing eggs, the vegetal end is the yolk bearing pole. (pertains to animals only - both vertebrate and invertebrate embryos). BSPO:PM An axis of a plant structure that is determined by the direction of apical growth, either by an apical meristem or an apical cell. Apical is toward the direction of apical growth: toward the tip of a growing shoot axis, root, thallus, or non-vascular leaf. Basal is away from the direction of apical growth: toward the root-shoot junction in the case of the primary root or stem, toward the primary root or stem for higher order roots or branches, toward the point of attachment for non-vascular leaves, and toward the original point of growth (as determined in the embryo) for thalli. spatial BSPO:0000200 Plant structures that do not grow from an apical meristem, such as vascular leaves or petals, should be described using the proximal-distal axis. The proximal-distal axis may also be used for branches or lateral roots, and, in those cases, is concordant with the apical-basal axis. apical-basal axis relative to direction of growth An axis of a plant structure that is determined by the direction of apical growth, either by an apical meristem or an apical cell. Apical is toward the direction of apical growth: toward the tip of a growing shoot axis, root, thallus, or non-vascular leaf. Basal is away from the direction of apical growth: toward the root-shoot junction in the case of the primary root or stem, toward the primary root or stem for higher order roots or branches, toward the point of attachment for non-vascular leaves, and toward the original point of growth (as determined in the embryo) for thalli. BSPO:RW Anatomical plane that is perpendicular to a radial plane. wasila.dahdul 2014-01-22T15:34:31Z spatial BSPO:0000201 Need to add logical definitions. tangential plane Anatomical plane that is perpendicular to a radial plane. BSPO:wd Anatomical plane that follows the two dimensions specified by an apical-basal axis relative to direction of growth and a medial-lateral axis. wasila.dahdul 2014-01-22T15:34:02Z spatial BSPO:0000202 Need to add logical definitions. radial plane Anatomical plane that follows the two dimensions specified by an apical-basal axis relative to direction of growth and a medial-lateral axis. BSPO:wd Anatomical surface that is located on the anterior side of the body or body part. FBql:00005848 spatial BSPO:0000371 anterior surface Anatomical surface that is located on the anterior side of the body or body part. BSPO:wd Anatomical surface that is located on the posterior side of the body or body part. FBql:00005849 spatial BSPO:0000372 posterior surface Anatomical surface that is located on the posterior side of the body or body part. BSPO:wd Anatomical surface that is located on the apical side of the body or body part. FBql:00005854 spatial BSPO:0000373 apical surface Anatomical surface that is located on the apical side of the body or body part. BSPO:wd Anatomical surface that is located on the basal side of the body or body part. FBql:00005855 spatial BSPO:0000374 basal surface Anatomical surface that is located on the basal side of the body or body part. BSPO:wd FBql:00005851 spatial BSPO:0000376 contralateral surface Anatomical surface that is located on the proximal side of the body or body part. FBql:00005852 spatial BSPO:0000377 proximal surface Anatomical surface that is located on the proximal side of the body or body part. BSPO:wd Anatomical surface that is located on the distal side of the body or body part. FBql:00005853 spatial BSPO:0000378 distal surface Anatomical surface that is located on the distal side of the body or body part. BSPO:wd Anatomical surface that located on the dorsal side of the body or body part. FBql:00005842 spatial BSPO:0000379 dorsal surface Anatomical surface that located on the dorsal side of the body or body part. BSPO:wd Anatomical surface that is located on the same side of an organism or structure. FBql:00005850 spatial BSPO:0000381 ipsilateral surface Anatomical surface that is located on the same side of an organism or structure. BSPO:wd Anatomical surface that located on the lateral side of the body or body part. FBql:00005844 spatial BSPO:0000382 lateral surface Anatomical surface that located on the lateral side of the body or body part. BSPO:wd Anatomical surface that located on the medial side of the body or body part. FBql:00005847 spatial BSPO:0000383 medial surface Anatomical surface that located on the medial side of the body or body part. BSPO:wd Anatomical surface that is located on the ventral side of the body or body part. FBql:00005843 spatial BSPO:0000384 ventral surface Anatomical surface that is located on the ventral side of the body or body part. BSPO:wd A flat 2D plane intersecting an anatomical continuant, dividing it into two adjacent portions. FMA:242982 anatomical cross-section anatomical section plane section spatial cross-section BSPO:0000400 These anatomical sections are applicable to most bilaterally symmetrical animals, but bipedal animals such as humans have more complex usage of these terms. For example, in post-embryonic humans a coronal plane is vertical and a transverse plane is horizontal, but for embryos and quadrupeds a coronal plane is horizontal and a transverse plane is vertical. anatomical plane A flat 2D plane intersecting an anatomical continuant, dividing it into two adjacent portions. BSPO:cjm Anatomical plane that divides a bilateral body into left and right parts, not necessarily of even size. FMA:11361 left/right plane median plane sagittal section spatial BSPO:0000417 sagittal plane Anatomical plane that divides a bilateral body into left and right parts, not necessarily of even size. BSPO:DOS BSPO:cjm BSPO:mah Anatomical margin that is located on the anterior side of a body or body part. spatial BSPO:0000671 anterior margin Anatomical margin that is located on the anterior side of a body or body part. BSPO:wd Anatomical margin that is located on the posterior side of the body or body part. spatial BSPO:0000672 posterior margin Anatomical margin that is located on the posterior side of the body or body part. BSPO:wd Anatomical margin that is located on the apical side of the body or body part. spatial BSPO:0000673 apical margin Anatomical margin that is located on the apical side of the body or body part. BSPO:wd Anatomical margin that is located on the basal side of the body or body part. spatial BSPO:0000674 basal margin Anatomical margin that is located on the basal side of the body or body part. BSPO:wd Anatomical margin that is located on the proximal region of the body or body part. spatial BSPO:0000677 proximal margin Anatomical margin that is located on the proximal region of the body or body part. BSPO:wd Anatomical margin that is located on the distal side of the body or body part. spatial BSPO:0000678 distal margin Anatomical margin that is located on the distal side of the body or body part. BSPO:wd Anatomical margin that is located on the dorsal side of body or body part. spatial BSPO:0000679 dorsal margin Anatomical margin that is located on the dorsal side of body or body part. BSPO:wd Anatomical margin that is located on the dorso-lateral region of the body or body part. dorsolateral margin spatial BSPO:0000680 dorso-lateral margin Anatomical margin that is located on the dorso-lateral region of the body or body part. BSPO:wd Anatomical margin that is located on the lateral side of the body or body part. spatial BSPO:0000682 lateral margin Anatomical margin that is located on the lateral side of the body or body part. BSPO:wd Anatomical margin that is located on the medial side of the body or body part. spatial BSPO:0000683 medial margin Anatomical margin that is located on the medial side of the body or body part. BSPO:wd Anatomical margin that is located on the ventral side of the body or body part. spatial BSPO:0000684 ventral margin Anatomical margin that is located on the ventral side of the body or body part. BSPO:wd Anatomical margin that is located on the ventro-lateral region of the body or body part. ventrolateral margin spatial BSPO:0000685 This is an example of a composition of two axis positions ventro-lateral margin Anatomical margin that is located on the ventro-lateral region of the body or body part. BSPO:wd Anatomical margin that is located on the antero-dorso region of the body or body part. anterodorsal margin spatial BSPO:0000686 antero-dorsal margin Anatomical margin that is located on the antero-dorso region of the body or body part. BSPO:wd Anatomical margin that is located on the postero-dorsal region of the body or body part. posterodorsal margin spatial BSPO:0000687 postero-dorsal margin Anatomical margin that is located on the postero-dorsal region of the body or body part. BSPO:wd Anatomical margin that is located on the antero-ventral region of the body or body part. anteroventral margin spatial BSPO:0000688 antero-ventral margin Anatomical margin that is located on the antero-ventral region of the body or body part. BSPO:wd Anatomical margin that is located on the postero-ventral region of the body or body part. posteroventral margin spatial BSPO:0000689 postero-ventral margin Anatomical margin that is located on the postero-ventral region of the body or body part. BSPO:wd An axis that extends from the center of organism to one or other side. http://upload.wikimedia.org/wikipedia/commons/3/34/Anatomical_Directions_and_Axes.JPG M-L axis ML axis medio-lateral axis mediolateral axis spatial proximal-distal axis BSPO:0001001 Properly, the ML axis is a half axis; practically, its usage is less clumsy and less linguistically biased than "left-right". The terms may still be used relatively to describe locations along the LR axis. The gills are medial to the operculum, but lateral to the heart. medial-lateral axis An axis that extends from the center of organism to one or other side. BSPO:cjm 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. spatial CARO:0000000 anatomical entity 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. CARO:MAH Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. spatial CARO:0000003 anatomical structure connected 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. CC:DOS An anatomical entity that has mass. spatial CARO:0000006 material anatomical entity material anatomical entity An anatomical entity that has mass. CC:DOS An anatomical entity that has no mass. spatial CARO:0000007 immaterial anatomical entity An anatomical entity that has no mass. CC:DOS A one dimensional, immaterial anatomical entity. spatial CARO:0000008 anatomical line A one dimensional, immaterial anatomical entity. CC:DOS A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures. spatial CARO:0000010 anatomical boundary A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures. CC:DOS biological entity molecular process molecular_function catalytic activity biological_process true kinase activity transferase activity transferase activity, transferring phosphorus-containing groups data item data item information content entity information content entity curation status specification The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) PERSON:Bill Bug GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 curation status specification data about an ontology part Data about an ontology part is a data item about a part of an ontology, for example a term Person:Alan Ruttenberg data about an ontology part obsolescence reason specification The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. PERSON: Alan Ruttenberg PERSON: Melanie Courtot obsolescence reason specification denotator type The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. A denotator type indicates how a term should be interpreted from an ontological perspective. Alan Ruttenberg Barry Smith, Werner Ceusters denotator type example to be eventually removed example to be eventually removed failed exploratory term The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job Person:Alan Ruttenberg failed exploratory term metadata complete Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. metadata complete organizational term Term created to ease viewing/sort terms for development purpose, and will not be included in a release organizational term ready for release Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." ready for release metadata incomplete Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete uncurated Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated pending final vetting All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. pending final vetting placeholder removed placeholder removed terms merged An editor note should explain what were the merged terms and the reason for the merge. terms merged term imported This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. term imported term split This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. term split universal Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. Alan Ruttenberg A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf universal defined class A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. Alan Ruttenberg defined class named class expression A named class expression is a logical expression that is given a name. The name can be used in place of the expression. named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions Alan Ruttenberg named class expression to be replaced with external ontology term Terms with this status should eventually replaced with a term from another ontology. Alan Ruttenberg group:OBI to be replaced with external ontology term requires discussion A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. Alan Ruttenberg group:OBI requires discussion 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 can't be added as a property chain because it causes a circularity violation for 'part of'. This can't be added as a property chain because it causes a circularity violation for 'part of'. This can't be added as a property chain because it causes a circularity violation for 'part of'. 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).