István Mikó (imiko) https://orcid.org/0000-0003-2938-9075
Jennifer C. Girón (jgiron) https://orcid.org/0000-0002-0851-6883
Luis A. González Montaña (lagonzalezmo) https://orcid.org/0000-0002-9136-9932
Sergei Tarasov (starasov) https://orcid.org/0000-0001-5237-2330
The ontology for the Anatomy of the Insect SkeletoMuscular system (AISM) contains terms used to describe the cuticle - as a single anatomical structure - and the skeletal muscle system, to be used in insect biodiversity research.
Ontology for the Anatomy of the Insect SkeletoMuscular system
2021-05-21
This annotation property defines a "sensu", which is the combination of a bibliographic reference, a label and a class (represented by verbatim and logical definitions). Given this model, independent observations can be inferred across to compute synonymy (multiple labels attached to one), homonymy (one label attached to multiple classes).
Yoder MJ, Mikó I, Seltmann KC, Bertone MA, Deans AR (2010) A Gross Anatomy Ontology for Hymenoptera. PLOS ONE 5: e15991.
https://doi.org/10.1371/journal.pone.0015991.g004
This annotation property is on the label of a class in owl.
sensu
This annotation property defines a "sensu", which is the combination of a bibliographic reference, a label and a class (represented by verbatim and logical definitions). Given this model, independent observations can be inferred across to compute synonymy (multiple labels attached to one), homonymy (one label attached to multiple classes).
Yoder MJ, Mikó I, Seltmann KC, Bertone MA, Deans AR (2010) A Gross Anatomy Ontology for Hymenoptera. PLOS ONE 5: e15991.
https://doi.org/10.1371/journal.pone.0015991.g004
This annotation property is on the label of a class in owl.
imiko
2020-11-17
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
IAO:0000116
uberon
editor_note
true
editor_note
editor note
editor note
curator note
An administrative note of use for a curator but of no use for a user
PERSON:Alan Ruttenberg
IAO:0000232
uberon
curator_notes
true
curator_notes
curator note
curator note
curator notes
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
uberon
dc-contributor
true
dc-contributor
contributor
uberon
dc-description
true
dc-description
description
uberon
dc-title
true
dc-title
title
uberon
dcterms-license
true
dcterms-license
license
subset_property
has_exact_synonym
lateral_to
lateral_to
imiko
2020-10-27
medial_to
medial_to
imiko
2020-10-27
imiko
encircles
imiko
2020-11-11
imiko
encircled by
imiko
2020-11-11
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 https://code.google.com/p/obo-relations/wiki/ROAndTime
Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)
A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
part_of
BFO:0000050
external
protein
quality
spatial
uberon
part_of
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)
Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2.
a core relation that holds between a whole and its part
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 https://code.google.com/p/obo-relations/wiki/ROAndTime
Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)
A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
has_part
BFO:0000051
chebi_ontology
external
protein
quality
spatial
uberon
has_part
false
has_part
We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'.
has part
has part
has_part
Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2.
PATOC:CJM
preceded by
X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X)
x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
is preceded by
preceded_by
http://www.obofoundry.org/ro/#OBO_REL:preceded_by
BFO:0000062
is preceded by
takes place after
uberon
preceded_by
preceded_by
preceded by
preceded_by
takes place after
Allen:precedes
is preceded by
SIO:000249
precedes
x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
BFO:0000063
uberon
precedes
precedes
precedes
precedes
occurs in
b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
occurs_in
unfolds in
unfolds_in
BFO:0000066
external
occurs_in
occurs_in
Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
occurs in
occurs in
site of
[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant
contains process
x anterior to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail.
x anterior_to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail: bearer
cjm
2009-07-31T02:15:46Z
BSPO:0000096
rostral_to
spatial
uberon
anterior_to
anterior_to
anterior to
anterior_to
x anterior to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail.
BSPO:cjm
x anterior_to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail: bearer
x distal to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal).
x distal_to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal).
BSPO:0000097
spatial
uberon
distal_to
distal_to
distal to
distal_to
x distal to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal).
BSPO:cjm
x distal_to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal).
x dorsal to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly).
x dorsal_to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly).
BSPO:0000098
spatial
uberon
dorsal_to
dorsal_to
dorsal to
dorsal_to
x dorsal to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly).
BSPO:cjm
x dorsal_to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly).
x posterior to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail.
x posterior_to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail.
BSPO:0000099
caudal to
caudal_to
spatial
uberon
posterior_to
posterior_to
posterior to
posterior_to
x posterior to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that extends through an organism from head end to opposite end of body or tail.
BSPO:cjm
x posterior_to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail.
caudal to
x proximal to y iff x is closer to the point of attachment with the body than y.
x proximal_to y iff x is closer to the point of attachment with the body than y.
BSPO:0000100
spatial
uberon
proximal_to
proximal_to
The elbow is proximal to the hand, but distal to the shoulder.
proximal to
proximal_to
x proximal to y iff x is closer to the point of attachment with the body than y.
BSPO:cjm
x proximal_to y iff x is closer to the point of attachment with the body than y.
x ventral to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly).
x ventral_to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly).
BSPO:0000102
spatial
uberon
ventral_to
ventral_to
ventral to
ventral_to
x ventral to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that extends through an organism from back (e.g. spinal column) to front (e.g. belly).
BSPO:cjm
x ventral_to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly).
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 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
uberon
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.
Near the outer surface of the organism. Thus, skin is superficial to the muscle layer.
BSPO:0000108
uberon
superficial_to
superficial_to
superficial_to
Near the outer surface of the organism. Thus, skin is superficial to the muscle layer.
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 posterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the posterior portion.
BSPO:0000122
uberon
in_posterior_side_of
in_posterior_side_of
in_posterior_side_of
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
uberon
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 proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion.
BSPO:0000124
uberon
in_proximal_side_of
in_proximal_side_of
in_proximal_side_of
X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion.
BSPO:PATO_mtg_2009
X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion.
BSPO:0000125
uberon
in_distal_side_of
in_distal_side_of
in_distal_side_of
X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion.
BSPO:PATO_mtg_2009
X in_lateral_side_of Y <=> if X is in_left_side_of Y or X is in_right_side_of Y. X is often, but not always a paired structure
BSPO:0000126
uberon
in_lateral_side_of
in_lateral_side_of
in_lateral_side_of
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
X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y
BSPO:0001106
uberon
proximalmost_part_of
proximalmost_part_of
proximalmost_part_of
X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y
This relation holds when both the deep_to and ajdacent_to relationship similarly hold.
BSPO:0001107
uberon
immediately_deep_to
immediately_deep_to
immediately_deep_to
This relation holds when both the deep_to and ajdacent_to relationship similarly hold.
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
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
This document is about information artifacts and their representations
A (currently) primitive relation that relates an information artifact to an entity.
7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive.
We will try to build it back up by elaborating the various subproperties that are more precisely defined.
Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
person:Alan Ruttenberg
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
is about
A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named.
A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically
2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive.
g denotes r =def
r is a portion of reality
there is some c that is a concretization of g
every c that is a concretization of g specifically denotes r
person:Alan Ruttenberg
Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
denotes
inverse of the relation 'denotes'
Person: Jie Zheng, Chris Stoeckert, Mike Conlon
denoted by
inheres in
this fragility inheres in this vase
this red color inheres in this apple
a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
A dependent inheres in its bearer at all times for which the dependent exists.
inheres_in
inheres in
bearer of
this apple is bearer of this red color
this vase is bearer of this fragility
a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence
A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
bearer_of
is bearer of
RO:0000053
uberon
bearer_of
bearer_of
bearer of
bearer of
participates in
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates_in
RO:0000056
protein
uberon
participates_in
false
participates_in
participates in
participates in
participates_in
has participant
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
a relation between a process and a continuant, in which the continuant is somehow involved in the process
Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
has_participant
http://www.obofoundry.org/ro/#OBO_REL:has_participant
has participant
RO:0000086
protein
has_quality
false
has_quality
has_quality
is location of
my head is the location of my brain
this cage is the location of this rat
a relation between two independent continuants, the location and the target, in which the target is entirely within the location
Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
location_of
RO:0001015
uberon
location_of
location_of
location of
location_of
contained in
Containment is location not involving parthood, and arises only where some immaterial continuant is involved.
Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):
Intended meaning:
domain: material entity
range: spatial region or site (immaterial continuant)
contained_in
contained in
contains
RO:0001019
uberon
contains
contains
contains
contains
located in
my brain is located in my head
this rat is located in this cage
a relation between two independent continuants, the target and the location, in which the target is entirely within the location
Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
located_in
http://www.obofoundry.org/ro/#OBO_REL:located_in
RO:0001025
protein
uberon
located_in
located_in
located in
located_in
This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.
This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.
the surface of my skin is a 2D boundary of my body
a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity
A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
2D_boundary_of
boundary of
is 2D boundary of
is boundary of
RO:0002000
uberon
boundary_of
boundary_of
2D boundary of
boundary of
my body has 2D boundary the surface of my skin
a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity
A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.
Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.
David Osumi-Sutherland
has boundary
has_2D_boundary
RO:0002002
uberon
has_boundary
has_boundary
has 2D boundary
has boundary
RO:0002007
uberon
bounding_layer_of
bounding_layer_of
A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane.
bounding layer of
A relation that holds between two linear structures that are approximately parallel to each other for their entire length and where either the two structures are adjacent to each other or one is part of the other.
Note from NCEAS meeting: consider changing primary label
David Osumi-Sutherland
Example: if we define region of chromosome as any subdivision of a chromosome along its long axis, then we can define a region of chromosome that contains only gene x as 'chromosome region' that coincident_with some 'gene x', where the term gene X corresponds to a genomic sequence.
coincident with
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
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
David Osumi-Sutherland
starts_at_end_of
A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251].
RO:0002087
directly preceded by
is directly preceded by
is immediately preceded by
starts_at_end_of
uberon
immediately_preceded_by
immediately_preceded_by
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
immediately preceded by
immediately_preceded_by
A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251].
SIO:000251
is immediately preceded by
SIO:000251
David Osumi-Sutherland
ends_at_start_of
meets
X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
immediately precedes
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
X continuous_with Y if and only if X and Y share a fiat boundary.
David Osumi-Sutherland
connected to
The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)
RO:0002150
uberon
continuous_with
continuous_with
continuous with
continuous_with
FMA:85972
lactation SubClassOf 'only in taxon' some 'Mammalia'
S only_in_taxon T iff: S SubClassOf in_taxon only T
U only_in_taxon T: U is a feature found in only in organisms of species of taxon T. The feature cannot be found in an organism of any species outside of (not subsumed by) that taxon. Down-propagates in U hierarchy, up-propagates in T hierarchy (species taxonomy). Implies applicable_to_taxon.
x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z.
The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.
'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria
Chris Mungall
RO:0002160
never_outside_taxon
specific_to
specific_to_taxon
protein
uberon
only_in_taxon
false
only_in_taxon
Down-propagates. The original name for this in the paper is 'specific_to'. Applicable to genes because some genes are lost in sub-species (strains) of a species.
only in taxon
only_in_taxon
S only_in_taxon T iff: S SubClassOf in_taxon only T
U only_in_taxon T: U is a feature found in only in organisms of species of taxon T. The feature cannot be found in an organism of any species outside of (not subsumed by) that taxon. Down-propagates in U hierarchy, up-propagates in T hierarchy (species taxonomy). Implies applicable_to_taxon.
ROC:Waclaw
x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed.
Chris Mungall
Jennifer Deegan
RO:0002162
uberon
in_taxon
in_taxon
Connects a biological entity to its taxon of origin.
in taxon
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
a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).
Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship.
a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b
RO:0002170
uberon
connected_to
connected_to
Connection does not imply overlaps.
connected to
connected to
https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern
https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern
Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship.
Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship.
this is currently used for both structural relationships (such as between a valve and the chamber it connects) and abstract relationships (anatomical lines and the entities they connect)
RO:0002176
uberon
connects
connects
connects
Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship.
a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b.
attached to part of (anatomical structure to anatomical structure)
RO:0002177
uberon
attaches_to_part_of
attaches_to_part_of
attached to part of
attaches_to_part_of
true
true
RO:0002179
drains blood from
drains from
uberon
drains
drains
source: Wikipedia
drains
w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit.
RO:0002180
protein
uberon
has_component
false
has_component
has component
has component
has_component
x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y
Chris Mungall
David Osumi-Sutherland
Melissa Haendel
Terry Meehan
RO:0002202
uberon
develops_from
develops_from
This is the transitive form of the develops from relation
develops from
develops_from
inverse of develops from
Chris Mungall
David Osumi-Sutherland
Terry Meehan
RO:0002203
uberon
develops_into
develops_into
develops into
develops_into
process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2.
We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit
Chris Mungall
David Hill
Tanya Berardini
GO
Regulation precludes parthood; the regulatory process may not be within the regulated process.
regulates (processual)
false
RO:0002211
external
regulates
regulates
regulates
regulates
Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
Chris Mungall
negatively regulates (process to process)
RO:0002212
external
negatively_regulates
negatively_regulates
negatively regulates
negatively regulates
Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
Chris Mungall
positively regulates (process to process)
RO:0002213
external
positively_regulates
positively_regulates
positively regulates
positively regulates
mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
osteoclast SubClassOf 'capable of' some 'bone resorption'
A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
Chris Mungall
has function realized in
For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)".
RO:0002215
protein
uberon
capable_of
false
capable_of
capable of
capable of
capable_of
c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
Chris Mungall
has function in
RO:0002216
uberon
capable_of_part_of
capable_of_part_of
capable of part of
capable of part of
true
x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x
x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y
Chris Mungall
RO:0002219
uberon
surrounded_by
surrounded_by
surrounded by
surrounded_by
x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y
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.
x adjacent_to y iff: x and y share a boundary
This relation acts as a join point with BSPO
Chris Mungall
RO:0002220
spatial
uberon
adjacent_to
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.
inverse of surrounded by
inverse of surrounded_by
Chris Mungall
RO:0002221
uberon
surrounds
surrounds
surrounds
surrounds
inverse of surrounded_by
Chris Mungall
Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporally related to
Relation between occurrents, shares a start boundary with.
RO:0002223
uberon
starts
starts
starts
Relation between occurrents, shares a start boundary with.
Allen:starts
RO:0002224
uberon
starts_with
starts_with
starts with
Relation between occurrents, shares an end boundary with.
RO:0002229
finishes
uberon
ends
ends
ends
Relation between occurrents, shares an end boundary with.
Allen:starts
ZFS:finishes
RO:0002230
uberon
ends_with
ends_with
ends with
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
Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]
x has developmental contribution from y iff x has some part z such that z develops from y
Chris Mungall
RO:0002254
uberon
has_developmental_contribution_from
has_developmental_contribution_from
has developmental contribution from
has developmental contribution from
inverse of has developmental contribution from
Chris Mungall
RO:0002255
uberon
developmentally_contributes_to
developmentally_contributes_to
developmentally contributes to
developmentally_contributes_to
t1 developmentally_induced_by t2 if there is a process of organ induction (GO:0001759) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor tissue type T to T', where T' develops_from T.
RO:0002256
uberon
developmentally_induced_by
developmentally_induced_by
sources for developmentally_induced_by relationships in Uberon: Developmental Biology, Gilbert, 8th edition, figure 6.5(F)
developmentally_induced_by
t1 developmentally_induced_by t2 if there is a process of organ induction (GO:0001759) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor tissue type T to T', where T' develops_from T.
GO:0001759
Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p
false
Chris Mungall
In general you should not use this relation to make assertions - use one of the more specific relations below this one
This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from
developmentally preceded by
A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.
c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.
acts upstream of
A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.
c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.
affects
acts upstream of or within
RO:0002285
uberon
developmentally_replaces
developmentally_replaces
developmentally_replaces
Inverse of developmentally preceded by
Chris Mungall
developmentally succeeded by
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 inheres in 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 inheres in part of
Chris Mungall
inheres in part of
true
A relationship that holds via some environmental process
Chris Mungall
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution.
evolutionarily related to
A mereological relationship or a topological relationship
Chris Mungall
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
mereotopologically related to
A relationship that holds between entities participating in some developmental process (GO:0032502)
Chris Mungall
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development
developmentally related to
a particular instances of akt-2 enables some instance of protein kinase activity
Chris Mungall
catalyzes
executes
has
is catalyzing
is executing
This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.
This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time.
enables
A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
Chris Mungall
This is a grouping relation that collects relations used for the purpose of connecting structure and function
RO:0002328
uberon
functionally_related_to
functionally_related_to
functionally related to
functionally related to
this relation holds between c and p when c is part of some c', and c' is capable of p.
Chris Mungall
false
RO:0002329
uberon
part_of_structure_that_is_capable_of
part_of_structure_that_is_capable_of
part of structure that is capable of
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
RO:0002350
uberon
member_of
member_of
member of
RO:0002351
uberon
has_member
has_member
has member
inverse of has input
Chris Mungall
input of
RO:0002353
protein
output_of
false
output_of
output_of
a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a
Chris Mungall
attached to (anatomical structure to anatomical structure)
RO:0002371
uberon
attaches_to
attaches_to
attached to
attaches_to
m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to.
m has_muscle_origin s iff m is attaches_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to.
Chris Mungall
Wikipedia:Insertion_(anatomy)
RO:0002372
uberon
has_muscle_origin
has_muscle_origin
The origin is the end of a muscle that attaches to the more fixed part of the skeleton, which is the proximal end in limb muscles
has muscle origin
has_muscle_origin
We need to import uberon muscle to create a stricter domain constraint
m has_muscle_origin s iff m is attaches_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to.
m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone.
RO:0002373
uberon
has_muscle_insertion
has_muscle_insertion
The insertion is the point of attachment of a muscle that moves the most when the muscle shortens, or the most distal end of limb muscles
has_muscle_insertion
m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone.
RO:0002376
uberon
drains into
tributary_of
tributary_of
tributary_of
drains into
dbpowl:drainsTo
A lump of clay and a statue
x spatially_coextensive_with y if and inly if x and y have the same location
Chris Mungall
This relation is added for formal completeness. It is unlikely to be used in many practical scenarios
spatially coextensive with
we need to check if FMA branch_of implies part_of. the relation we intend to use here should - for example, see vestibulocochlear nerve
RO:0002380
uberon
branching_part_of
branching_part_of
branching_part_of
x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction).
Chris Mungall
has developmental potential involving
x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y
x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y
Chris Mungall
RO:0002385
uberon
has_potential_to_developmentally_contribute_to
has_potential_to_developmentally_contribute_to
has potential to developmentally contribute to
has potential to developmentally contribute to
x has the potential to develop into y iff x develops into y or if x is capable of developing into y
x has the potential to develop into y iff x develops into y or if x is capable of developing into y
Chris Mungall
RO:0002387
uberon
has_potential_to_develop_into
has_potential_to_develop_into
has potential to develop into
has potential to develop into
x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y
Chris Mungall
has potential to directly develop into
inverse of upstream of
Chris Mungall
causally downstream of
Chris Mungall
immediately causally downstream of
This relation groups causal relations between material entities and causal relations between processes
This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.
To define causal relations in an activity-flow type network, we make use of 3 primitives:
* Temporal: how do the intervals of the two occurrents relate?
* Is the causal relation regulatory?
* Is the influence positive or negative
The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.
For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.
For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.
Each of these 3 primitives can be composed to yield a cross-product of different relation types.
Chris Mungall
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causally related to
p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain
Chris Mungall
causally upstream of
p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q.
Chris Mungall
immediately causally upstream of
p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q.
We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
Chris Mungall
influences (processual)
affects
causally upstream of or within
inverse of causally upstream of or within
Chris Mungall
causally downstream of or within
c involved in regulation of p if c is involved in some p' and p' regulates some p
Chris Mungall
involved in regulation of
c involved in regulation of p if c is involved in some p' and p' positively regulates some p
Chris Mungall
involved in positive regulation of
c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
Chris Mungall
involved in negative regulation of
c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p
OWL does not allow defining object properties via a Union
Chris Mungall
involved in or reguates
involved in or involved in regulation of
A protein that enables activity in a cytosol.
c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
Chris Mungall
executes activity in
enables activity in
is active in
true
c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.
GOC:cjm
GOC:dos
RO:0002433
uberon
contributes_to_morphology_of
contributes_to_morphology_of
contributes to morphology of
A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
Considering relabeling as 'pairwise interacts with'
This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.
Chris Mungall
Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.
in pairwise interaction with
interacts with
http://purl.obolibrary.org/obo/MI_0914
https://github.com/oborel/obo-relations/wiki/InteractionRelations
An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.
Chris Mungall
binds
molecularly binds with
molecularly interacts with
http://purl.obolibrary.org/obo/MI_0915
Axiomatization to GO to be added later
Chris Mungall
An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y.
phosphorylates
The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.
A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.
Chris Mungall
Vasundra Touré
molecularly controls
directly regulates activity of
The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B.
For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.
Chris Mungall
Vasundra Touré
directly inhibits
molecularly decreases activity of
directly negatively regulates activity of
The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B.
For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.
Chris Mungall
Vasundra Touré
directly activates
molecularly increases activity of
directly positively regulates activity of
Chris Mungall
This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning.
helper property (not for use in curation)
x composed_primarily_of y iff: more than half of the mass of x is made from parts of y
RO:0002473
uberon
RO:0002473
composed_primarily_of
composed_primarily_of
composed primarily of
p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c.
Chris Mungall
has part that occurs in
true
Chris Mungall
is kinase activity
Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s.
RO:0002488
begins_to_exist_during
uberon
RO:0002488
existence_starts_during
existence_starts_during
existence starts during
Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s.
Relation between continuant and occurrent, such that c comes into existence at the start of p.
RO:0002489
uberon
existence_starts_with
existence_starts_with
existence starts with
Relation between continuant and occurrent, such that c comes into existence at the start of p.
RO:0002491
uberon
existence_starts_and_ends_during
existence_starts_and_ends_during
existence starts and ends during
Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely.
RO:0002492
ceases_to_exist_during
uberon
RO:0002492
existence_ends_during
existence_ends_during
existence ends during
Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely.
Relation between continuant and occurrent, such that c ceases to exist at the end of p.
RO:0002493
uberon
existence_ends_with
existence_ends_with
existence ends with
Relation between continuant and occurrent, such that c ceases to exist at the end of p.
RO:0002494
transforms from
uberon
transformation_of
transformation_of
transformation of
transforms from
SIO:000657
RO:0002495
direct_transformation_of
immediately transforms from
uberon
immediate_transformation_of
immediate_transformation_of
immediate transformation of
direct_transformation_of
immediately transforms from
SIO:000658
RO:0002496
uberon
existence_starts_during_or_after
existence_starts_during_or_after
existence starts during or after
RO:0002497
uberon
existence_ends_during_or_before
existence_ends_during_or_before
existence ends during or before
A relationship between a material entity and a process where the material entity has some causal role that influences the process
causal agent in process
p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q.
Chris Mungall
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causal relation between processes
Chris Mungall
depends on
The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch
Chris Mungall
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causal relation between entities
A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision.
RO:0002551
uberon
has sekeletal support
has supporting framework
has_skeleton
has_skeleton
has skeleton
A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision.
Chris Mungall
causally influenced by (entity-centric)
causally influenced by
Chris Mungall
interaction relation helper property
https://github.com/oborel/obo-relations/wiki/InteractionRelations
Chris Mungall
molecular interaction relation helper property
The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).
Chris Mungall
Vasundra Touré
causally influences (entity-centric)
causally influences
A relation that holds between elements of a musculoskeletal system or its analogs.
Chris Mungall
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes.
biomechanically related to
RO:0002569
uberon
has_branching_part
has_branching_part
has branching part
RO:0002572
uberon
luminal_space_of
luminal_space_of
luminal space of
RO:0002576
uberon
skeleton_of
skeleton_of
skeleton of
Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
Chris Mungall
directly regulates (processual)
directly regulates
gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'
s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p
Chris Mungall
has part structure that is capable of
A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
Chris Mungall
causal relation between material entity and a process
pyrethroid -> growth
Holds between c and p if and only if c is capable of some activity a, and a regulates p.
capable of regulating
Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
capable of negatively regulating
renin -> arteriolar smooth muscle contraction
Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.
capable of positively regulating
Inverse of 'causal agent in process'
process has causal agent
Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2.
directly positively regulates (process to process)
directly positively regulates
Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2.
directly negatively regulates (process to process)
directly negatively regulates
a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix.
Melissa Haendel
RO:0003000
uberon
produces
produces
Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue.
produces
produces
a produced_by b iff some process that occurs_in b has_output a.
Melissa Haendel
RO:0003001
uberon
produced_by
produced_by
produced by
produced_by
Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P.
cjm
2018-01-25T23:20:13Z
enables subfunction
cjm
2018-01-26T23:49:30Z
acts upstream of or within, positive effect
cjm
2018-01-26T23:49:51Z
acts upstream of or within, negative effect
c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive
cjm
2018-01-26T23:53:14Z
acts upstream of, positive effect
c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative
cjm
2018-01-26T23:53:22Z
acts upstream of, negative effect
cjm
2018-03-13T23:55:05Z
causally upstream of or within, negative effect
cjm
2018-03-13T23:55:19Z
causally upstream of or within, positive effect
The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.
Vasundra Touré
regulates activity of
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
q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
quality
decreased_in_magnitude_relative_to
This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'.
decreased_in_magnitude_relative_to
q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
PATOC:CJM
q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
quality
different_in_magnitude_relative_to
different_in_magnitude_relative_to
q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
PATOC:CJM
s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2.
quality
has_cross_section
Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round.
has_cross_section
s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2.
PATOC:CJM
q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
quality
increased_in_magnitude_relative_to
This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'.
increased_in_magnitude_relative_to
q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
PATOC:CJM
q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
quality
similar_in_magnitude_relative_to
similar_in_magnitude_relative_to
q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
PATOC:CJM
protein
has_gene_template
false
has_gene_template
x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y.
uberon
anteriorly_connected_to
anteriorly connected to
x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y.
carries
uberon
channel_for
channel for
uberon
channels_from
channels_from
x is a conduit for y iff y passes through the lumen of x.
uberon
conduit_for
conduit for
Relationship between a fluid and a material entity, where the fluid is the output of a realization of a filtration role that inheres in the material entity.
uberon
filtered_through
Relationship between a fluid and a filtration barrier, where the portion of fluid arises as a transformation of another portion of fluid on the other side of the barrier, with larger particles removed
filtered through
x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y.
uberon
posteriorly_connected_to
posteriorly connected to
x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y.
uberon
protects
protects
uberon
subdivision_of
placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B
subdivision of
.
uberon
transitively_anteriorly_connected_to
transitively anteriorly connected to
.
uberon
transitively_connected_to
transitively_connected to
A protein coding gene resilin in fruit fly.
gene
FlyBase:FBgn0034157
Category=external.
resilin (fruit fly)
A protein coding gene resilin in fruit fly.
PRO:DNx
The projection of the inner surface of the cuticle.
cuticular internal depression
imiko
jgiron
The projection of the inner surface of the cuticle.
2021 05 19
jgiron
The region of the cuticle that is composed two articular surfaces that are adjacent to each other.
Articulations are `anatomical clusters`, collections of not direclty connected (continuous) sclerite surfaces that are adjacent to another sclerite. The cranio-mandibular articulation is the articular surface of the cranium and the adjacent articular surface of the mandible. The articular surfaces are sometimes located on the same sclerite.
insect articulation
imiko
imiko
The region of the cuticle that is composed two articular surfaces that are adjacent to each other.
imiko
2020-10-27
Articulations are `anatomical clusters`, collections of not direclty connected (continuous) sclerite surfaces that are adjacent to another sclerite. The cranio-mandibular articulation is the articular surface of the cranium and the adjacent articular surface of the mandible. The articular surfaces are sometimes located on the same sclerite.
imiko
The region of the insect cuticle that is less flexible than the neighboring conjunctiva(e) (conjunctiva(e) that the sclerite is continuous with).
sclerite
imiko
imiko
The region of the insect cuticle that is less flexible than the neighboring conjunctiva(e) (conjunctiva(e) that the sclerite is continuous with).
imiko
2020-10-27
sclerite
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Sclerite: distinctly sclerotized region of the integument, with thick layer of exocuticle."
The region of the insect cuticle that is more flexible than the neighboring sclerite(s) (sclerite(s) that the conjunctiva is continuous with).
Conjunctivae are more flexible and usually less thick than sclerties of the cuticle allowing the sclerites to move relative to each other.
Micro-CT based methods cannot be used to accurately differentiate slcerites from conjunctiuvae. CLSM (the excitation wavelengths of sclerites and conjunctivae are different in response of 488 nm emission vawelength), histological sections or simple dissections need to be applied to define relative flexibility of the insect cuticle.
If a conjunctiva entirelly encircles a sclerite, then the 'encircles' and 'encircled by' object properties are used to link the sclerite and the conjunctiva even in cases in which the encircled sclerites or conjunctivae are part of an evagination allowing to model spatial relationship between appendage segments: the pedicel is encircled by the scapal-pedicellar conjunctiva, which is encircled by the scape or the the coxa encircles the coxo-femoral conjunctiuva that encircels the femur.
membrane
conjunctiva
imiko
jgiron
imiko
imiko
The region of the insect cuticle that is more flexible than the neighboring sclerite(s) (sclerite(s) that the conjunctiva is continuous with).
imiko
2020-10-27
Conjunctivae are more flexible and usually less thick than sclerties of the cuticle allowing the sclerites to move relative to each other.
Micro-CT based methods cannot be used to accurately differentiate slcerites from conjunctiuvae. CLSM (the excitation wavelengths of sclerites and conjunctivae are different in response of 488 nm emission vawelength), histological sections or simple dissections need to be applied to define relative flexibility of the insect cuticle.
If a conjunctiva entirelly encircles a sclerite, then the 'encircles' and 'encircled by' object properties are used to link the sclerite and the conjunctiva even in cases in which the encircled sclerites or conjunctivae are part of an evagination allowing to model spatial relationship between appendage segments: the pedicel is encircled by the scapal-pedicellar conjunctiva, which is encircled by the scape or the the coxa encircles the coxo-femoral conjunctiuva that encircels the femur.
imiko
membrane
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Membrane: very flexible, unsclerotized area of the integument."
The region of the cuticle that corresponds to a concave surface.
The surface of the cuticle in insects is the entire surface of an organism, and it is composed of flat, concave and convex regions. Concavities sometimes correspons with invaginations of the cuticle and the underlaying sinlge layer epidermis, somtimes correspond to a decreased cuticular thickness.
cuticular depression
imiko
imiko
The region of the cuticle that corresponds to a concave surface.
imiko
2020-10-27
The surface of the cuticle in insects is the entire surface of an organism, and it is composed of flat, concave and convex regions. Concavities sometimes correspons with invaginations of the cuticle and the underlaying sinlge layer epidermis, somtimes correspond to a decreased cuticular thickness.
imiko
The region of cuticle that corresponds with an invagination of the single layer epidermis (epidermal fold). The cuticular invagination sometimes corresponds to a cuticular depression (concavity on the surface of the cuticle).
cuticular invagination
imiko
imiko
imiko
The region of cuticle that corresponds with an invagination of the single layer epidermis (epidermal fold). The cuticular invagination sometimes corresponds to a cuticular depression (concavity on the surface of the cuticle).
imiko
2020-10-27
The region of the cuticle with higher content of resilin.
elastic cuticle
imiko
imiko
The region of the cuticle with higher content of resilin.
jgiron
2021-04-21
elastic cuticle
2020-10-27
The region of the cuticle that corresponds to a convex surface.
The surface of the cuticle in insects is the entire surface of an organism, and it is composed of flat, concave and convex regions. Convexities sometimes correspons with evaginations of the cuticle and the underlaying sinlge layer epidermis and sometimes correspond to an increased cuticular thickness."
cuticular protrusion
imiko
imiko
The region of the cuticle that corresponds to a convex surface.
imiko
2020-10-27
The surface of the cuticle in insects is the entire surface of an organism, and it is composed of flat, concave and convex regions. Convexities sometimes correspons with evaginations of the cuticle and the underlaying sinlge layer epidermis and sometimes correspond to an increased cuticular thickness."
imiko
A part or structure that is produced by evagination.
evaginated
imiko
A part or structure that is produced by evagination.
imiko
2021-04-21
evaginated
imiko
2020-10-27
The articulation between the mandible and the cranium.
cranio-mandibular articulation
imiko
imiko
imiko
The articulation between the mandible and the cranium.
imiko
2020-10-27
The articulation between the cardo and the cranium.
cranio-cardinal articulation
imiko
imiko
imiko
The articulation between the cardo and the cranium.
imiko
2020-10-27
The articulation between the scapus and the cranium.
cranio-antennal articulation
imiko
imiko
imiko
The articulation between the scapus and the cranium.
imiko
2020-10-27
The articulation between the head and the neck.
head-cervical articulation
imiko
imiko
imiko
The articulation between the head and the neck.
imiko
2020-10-27
Is the sclerite of the insect maxilla that is attached to the head capsule by the oral foraminal conjunctiva and to the stipes by the stipito-cardinal conjunctiva.
cardo
imiko
jgiron
imiko
imiko
jgiron
imiko
Is the sclerite of the insect maxilla that is attached to the head capsule by the oral foraminal conjunctiva and to the stipes by the stipito-cardinal conjunctiva.
jgiron
2021-02-19
cardo
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Cardo: basal element of maxilla, articulating with head capsule; usually moved by one cranial muscle and one tentorial muscle."
Is the sclerite of the insect head that is attached to the neck membrane and the oral foraminal conjunctiva, bears the eye cuticle and surrounds the brain
insect cranium
head capsule
imiko
imiko
jgiron
imiko
imiko
imiko
Is the sclerite of the insect head that is attached to the neck membrane and the oral foraminal conjunctiva, bears the eye cuticle and surrounds the brain
jgiron
2021-02-19
insect cranium
imiko
head capsule
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"The head capsule is almost always a rigid, well sclerotized structural unit, equipped with a defined set of appendages. It is reinforced by strengthening ridges and the endoskeletal tentorium"
The axillary sclerite that is on the dorsal region of the basal wing conjunctiva and lateral to the first axillary sclerite.
dorsal second axillary sclerite
imiko
imiko
jgiron
The axillary sclerite that is on the dorsal region of the basal wing conjunctiva and lateral to the first axillary sclerite.
jgiron
2021-04-10
Is the abdominal tergite of the preabdomen that is attached to the posterior margin of the tergum by the metanoto-abdominal tergite I conjunctiva and to the anterior margin of the abdominal tergite II by the abdominal tergite I-abdominal tergite II conjunctiva.
abdominal tergite I
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
Is the abdominal tergite of the preabdomen that is attached to the posterior margin of the tergum by the metanoto-abdominal tergite I conjunctiva and to the anterior margin of the abdominal tergite II by the abdominal tergite I-abdominal tergite II conjunctiva.
jgiron
2021-03-18
The axillary sclerite that is part of the dorsal region of the basal wing conjunctiva and is anterior to the third axillary sclerite.
first axillary sclerite
imiko
imiko
imiko
The axillary sclerite that is part of the dorsal region of the basal wing conjunctiva and is anterior to the third axillary sclerite.
jgiron
2021-04-10
Is the sclerite of the insect maxilla that is attached to the stipes by the stipito-galeal conjunctiva.
galea
jgiron
jgiron
jgiron
Is the sclerite of the insect maxilla that is attached to the stipes by the stipito-galeal conjunctiva.
jgiron
2021-02-19
galea
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Galea: outer endite lobe of maxilla, usually semimembranous and equipped with sensilla (mainly chemoreceptors)."
Is the appendage of the labium that is attached to the palpiger by the palpigero-palpal conjunctiva.
labial palpus
imiko
jgiron
jgiron
jgiron
Is the appendage of the labium that is attached to the palpiger by the palpigero-palpal conjunctiva.
jgiron
2021-02-19
labial palpus
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Labial palp: tactile appendage of the labium."
Is the sclerite of the insect maxilla that is attached to the stipes by the stipito-lacinial conjunctiva.
lacinia
jgiron
imiko
jgiron
jgiron
Is the sclerite of the insect maxilla that is attached to the stipes by the stipito-lacinial conjunctiva.
jgiron
2021-02-19
lacinia
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Lacinia: inner endite lobe of maxilla, usually firmly connected or fused with stipes; usually sclerotized, with mesally curved apex and articulated spines arranged along mesal edge."
The region of cuticle that corresponds with an evagination of the cuticle and the single layer epidermis (epidermal fold). The cuticular evagination usually corresponds to a cuticular protrusion (convexity on the surface of the cuticle).
cuticular evagination
imiko
imiko
imiko
The region of cuticle that corresponds with an evagination of the cuticle and the single layer epidermis (epidermal fold). The cuticular evagination usually corresponds to a cuticular protrusion (convexity on the surface of the cuticle).
imiko
2020-11-11
The cuticular protrusion that does not correspond to an evagination.
solid cuticular protrusion
imiko
imiko
The cuticular protrusion that does not correspond to an evagination.
imiko
2021-04-21
solid cuticular protrusion
2020-11-11
The evagination of the cuticle that is musculated (connected to the body via muscles).
appendage
imiko
imiko
The evagination of the cuticle that is musculated (connected to the body via muscles).
imiko
2020-11-11
Is the paired appendage of the insect thorax that is composed of coxa, trochanter, femur, tibia, tarsus, and pretarsus.
insect leg
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
Is the paired appendage of the insect thorax that is composed of coxa, trochanter, femur, tibia, tarsus, and pretarsus.
jgiron
2021-03-18
Is the appendage of the head capsule that is connected by the antenniferal-scapal conjunctiva to the scapus, which is connected by the scapal-pedicellar conjunctiva to the pedicellus; the pedicellus is connected by the pedicellar-first flagellomeral conjunctiva to the first flagellomere; the first flagellomere is connected by interflagellomeral conjunctiva to the next flagellomere. Further flagellomeres are connected to each other by interflagellomeral conjunctiva.
antenna
imiko
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
Is the appendage of the head capsule that is connected by the antenniferal-scapal conjunctiva to the scapus, which is connected by the scapal-pedicellar conjunctiva to the pedicellus; the pedicellus is connected by the pedicellar-first flagellomeral conjunctiva to the first flagellomere; the first flagellomere is connected by interflagellomeral conjunctiva to the next flagellomere. Further flagellomeres are connected to each other by interflagellomeral conjunctiva.
jgiron
2021-02-19
antenna
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Antenna: head appendage of segment 2, innervated by deutocerebrum; in Insecta composed of scapus, pedicellus and flagellum; primarily multisegmented and filiform."
The flat, paired appendage on the dorso-lateral region of the pterothorax.
insect wing
imiko
imiko
imiko
imiko
The flat, paired appendage on the dorso-lateral region of the pterothorax.
jgiron
2021-04-21
The paired appendage of the prothorax that is anterior to a mid leg and composed of procoxa, protrochanter, profemur, protibia, protarsus, and propretarsus.
fore leg
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
The paired appendage of the prothorax that is anterior to a mid leg and composed of procoxa, protrochanter, profemur, protibia, protarsus, and propretarsus.
jgiron
2021-04-03
The paired appendage of the mesothorax that is posterior to a fore leg, anterior to a hind leg, and composed of mesocoxa, mesotrochanter, mesofemur, mesotibia, mesotarsus, and mesopretarsus.
mid leg
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
The paired appendage of the mesothorax that is posterior to a fore leg, anterior to a hind leg, and composed of mesocoxa, mesotrochanter, mesofemur, mesotibia, mesotarsus, and mesopretarsus.
jgiron
2021-04-03
The paired appendage of the metathorax that is posterior to a mid leg and composed of metacoxa, metatrochanter, metafemur, metatibia, metatarsus, and metapretarsus.
hind leg
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
The paired appendage of the metathorax that is posterior to a mid leg and composed of metacoxa, metatrochanter, metafemur, metatibia, metatarsus, and metapretarsus.
jgiron
2021-04-03
The paired insect wing that is continuous with the mesonotum.
fore wing
imiko
jgiron
imiko
The paired insect wing that is continuous with the mesonotum.
jgiron
2021-04-21
The paired insect wing that is continuous with the metanotum.
hind wing
imiko
jgiron
imiko
The paired insect wing that is continuous with the metanotum.
jgiron
2021-04-21
The unicellular cuticular evagination that constitutes a sclerite with its base surrounded by socket membrane.
seta
imiko
imiko
imiko
The unicellular cuticular evagination that constitutes a sclerite with its base surrounded by socket membrane.
jgiron
2021-04-21
seta
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Seta (=macrotrichium): articulated hair with socket, formed by trichogen cell."
2020-11-11
The multicellular evagination of the cuticle that corresponds to an epithelial fold, composed of a single sclerite that is encricled by a conjunctiva (moveable), and not musculated.
The difference between an appendage and a spur is the lack of muscles attached to the spur, otherwise, the mandible would be also a spur. Spines are multicellular evaginations that are not encircled by conjunctivae. Moveable beetle horns are spurs while not moveable beetle horns are spines.
spur
imiko
imiko
imiko
imiko
The multicellular evagination of the cuticle that corresponds to an epithelial fold, composed of a single sclerite that is encricled by a conjunctiva (moveable), and not musculated.
imiko
2020-11-11
The difference between an appendage and a spur is the lack of muscles attached to the spur, otherwise, the mandible would be also a spur. Spines are multicellular evaginations that are not encircled by conjunctivae. Moveable beetle horns are spurs while not moveable beetle horns are spines.
imiko
2020-11-11
spur
Richards AG, Richards PA (1979) The cuticular protuberances of insects. International Journal of Insect Morphology and Embryology 8: 143–157.
"Multicellular protuberances without differentiation of specialized cells"
https://doi.org/10.1016/0020-7322(79)90013-8
The seta that is flat.
scale
imiko
imiko
The seta that is flat.
imiko
2020-11-11
Is the mouthpart and appendage that is attached to the clypeus by the clypeo-labral conjunctiva and to the proximal margin of the epipharynx.
labrum
imiko
jgiron
jgiron
jgiron
Is the mouthpart and appendage that is attached to the clypeus by the clypeo-labral conjunctiva and to the proximal margin of the epipharynx.
jgiron
2021-02-19
labrum
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Labrum: unpaired upper lip, connected with distal edge of clypeus."
Is a mouthpart and sclerite between the labrum and the insect maxilla that is attached to the head capsule by the oral foraminal conjunctiva and the cranio-mandibular muscle.
insect mandible
imiko
imiko
imiko
jgiron
imiko
jgiron
jgiron
Is a mouthpart and sclerite between the labrum and the insect maxilla that is attached to the head capsule by the oral foraminal conjunctiva and the cranio-mandibular muscle.
jgiron
2021-02-19
insect mandible
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"The mandibles are the paired appendages of the 4th head segment and receive their innervation from the anterior part of the suboesophageal ganglion [...] They are primarily a compact, undivided and strongly sclerotized element without appendages."
Is a mouthpart appendage of the head capsule, between the insect mandible and the labium, composed of cardo, which is attached to the stipes by the cardo-stipital conjunctiva; the stipes, which is attached to the galea by the stipito-galeal conjunctiva, to the lacinia by the stipito-lacinial conjunctiva, and to the palpifer by the stipito-palpiferal conjunctiva; the palpifer is attached to the maxillary palpus by the palpifero-palpal conjunctiva.
insect maxilla
imiko
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
Is a mouthpart appendage of the head capsule, between the insect mandible and the labium, composed of cardo, which is attached to the stipes by the cardo-stipital conjunctiva; the stipes, which is attached to the galea by the stipito-galeal conjunctiva, to the lacinia by the stipito-lacinial conjunctiva, and to the palpifer by the stipito-palpiferal conjunctiva; the palpifer is attached to the maxillary palpus by the palpifero-palpal conjunctiva.
jgiron
2021-02-19
insect maxilla
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Maxilla: head appendage of segment 5, innervated by maxillary nerve originating from intermediate part of suboesophageal complex; primarily composed of cardo, stipes, endite lobes (lacinia, galea) and maxillary palp."
The conjunctiva of the insect thorax that connects the mesothorax and the metathorax.
mesothoracic-metathoracic conjunctiva
imiko
jgiron
imiko
imiko
The conjunctiva of the insect thorax that connects the mesothorax and the metathorax.
jgiron
2021-03-18
The conjunctiva of the insect thorax joining the prothorax and the mesothorax.
prothoracic-mesothoracic conjunctiva
jgiron
jgiron
jgiron
jgiron
The conjunctiva of the insect thorax joining the prothorax and the mesothorax.
jgiron
2020-03-18
The appendage of the leg that is attached to the tarsus by the tarso-pretarsal conjunctiva.
ungues
pretarsus
jgiron
jgiron
jgiron
jgiron
The appendage of the leg that is attached to the tarsus by the tarso-pretarsal conjunctiva.
jgiron
2021-03-18
ungues
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Ungues: pretarsal claws; unpaired in Collembola and Protura, usually paired in Diplura and Insecta."
Is the appendage of the labium composed of the glossa and paraglossa jointly.
ligula
imiko
imiko
jgiron
jgiron
Is the appendage of the labium composed of the glossa and paraglossa jointly.
jgiron
2021-02-19
ligula
Snodgrass RE (1993) Principles of Insect Morphology. Cornell University Press, 768 pp.
https://www.jstor.org/stable/10.7591/j.ctv1nhm1j
"Ligula - The terminal lobes of the labium collectively, or a terminal part of the labium formed by the union of the lobes."
Is the appendage of the labium, and part of the ligula, that is attached to the prementum by the premental-glossal conjunctiva.
glossa
imiko
imiko
jgiron
jgiron
Is the appendage of the labium, and part of the ligula, that is attached to the prementum by the premental-glossal conjunctiva.
jgiron
2021-02-19
glossa
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Glossa: paired inner endite lobes of the prementum."
Is the appendage of the labium, and part of the ligula, that is attached to the prementum by the premental-paraglossal conjunctiva.
paraglossa
imiko
jgiron
jgiron
jgiron
Is the appendage of the labium, and part of the ligula, that is attached to the prementum by the premental-paraglossal conjunctiva.
jgiron
2021-02-19
paraglossa
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Paraglossa: paired outer endite lobes of the prementum (labium)."
Is the appendage of the insect maxilla that is attached to the palpifer by the palpifero-palpal conjunctiva.
maxillary palpus
imiko
jgiron
jgiron
jgiron
jgiron
Is the appendage of the insect maxilla that is attached to the palpifer by the palpifero-palpal conjunctiva.
jgiron
2021-02-19
maxillary palpus
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Palp: tactile appendage of maxilla"
The notum or sclerite on the dorsal region of the mesothorax that is posterior to the pronotum, connected via the mesonoto-mesopleural conjuntiva to the dorsal margin of the mesopleuron, that is not adjacent to the mesocoxa, but attached to it by the mesocoxal muscle.
mesonotum
jcgiron
imiko
jcgiron
jgiron
jcgiron
jcgiron
jcgiron
jcgiron
The notum or sclerite on the dorsal region of the mesothorax that is posterior to the pronotum, connected via the mesonoto-mesopleural conjuntiva to the dorsal margin of the mesopleuron, that is not adjacent to the mesocoxa, but attached to it by the mesocoxal muscle.
jgiron
2021-04-21
The sclerite that is continuous with the basal mesocoxal conjunctiva and the basal wing conjunctiva and contains the mesofurca.
mesopectus
imiko
imiko
imiko
imiko
The sclerite that is continuous with the basal mesocoxal conjunctiva and the basal wing conjunctiva and contains the mesofurca.
imiko
2021-04-21
mesopectus
2020-11-11
The trochantin that is located on the ventro-lateral region of the mesothorax and is attached to a mesocoxa and surrounded by the basal mesocoxal conjunctiva.
mesotrochantin
imiko
jgiron
jgiron
jgiron
The trochantin that is located on the ventro-lateral region of the mesothorax and is attached to a mesocoxa and surrounded by the basal mesocoxal conjunctiva.
jgiron
2021-04-21
mesotrochantin
2020-11-11
The trochantin that is located on the ventro-lateral region of the prothorax and is attached to a procoxa and surrounded by the basal procoxal conjunctiva.
protrochantin
imiko
jgiron
jgiron
jgiron
The trochantin that is located on the ventro-lateral region of the prothorax and is attached to a procoxa and surrounded by the basal procoxal conjunctiva.
jgiron
2021-04-21
protrochantin
2020-11-11
The trochantin that is located on the ventro-lateral region of the metathorax and is attached to a metacoxa and surrounded by the basal metacoxal conjunctiva.
metatrochantin
imiko
jgiron
jgiron
jgiron
The trochantin that is located on the ventro-lateral region of the metathorax and is attached to a metacoxa and surrounded by the basal metacoxal conjunctiva.
jgiron
2021-04-21
metatrochantin
2020-11-11
Is the sclerite of the labium that is connected to the mentum by the mental-premental conjunctiva, to the palpiger by the premental-palpigeral conjunctiva, to the paraglossa by the premental-paraglossal conjunctiva, and to the glossa by the premental-glossal conjunctiva.
prementum
imiko
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
Is the sclerite of the labium that is connected to the mentum by the mental-premental conjunctiva, to the palpiger by the premental-palpigeral conjunctiva, to the paraglossa by the premental-paraglossal conjunctiva, and to the glossa by the premental-glossal conjunctiva.
jgiron
2021-02-19
prementum
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Prementum: distal main element of labium, bearing the endite lobes (glossa and paraglossa) and the labial palp."
The sclerite that is posterior to the pronotum and receives the site of attachment of the dilutor muscle of the first thoracic spiracle.
prepectus
imiko
imiko
imiko
The sclerite that is posterior to the pronotum and receives the site of attachment of the dilutor muscle of the first thoracic spiracle.
imiko
2021-04-21
prepectus
2020-11-11
The sclerite that is attached to cranial muscles, procoxal muscles, contiuous posterioirly with the neck membrane and with pronoto-propleural conjunctiva and not adjacent (not touching) to the procoxa.
pronotum
imiko
imiko
imiko
jgiron
imiko
imiko
imiko
imiko
imiko
The sclerite that is attached to cranial muscles, procoxal muscles, contiuous posterioirly with the neck membrane and with pronoto-propleural conjunctiva and not adjacent (not touching) to the procoxa.
imiko
2021-03-18
pronotum
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Pronotum: prothoracic tergum."
The mere that is part of the labial palpus.
labial palpomere
jgiron
jgiron
The mere that is part of the labial palpus.
jgiron
2021-04-21
The sclerite on the ventral region of the prothorax that bears the profurca and us attached to the propleuro-prosternal conjunctiva.
prosternum
imiko
jgiron
imiko
imiko
The sclerite on the ventral region of the prothorax that bears the profurca and us attached to the propleuro-prosternal conjunctiva.
jgiron
2021-04-09
The sclerite that is cylindrical and encircles and is encircled by conjunctiva.
ring sclerite
The sclerite that is cylindrical and encircles and is encircled by conjunctiva.
imiko
2021-04-21
imiko
imiko
jgiron
The ring sclerite that is part of an appendage and is attached to muscle.
appendage segment
imiko
imiko
imiko
The ring sclerite that is part of an appendage and is attached to muscle.
imiko
2021-04-21
The segment of the mid leg that is attached to the latero-ventral region of the mesothorax by the basal mesocoxal conjunctiva and to the mesotrochanter by the mesocoxal-mesotrochanteral conjunctiva.
mesocoxa
imiko
jgiron
imiko
imiko
jgiron
jgiron
The segment of the mid leg that is attached to the latero-ventral region of the mesothorax by the basal mesocoxal conjunctiva and to the mesotrochanter by the mesocoxal-mesotrochanteral conjunctiva.
jgiron
2021-03-18
The segment of the hind leg that is attached to the latero-ventral region of the metathorax by the basal metacoxal conjunctiva and to the metatrochanter by the metacoxal-metatrochanteral conjunctiva.
metacoxa
imiko
jgiron
imiko
imiko
jgiron
jgiron
The segment of the hind leg that is attached to the latero-ventral region of the metathorax by the basal metacoxal conjunctiva and to the metatrochanter by the metacoxal-metatrochanteral conjunctiva.
jgiron
2021-03-18
The segment of the fore leg that is attached to the latero-ventral region of the prothorax by the basal procoxal conjunctiva and to the protrochanter by the procoxal-protrochanteral conjunctiva.
procoxa
imiko
jgiron
imiko
imiko
jgiron
jgiron
The segment of the fore leg that is attached to the latero-ventral region of the prothorax by the basal procoxal conjunctiva and to the protrochanter by the procoxal-protrochanteral conjunctiva.
jgiron
2021-03-18
The segment of a fore leg attached to the distal margin of the profemur by the profemoro-protibial conjunctiva and to the proximal margin of the protarsus by the protibio-protarsal conjunctiva.
protibia
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
The segment of a fore leg attached to the distal margin of the profemur by the profemoro-protibial conjunctiva and to the proximal margin of the protarsus by the protibio-protarsal conjunctiva.
jgiron
2021-04-03
The segment of a mid leg attached to the distal margin of the mesofemur by the mesofemoro-mesotibial conjunctiva and to the proximal margin of the mesotarsus by the mesotibio-mesotarsal conjunctiva.
mesotibia
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
The segment of a mid leg attached to the distal margin of the mesofemur by the mesofemoro-mesotibial conjunctiva and to the proximal margin of the mesotarsus by the mesotibio-mesotarsal conjunctiva.
jgiron
2021-04-03
The segment of a hind leg attached to the distal margin of the metafemur by the metafemoro-metatibial conjunctiva and to the proximal margin of the metatarsus by the metatibio-metatarsal conjunctiva.
metatibia
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
The segment of a hind leg attached to the distal margin of the metafemur by the metafemoro-metatibial conjunctiva and to the proximal margin of the metatarsus by the metatibio-metatarsal conjunctiva.
jgiron
2021-04-03
The segment of a fore leg attached to the distal margin of the protrochanter by the protrochantero-profemoral conjunctiva and to the proximal margin of the protibia by the profemoro-protibial conjunctiva.
profemur
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
The segment of a fore leg attached to the distal margin of the protrochanter by the protrochantero-profemoral conjunctiva and to the proximal margin of the protibia by the profemoro-protibial conjunctiva.
jgiron
2021-03-18
The segment of a mid leg attached to the distal margin of the mesotrochanter by the mesotrochantero-mesofemoral conjunctiva and to the proximal margin of the mesotibia by the mesofemoro-mesotibial conjunctiva.
mesofemur
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
The segment of a mid leg attached to the distal margin of the mesotrochanter by the mesotrochantero-mesofemoral conjunctiva and to the proximal margin of the mesotibia by the mesofemoro-mesotibial conjunctiva.
jgiron
2021-03-18
The segment of a hind leg attached to the distal margin of the metatrochanter by the metatrochantero-metafemoral conjunctiva and to the proximal margin of the metatibia by the metafemoro-metatibial conjunctiva.
metafemur
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
The segment of a hind leg attached to the distal margin of the metatrochanter by the metatrochantero-metafemoral conjunctiva and to the proximal margin of the metatibia by the metafemoro-metatibial conjunctiva.
jgiron
2021-03-18
The ring sclerite that is part of an appendage and is not attached to skeletal muscle tissue.
mere
imiko
imiko
imiko
The ring sclerite that is part of an appendage and is not attached to skeletal muscle tissue.
jgiron
2021-04-21
The mere that is part of the tarsus.
tarsomere
imiko
jgiron
The mere that is part of the tarsus.
jgiron
2021-04-21
tarsomere
"Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Tarsomere: subelement of tarsus in Insecta; number often taxon-specific, sometimes differing on legs of different segments (diagnostic value: tarsal formula)."
The segment of a leg attached to the distal margin of the femur by the femoro-tibial conjunctiva and to the proximal margin of the tarsus by the tibio-tarsal conjunctiva.
tibia
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
The segment of a leg attached to the distal margin of the femur by the femoro-tibial conjunctiva and to the proximal margin of the tarsus by the tibio-tarsal conjunctiva.
jgiron
2021-04-03
tibia
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Tibia: 4th element of leg; usually cylindrical and equipped with paired terminal spurs, often with rows of spines."
The segment of a leg attached to the distal margin of the trochanter by the trochantero-femoral conjunctiva and to the proximal margin of the tibia by the femoro-tibial conjunctiva.
femur
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
The segment of a leg attached to the distal margin of the trochanter by the trochantero-femoral conjunctiva and to the proximal margin of the tibia by the femoro-tibial conjunctiva.
jgiron
2021-03-18
femur
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Femur: 3rd element of leg, often largest part."
The segment of the leg that is attached to the latero-ventral region of the insect thorax by the basal coxal conjunctiva and to the trochanter by the coxal-trochanteral conjunctiva.
coxa
imiko
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
The segment of the leg that is attached to the latero-ventral region of the insect thorax by the basal coxal conjunctiva and to the trochanter by the coxal-trochanteral conjunctiva.
jgiron
2021-03-18
coxa
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Coxa: basal element of leg; articulated with pleural, sternal and usually also trochantinal elements of thoracic segment."
The skeletal muscle continuous with the head capsule.
insect cranial muscle
The skeletal muscle continuous with the head capsule.
lagonzalezmo
2021-04-04
The skeletal muscle continuous with the head capsule and the antenna.
cranio-antennal muscle
lagonzalezmo
lagonzalezmo
The skeletal muscle continuous with the head capsule and the antenna.
lagonzalezmo
2021-04-04
The skeletal muscle continuous with the head capsule and the insect mandible.
cranio-mandibular muscle
imiko
lagonzalezmo
The skeletal muscle continuous with the head capsule and the insect mandible.
lagonzalezmo
2021-04-04
The skeletal muscle continuous with the head capsule and the labium.
cranio-labial muscle
lagonzalezmo
lagonzalezmo
The skeletal muscle continuous with the head capsule and the labium.
lagonzalezmo
2021-04-04
The skeletal muscle continuous with the head capsule and the labrum.
cranio-labral muscle
lagonzalezmo
lagonzalezmo
The skeletal muscle continuous with the head capsule and the labrum.
lagonzalezmo
2021-04-04
The coxal muscle of the mesocoxa.
mesocoxal muscle
imiko
imiko
The coxal muscle of the mesocoxa.
jgiron
2021-04-21
mesocoxal muscle
2020-11-11
The skeletal muscle that inserts in the coxa.
All of the coxal muscles, except the second sternal-metacoxal muscle, are attached to the thorax.
coxal muscle
imiko
imiko
The skeletal muscle that inserts in the coxa.
imiko
2021-04-21
All of the coxal muscles, except the second sternal-metacoxal muscle, are attached to the thorax.
imiko
Is the mouthpart appendage composed of the submentum, which is attached by the submental-mental conjunctiva to the mentum, which is attached by the mental-premental conjunctiva to the prementum, which is attached to the palpiger by the premental-palpigeral conjunctiva, the paraglossa by the premental-paraglossal conjunctiva, and the glossa by the premental-glossal conjunctiva; the palpiger is attached by the palpigero-palpal conjunctiva to the labial palpus.
labium
imiko
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
Is the mouthpart appendage composed of the submentum, which is attached by the submental-mental conjunctiva to the mentum, which is attached by the mental-premental conjunctiva to the prementum, which is attached to the palpiger by the premental-palpigeral conjunctiva, the paraglossa by the premental-paraglossal conjunctiva, and the glossa by the premental-glossal conjunctiva; the palpiger is attached by the palpigero-palpal conjunctiva to the labial palpus.
jgiron
2021-02-19
labium
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"The labium or lower lip forms the posterior (orthognathous head) or ventral (prognathous head) closure of the preoral space and of the salivarium. It is homologous to the maxilla (2nd maxilla) of crustaceans, but its proximal
parts form a structural unit without a recognizable median line or suture."
The elastic cuticle of the head capsule that is transparent and covers the eye.
eye cuticle
imiko
jgiron
imiko
The elastic cuticle of the head capsule that is transparent and covers the eye.
jgiron
2021-04-21
eye cuticle
2020-11-11
The resilin rich region that connects two sclerites.
ligament
imiko
imiko
imiko
The resilin rich region that connects two sclerites.
imiko
2021-04-21
ligament
2020-11-11
The usually cylindircal evagination of the cuticle that is resilin rich and is continuous with skeletal muscles.
cuticular tendon
imiko
imiko
imiko
The usually cylindircal evagination of the cuticle that is resilin rich and is continuous with skeletal muscles.
imiko
2020-11-11
cuticular tendon
Klass K-D (2001) The female abdomen of the viviparous earwig Hemimerus vosseleri (Insecta: Dermaptera: Hemimeridae), with a discussion of the postgenital abdomen of Insecta. Zoological Journal of the Linnean Society 131: 251–307.
https://doi.org/10.1111/j.1096-3642.2001.tb02239.x
"tendon is used herein to designate membranous internal cuticular projections"
The branching invagination of elastic cuticle that is cylindrical and contains taenidia.
trachea
imiko
imiko
imiko
imiko
The branching invagination of elastic cuticle that is cylindrical and contains taenidia.
imiko
2020-11-11
trachea
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Trachea: tube-shaped elements of the tracheal system."
The conjunctiva of the insect head that is attached to the salivarium and to the oral foraminal conjunctiva.
hypopharynx
imiko
jgiron
jgiron
jgiron
The conjunctiva of the insect head that is attached to the salivarium and to the oral foraminal conjunctiva.
jgiron
2021-02-19
hypopharynx
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Hypopharynx: median unpaired lobe between mouthparts and epipharynx; anterior (dorsal) surface continuous with anterior pharynx."
The conjunctiva of the insect thorax that joins the mesopleuron and the metapleuron.
mesopleuro-metapleural conjunctiva
imiko
jgiron
jgiron
jgiron
The conjunctiva of the insect thorax that joins the mesopleuron and the metapleuron.
jgiron
2021-04-09
The conjunctiva of the mesothorax that joins the metasternum and the metacoxa.
metasterno-metacoxal conjunctiva
imiko
jgiron
jgiron
jgiron
The conjunctiva of the mesothorax that joins the metasternum and the metacoxa.
jgiron
2021-04-09
The conjunctiva of the prothorax that joins the prosternum and the procoxa.
prosternal-procoxal conjunctiva
jgiron
jgiron
jgiron
jgiron
The conjunctiva of the prothorax that joins the prosternum and the procoxa.
jgiron
2021-04-09
The conjunctiva of the metathorax that joins the metapleuron and the metacoxa.
metapleuro-metacoxal conjunctiva
imiko
jgiron
jgiron
jgiron
The conjunctiva of the metathorax that joins the metapleuron and the metacoxa.
jgiron
2021-04-09
The conjuctiva that is continuous with the posterior margin of the head capsule and with the anterior margin of the prnotum, and bears cervical sclerites.
cervical membrane
neck membrane
imiko
jgiron
jgiron
imiko
The conjuctiva that is continuous with the posterior margin of the head capsule and with the anterior margin of the prnotum, and bears cervical sclerites.
imiko
2020-11-11
cervical membrane
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Cervical membrane: membrane connecting the head and prothorax."
The conjunctiva of the insect head that connects the head capsule and the mouthparts.
oral foraminal conjunctiva
imiko
jgiron
jgiron
jgiron
The conjunctiva of the insect head that connects the head capsule and the mouthparts.
jgiron
2021-04-03
The conjunctiva of the insect thorax that joins the pronotum and the mesonotum.
pronoto-mesonotal conjunctiva
imiko
jgiron
jgiron
jgiron
The conjunctiva of the insect thorax that joins the pronotum and the mesonotum.
jgiron
2021-04-09
The conjunctiva that is attached to the pronotum and the mesopectus.
pronoto-mesopectal conjunctiva
imiko
jgiron
jgiron
The conjunctiva that is attached to the pronotum and the mesopectus.
jgiron
2021-04-21
The conjunctiva that encircles a ring sclerite.
ring conjunctiva
imiko
imiko
The conjunctiva that encircles a ring sclerite.
jgiron
2021-04-03
The conjunctiva that encircles the mesocoxa and connects it to the ventral and lateral regions of the mesothorax.
basal mesocoxal conjunctiva
imiko
imiko
jgiron
The conjunctiva that encircles the mesocoxa and connects it to the ventral and lateral regions of the mesothorax.
imiko
2020-11-11
The conjunctiva that encircles the metacoxa and connects it to the ventral and lateral regions of the metathorax.
basal metacoxal conjunctiva
jgiron
jgiron
jgiron
The conjunctiva that encircles the metacoxa and connects it to the ventral and lateral regions of the metathorax.
jgiron
2021-03-18
The conjunctiva of the insect head that is connected to the oral foraminal conjunctiva and to the distal margin of the labrum.
epipharynx
imiko
jgiron
imiko
imiko
The conjunctiva of the insect head that is connected to the oral foraminal conjunctiva and to the distal margin of the labrum.
jgiron
2021-02-19
epipharynx
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Epipharynx: semimembranous or membranous posterior wall of labrum and roof of cibarium."
The conjunctiva that encircles the procoxa and connects it to the ventral and lateral regions of the prothorax.
basal procoxal conjunctiva
jgiron
jgiron
jgiron
The conjunctiva that encircles the procoxa and connects it to the ventral and lateral regions of the prothorax.
jgiron
2021-03-18
The cuticular region that is anterior (distal) to the neck membrane (encircled by the neck membrane) and contains the head capsule, the antenna, the eyes, mouthparts and surrounds the brain.
insect head
imiko
imiko
imiko
imiko
imiko
jgiron
jgiron
jgiron
imiko
jgiron
imiko
imiko
The cuticular region that is anterior (distal) to the neck membrane (encircled by the neck membrane) and contains the head capsule, the antenna, the eyes, mouthparts and surrounds the brain.
imiko
2020-11-11
insect head
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"The head is a compact and complex tagma with a concentration of a broad array of structures und functions. It is equipped with sense organs such as the highly complex compound eyes and the antennae, an elaborate set of mouthparts, and a complex muscle apparatus. It also contains central elements of the nervous system, the anterior part of the digestive tract including the cibarium (preoral cavity) and the salivarium, and also neurohaemal organs."
The region of cuticle that is connected to some muscles of the fore and hind legs and is posterior to the neck membrane and aterior to the first abdominal spiracle.
The hind leg muscles sometimes attach to the second abdominal sternite. The abdominal sopiracles are different in their structure from tghe thoracic spiracles as they are opened and closed by two articulating sclerites that are moved by two sets of muscles whereas the thoracic spiracles are closed by only one occlusor muscle and opened by the flexibility of the distal tracheal region. The border between the thorax and the abdomen is sometimes marked by the anterior first abdmonial tergal conjunctiva. In Hymenoptera, the border between the abdomen and the thorax cannot be defined as the anterior first abdmonial tergal conjunctiva is absent, the sclerite that receives muscles from the metacoxa also contains the first abdominal spiracle.
insect thorax
imiko
imiko
imiko
imiko
jgiron
jgiron
jgiron
imiko
jgiron
jgiron
The region of cuticle that is connected to some muscles of the fore and hind legs and is posterior to the neck membrane and aterior to the first abdominal spiracle.
imiko
2020-11-11
The hind leg muscles sometimes attach to the second abdominal sternite. The abdominal sopiracles are different in their structure from tghe thoracic spiracles as they are opened and closed by two articulating sclerites that are moved by two sets of muscles whereas the thoracic spiracles are closed by only one occlusor muscle and opened by the flexibility of the distal tracheal region. The border between the thorax and the abdomen is sometimes marked by the anterior first abdmonial tergal conjunctiva. In Hymenoptera, the border between the abdomen and the thorax cannot be defined as the anterior first abdmonial tergal conjunctiva is absent, the sclerite that receives muscles from the metacoxa also contains the first abdominal spiracle.
imiko
2020-11-11
The region of the cuticle that is posterior to the thorax.
The thorax is defined based on local properties (e.g. attachment sites of coxal muscles) and therefore we can reference this class for the definition of the abdomen.
insect abdomen
imiko
imiko
jgiron
jgiron
imiko
The region of the cuticle that is posterior to the thorax.
imiko
2020-11-11
The thorax is defined based on local properties (e.g. attachment sites of coxal muscles) and therefore we can reference this class for the definition of the abdomen.
imiko
2020-11-11
The conjunctiva of the insect maxilla that connects the cardo and the stipes.
cardo-stipital conjunctiva
imiko
jgiron
imiko
jgiron
The conjunctiva of the insect maxilla that connects the cardo and the stipes.
jgiron
2021-02-19
Is the sclerite of the insect maxilla that is attached to the cardo by the cardo-stipital conjunctiva, attached to the lacinia by the stipito-lacinial conjunctiva, attached to the palpifer by the stipito-palpiferal conjunctiva, and attached to the galea by the stipito-galeal conjunctiva.
stipes
imiko
jgiron
imiko
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
Is the sclerite of the insect maxilla that is attached to the cardo by the cardo-stipital conjunctiva, attached to the lacinia by the stipito-lacinial conjunctiva, attached to the palpifer by the stipito-palpiferal conjunctiva, and attached to the galea by the stipito-galeal conjunctiva.
jgiron
2021-02-19
stipes
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Stipes: second element of maxilla, connected with cardo by a hinge; bearing endite lobes (galea and lacinia) and maxillary palp."
The conjunctiva that encircles the base of the antenna (scape) and is encircled by the head capsule as the antennal foramen.
cranio-antennal conjunctiva
imiko
imiko
imiko
imiko
The conjunctiva that encircles the base of the antenna (scape) and is encircled by the head capsule as the antennal foramen.
imiko
2020-11-11
The segment of the antenna that is connected to the head capsule and the antennifer by the basal antennal conjunctiva and to the pedicellus by the scapal-pedicellar conjunctiva.
scapus
imiko
imiko
imiko
jgiron
jgiron
jgiron
jgiron
The segment of the antenna that is connected to the head capsule and the antennifer by the basal antennal conjunctiva and to the pedicellus by the scapal-pedicellar conjunctiva.
jgiron
2021-02-19
scapus
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
Scapus: basal element of antenna, with two muscles attached to the pedicellus.
The conjunctiva of the antenna that connects the scapus and the pedicellus.
scapal-pedicellar conjunctiva
imiko
jgiron
jgiron
jgiron
The conjunctiva of the antenna that connects the scapus and the pedicellus.
jgiron
2021-02-19
Is the segment of the antenna that is attached to the scapus by the scapal-pedicellar conjunctiva and to the first flagellomere by the pedicel-first flagellomere conjunctiva.
pedicellus
imiko
imiko
jgiron
jgiron
Is the segment of the antenna that is attached to the scapus by the scapal-pedicellar conjunctiva and to the first flagellomere by the pedicel-first flagellomere conjunctiva.
jgiron
2021-02-19
pedicellus
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Pedicellus: second antennal segment in Insecta; contains Johnston’s organ and lacks intrinsic muscles."
The mere that is part of the antenna.
flagellomere
imiko
imiko
The mere that is part of the antenna.
jgiron
2021-04-21
The first flagellomere of the antenna, attached to the pedicel by the pedicel-first flagellomere conjunctiva.
first flagellomere
jgiron
jgiron
jgiron
The first flagellomere of the antenna, attached to the pedicel by the pedicel-first flagellomere conjunctiva.
jgiron
2021-02-19
first flagellomere
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Flagellomere: segment of the flagellum."
The conjunctiva of the antenna that connects the pedicellus and the first flagellomere.
pedicellar-first flagellomeral conjunctiva
imiko
imiko
jgiron
jgiron
The conjunctiva of the antenna that connects the pedicellus and the first flagellomere.
jgiron
2021-02-19
The region of the cuticle on the lateral region of the metathorax that is attached to the metanotum and the metasternum, and is attached to the metacoxa by the metacoxal muscle and the basal metacoxal conjunctiva.
metapleuron
imiko
jgiron
imiko
jgiron
jgiron
jgiron
The region of the cuticle on the lateral region of the metathorax that is attached to the metanotum and the metasternum, and is attached to the metacoxa by the metacoxal muscle and the basal metacoxal conjunctiva.
jgiron
2021-04-21
The conjunctiva of the prothorax that joins the propleuron and the procoxa.
propleuro-procoxal conjunctiva
imiko
jgiron
jgiron
jgiron
The conjunctiva of the prothorax that joins the propleuron and the procoxa.
jgiron
2021-04-09
The sclerite on the ventral region of the mesothorax that bears the mesofurca and is attached to the mesopleuro-mesosternal conjunctiva.
mesosternum
jgiron
jgiron
jgiron
jgiron
The sclerite on the ventral region of the mesothorax that bears the mesofurca and is attached to the mesopleuro-mesosternal conjunctiva.
jgiron
2021-04-09
The conjunctiva of the fore leg joining the distal margin of a procoxa and the proximal margin of a protrochanter.
procoxal-protrochanteral conjunctiva
jgiron
jgiron
jgiron
jgiron
The conjunctiva of the fore leg joining the distal margin of a procoxa and the proximal margin of a protrochanter.
jgiron
2021-03-18
The conjunctiva of the mid leg joining the distal margin of a mesocoxa and the proximal margin of a mesotrochanter.
mesocoxal-mesotrochanteral conjunctiva
imiko
jgiron
imiko
jgiron
The conjunctiva of the mid leg joining the distal margin of a mesocoxa and the proximal margin of a mesotrochanter.
jgiron
2021-03-18
The conjunctiva of the hind leg joining the distal margin of a metacoxa and the proximal margin of a metatrochanter.
metacoxal-metatrochanteral conjunctiva
jgiron
jgiron
jgiron
jgiron
The conjunctiva of the hind leg joining the distal margin of a metacoxa and the proximal margin of a metatrochanter.
jgiron
2021-03-18
The conjunctiva that corresponds to one epithelial cell and surrounds a sclerotized unicellular cuticular evagination.
Should coincide with 'exactly one' epithelial cell, but that violates OWL specs.
socket membrane
imiko
imiko
imiko
The conjunctiva that corresponds to one epithelial cell and surrounds a sclerotized unicellular cuticular evagination.
jgiron
2021-04-21
Should coincide with 'exactly one' epithelial cell, but that violates OWL specs.
jgiron
2021-04-26
socket membrane
2020-11-11
The cuticular evagination that corresponds to the evagination on the membrane of a single cell and not to the evagination of a cell layer.
Should coincide with 'exactly one' epithelial cell, but that violates OWL specs.
unicellular cuticular evagination
imiko
imiko
The cuticular evagination that corresponds to the evagination on the membrane of a single cell and not to the evagination of a cell layer.
imiko
2020-11-11
Should coincide with 'exactly one' epithelial cell, but that violates OWL specs.
jgiron
2021-04-26
The region of cuticle that corresponds to the evagination of the single layer epithelium.
multicellular cuticular evagination
imiko
The region of cuticle that corresponds to the evagination of the single layer epithelium.
imiko
2021-04-21
multicellular cuticular evagination
2020-11-11
The seta that has one opening distally.
Should coincide with 'exactly one' pore canal, but that violates OWL specs.
uniporous sensillum
imiko
imiko
The seta that has one opening distally.
imiko
2020-11-11
Should coincide with 'exactly one' pore canal, but that violates OWL specs.
imiko
2021-04-23
The seta that has multiple cuticular pores (openings of class III exocrine glands).
multiporous sensillum
imiko
imiko
The seta that has multiple cuticular pores (openings of class III exocrine glands).
imiko
2021-04-21
multiporous sensillum
Ando, T., Sekine, S., Inagaki, S., Misaki, K., Badel, L., Moriya, H., Sami, M.M., Itakura, Y., Chihara, T., Kazama, H. and Yonemura, S., 2019. Nanopore formation in the cuticle of an insect olfactory sensillum. Current Biology, 29(9), pp.1512-1520.
https://www.sciencedirect.com/science/article/pii/S0960982219303410#fig4
2020-11-11
The multiporous plate that is elongated.
placoid sensillum
imiko
imiko
The multiporous plate that is elongated.
imiko
2021-04-21
placoid sensillum
2020-11-11
The multiporous sensillum that is flat.
multiporous plate
imiko
imiko
The multiporous sensillum that is flat.
imiko
2021-04-21
multiporous plate
2020-11-11
The branching cuticular invagination that corresponds to the invagination of the membrane of a single cell and does not contain taenidia.
Should coincide with 'exactly one' epithelial cell, but that violates OWL specs.
exocrine gland duct
imiko
imiko
imiko
The branching cuticular invagination that corresponds to the invagination of the membrane of a single cell and does not contain taenidia.
imiko
2021-04-21
Should coincide with 'exactly one' epithelial cell, but that violates OWL specs.
jgiron
2021-04-26
exocrine gland duct
2020-11-11
The region of the cuticle that is continuous to the proximal region of the trachea and can be closed by muscles.
spiracle
imiko
imiko
imiko
The region of the cuticle that is continuous to the proximal region of the trachea and can be closed by muscles.
imiko
2021-04-21
spiracle
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Spiracle: external opening of the tracheal system."
The cuticular ivagination that is branched into umerous branches.
Branching cuticular invaginations porvide important models for branchig morphogenesis.
branching cuticular invagination
imiko
imiko
The cuticular ivagination that is branched into umerous branches.
imiko
2020-11-11
Branching cuticular invaginations porvide important models for branchig morphogenesis.
imiko
2020-11-11
The branching cuticular invagination that is located between the mid and hindgut.
malphigian tube
imiko
The branching cuticular invagination that is located between the mid and hindgut.
imiko
2021-04-21
malphigian tube
2020-11-11
The cuticular invagination that is hollow.
The apophysis in HAO refers to an ivagination of the cuticle that is cylindrical as opposed to a ridge that is elongate. Beutel et al. 2014 differentiate apodemes from apophyses in that apodemes are solid and apophyses are hollow.
apophysis
imiko
imiko
imiko
The cuticular invagination that is hollow.
imiko
2021-04-21
The apophysis in HAO refers to an ivagination of the cuticle that is cylindrical as opposed to a ridge that is elongate. Beutel et al. 2014 differentiate apodemes from apophyses in that apodemes are solid and apophyses are hollow.
imiko
2020-11-11
apophysis
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Apophysis: hollow cuticular invagination."
The coiled ridge in the wall of the trachea.
taenidium
imiko
imiko
The coiled ridge in the wall of the trachea.
imiko
2021-04-21
taenidium
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Taenidium: spiral-shaped strengthening ridge of the tracheae."
2020-11-11
The furca of the mesothorax that is attached to the mesocoxa via muscle.
mesofurca
imiko
jgiron
imiko
The furca of the mesothorax that is attached to the mesocoxa via muscle.
jgiron
2021-04-21
The furca of the metathorax that is attached to the metacoxa via muscle.
metafurca
imiko
jgiron
imiko
The furca of the metathorax that is attached to the metacoxa via muscle.
jgiron
2021-04-21
The furca of the prothorax that is attached to the procoxa via muscle.
profurca
imiko
jgiron
imiko
The furca of the prothorax that is attached to the procoxa via muscle.
jgiron
2021-04-21
The apophysis that is located ventromedially on the thorax and is connected to the coxa via muscles.
furca
imiko
imiko
imiko
imiko
imiko
The apophysis that is located ventromedially on the thorax and is connected to the coxa via muscles.
imiko
2020-11-11
furca
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Furca (=sternal apophysis, endosternite): endoskeletal element (entapophysis) of furcasternum; paired furcal arms often connected with pleural ridge by short muscle."
The coxal muscle of the procoxa.
procoxal muscle
imiko
imiko
The coxal muscle of the procoxa.
jgiron
2021-04-21
procoxal muscle
2020-11-11
The coxal muscle of the metacoxa.
metacoxal muscle
imiko
imiko
The coxal muscle of the metacoxa.
jgiron
2021-04-21
metacoxal muscle
2020-11-11
The skeletal muscle that inserts in the femur.
femoral muscle
lagonzalezmo
imiko
The skeletal muscle that inserts in the femur.
jgiron
2021-04-21
The skeletal muscle that inserts in the tibia.
tibial muscle
imiko
imiko
The skeletal muscle that inserts in the tibia.
jgiron
2021-04-21
The skeletal muscle that inserts on the pretarsus.
There are usually two muscle bands of the pretarsal muscle, one is arising from the femur, the other from the tibia. The muscle usually inserts on a resilin rich basal sclerite of the pretarsus, the unguitractor plate.
pretarsal muscle
The skeletal muscle that inserts on the pretarsus.
imiko
2020-11-11
There are usually two muscle bands of the pretarsal muscle, one is arising from the femur, the other from the tibia. The muscle usually inserts on a resilin rich basal sclerite of the pretarsus, the unguitractor plate.
imiko
2020-11-11
The skeletal muscle that inserts in the profemur.
profemoral muscle
imiko
imiko
The skeletal muscle that inserts in the profemur.
jgiron
2021-04-21
The skeletal muscle that inserts in the mesofemur.
mesofemoral muscle
imiko
imiko
The skeletal muscle that inserts in the mesofemur.
jgiron
2021-04-21
The skeletal muscle that inserts in the metafemur.
metafemoral muscle
imiko
imiko
The skeletal muscle that inserts in the metafemur.
jgiron
2021-04-21
The skeletal muscle that inserts in the protibia.
protibial muscle
imiko
imiko
The skeletal muscle that inserts in the protibia.
jgiron
2021-04-21
The skeletal muscle that inserts in the mesotibia.
mesotibial muscle
imiko
imiko
The skeletal muscle that inserts in the mesotibia.
jgiron
2021-04-21
The skeletal muscle that inserts in the metatibia.
metatibial muscle
imiko
imiko
The skeletal muscle that inserts in the metatibia.
jgiron
2021-04-21
The cuticular depression that is circular.
fovea
imiko
imiko
imiko
The cuticular depression that is circular.
imiko
2020-11-11
The cuticular depression that does not correspond to an epithelial fold.
The cuticular depression (concavity on the surface of the cuticle) that does not correspond to a cuticular invagination (epithelial fold). The cuticule is less thick at the site of a cuticular impression.
impression
imiko
imiko
imiko
The cuticular depression that does not correspond to an epithelial fold.
jgiron
2021-04-21
The cuticular depression (concavity on the surface of the cuticle) that does not correspond to a cuticular invagination (epithelial fold). The cuticule is less thick at the site of a cuticular impression.
imiko
2020-11-11
The invagination on a sclerite that is elongated.
ridge
imiko
imiko
The invagination on a sclerite that is elongated.
imiko
2020-11-11
ridge
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Ridge: cuticular strengthening ridge."
"They are not lines of fusion or molting lines."(p. 12)
Is the conjunctiva in the head capsule that forms a pouch between the hypopharynx and the labium and bears the exocrine gland duct.
salivarium
jgiron
imiko
jgiron
imiko
imiko
imiko
Is the conjunctiva in the head capsule that forms a pouch between the hypopharynx and the labium and bears the exocrine gland duct.
jgiron
2021-02-19
salivarium
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Salivarium: posterior part of preoral space between hypopharynx and labium, with opening of salivary ducts."
The invagination of the cuticle that is largely membraneous.
pouch
imiko
imiko
The invagination of the cuticle that is largely membraneous.
imiko
2020-11-12
The ridge that is in the sagittal line of the ventral part thorax.
discrimenal lamella
imiko
imiko
imiko
The ridge that is in the sagittal line of the ventral part thorax.
imiko
2020-11-12
The cuticular depression (concavity on cuticle surface) that corresponds with a ridge (an elongate cuticular invagination).
sulcus
imiko
imiko
The cuticular depression (concavity on cuticle surface) that corresponds with a ridge (an elongate cuticular invagination).
imiko
2020-11-12
The ridge that corresponds to the discrimenal lamella.
discrimen
imiko
imiko
The ridge that corresponds to the discrimenal lamella.
imiko
2020-11-12
discrimen
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Discrimen: longitudinal ridge medially dividing the sternum"
The appendage of the insect head that is encircled by the oral foraminal conjunctiva.
mouthpart
imiko
imiko
jgiron
The appendage of the insect head that is encircled by the oral foraminal conjunctiva.
imiko
2021-04-21
mouthpart
2020-11-17
The insect articulation between the propleuron and the procoxa.
propleuro-procoxal artiulation
imiko
imiko
The insect articulation between the propleuron and the procoxa.
jgiron
2021-04-21
The anatomical surface where two sclerites meet.
articular surface
imiko
imiko
The anatomical surface where two sclerites meet.
jgiron
2021-04-21
The sclerite of the salivarium.
salivary sclerite
imiko
imiko
The sclerite of the salivarium.
jgiron
2021-04-21
The notum or sclerite on the dorsal region of the metathorax that is posterior to the mesonotum, connected via the metanoto-metapleural conjuntiva to the dorsal margin of the metapleuron, that is not adjacent to the metacoxa, but attached to it by the metacoxal muscle.
metanotum
imiko
imiko
jcgiron
jgiron
jcgiron
jcgiron
jcgiron
jcgiron
The notum or sclerite on the dorsal region of the metathorax that is posterior to the mesonotum, connected via the metanoto-metapleural conjuntiva to the dorsal margin of the metapleuron, that is not adjacent to the metacoxa, but attached to it by the metacoxal muscle.
jcgiron
2021-04-21
The sclerite that is continuous with the basal metacoxal conjunctiva and the basal wing conjunctiva and contains the metafurca.
metapectus
imiko
imiko
imiko
imiko
The sclerite that is continuous with the basal metacoxal conjunctiva and the basal wing conjunctiva and contains the metafurca.
imiko
2021-04-21
The conjunctiva is encircled by a tarsomere that encircles another tarsomere.
intertarsomeral conjunctiva
jgiron
jgiron
jgiron
jgiron
The conjunctiva is encircled by a tarsomere that encircles another tarsomere.
jgiron
2021-03-18
The conjunctiva that encircles the coxa and connects them to the ventral and lateral thoracic regions.
These conjunctivae can be used as stable reference points in insects that poseess legs, and can be used to define sclerites on the lateral side of the thorax.
basal coxal conjunctiva
imiko
jgiron
imiko
jgiron
The conjunctiva that encircles the coxa and connects them to the ventral and lateral thoracic regions.
imiko
2020-11-17
These conjunctivae can be used as stable reference points in insects that poseess legs, and can be used to define sclerites on the lateral side of the thorax.
imiko
2020-11-17
The region of the insect integument that is part of the insect cuticle.
The AISM focuses on anatomical structures that are part of the insect (chitinous) cuticle. These structures are acellular regions of the integument. Regions of the insect cuticle with different mechanical properties (i.e. increased and descresed flexinility, thickness and elasticity) are continuous with each other (e.g. sclerites are continuous with conjunctivae or resilin rich regions are continuou with regions with less resilin content).
region of cuticle
imiko
imiko
The region of the insect integument that is part of the insect cuticle.
imiko
2020-11-23
The AISM focuses on anatomical structures that are part of the insect (chitinous) cuticle. These structures are acellular regions of the integument. Regions of the insect cuticle with different mechanical properties (i.e. increased and descresed flexinility, thickness and elasticity) are continuous with each other (e.g. sclerites are continuous with conjunctivae or resilin rich regions are continuou with regions with less resilin content).
imiko
2020-11-23
The anatomical space that is contained by the cuticle and connects the inside of the insect with the outside, is tubular, and whose diameter is smaller than 100 nm.
Should coincide with 'exactly one' epithelial cell, but that violates OWL specs.
pore canal
imiko
imiko
imiko
imiko
The anatomical space that is contained by the cuticle and connects the inside of the insect with the outside, is tubular, and whose diameter is smaller than 100 nm.
imiko
2021-02-04
Should coincide with 'exactly one' epithelial cell, but that violates OWL specs.
jgiron
2021-04-26
pore canal
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Pore canals: thin perforations of the cuticle."
The solid cuticular protrusion that coincides with only one epidermal cell (smaller than the diameter of the epidermal cell).
Should coincide with 'exactly one' epithelial cell, but that violates OWL specs.
acantha
imiko
imiko
imiko
The solid cuticular protrusion that coincides with only one epidermal cell (smaller than the diameter of the epidermal cell).
imiko
2021-02-04
Should coincide with 'exactly one' epithelial cell, but that violates OWL specs.
2021-04-26
jgiron
acantha
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Acanthae: hairs without sockets, one per hypodermal cell."
Hairlike seta that is short and thick walled.
sensillum chaeticum
imiko
imiko
imiko
Hairlike seta that is short and thick walled.
imiko
2021-02-08
sensillum chaeticum
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Sensillum chaeticum: shorter than sensillum trichodeum, thick-walled."
Hairlike seta that is long.
sensillum trichodeum
imiko
imiko
imiko
Hairlike seta that is long.
imiko
2021-02-08
sensillum trichodeum
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Sensillum trichodeum: hair-like sensilla, seta associated with sensory cell."
Seta that is located in the middle of a depression with narrowed external opening.
sensillum coeloconicum
imiko
imiko
Seta that is located in the middle of a depression with narrowed external opening.
imiko
2021-02-08
sensillum coeloconicum
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Sensillum coeloconicum: sensillum with modified seta in a cavity, with narrowed external opening of surrounding cuticle."
The solid cuticular invagination of a sclerite.
apodeme
imiko
imiko
imiko
The solid cuticular invagination of a sclerite.
jgiron
2021-04-21
apodeme
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Apodeme: solid cuticular invagination serving as muscle insertion area."
Klass K-D (2001) The female abdomen of the viviparous earwig Hemimerus vosseleri (Insecta: Dermaptera: Hemimeridae), with a discussion of the postgenital abdomen of Insecta. Zoological Journal of the Linnean Society 131: 251–307.
https://doi.org/10.1111/j.1096-3642.2001.tb02239.x
"tendon is used herein to designate sclerotized internal cuticular projections"
The seta that is conical.
sensillum basiconicum
imiko
imiko
The seta that is conical.
jgiron
2021-04-21
sensillum basiconicum
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Sensillum basiconicum: sensillum with rounded, conical seta."
The cuticular protrusion (process, protuberace) that bears the cranial articular surface of the cranio-antennal articulation.
antennifer
imiko
jgiron
jgiron
imiko
The cuticular protrusion (process, protuberace) that bears the cranial articular surface of the cranio-antennal articulation.
imiko
2021-02-08
antennifer
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Antennifer: small cephalic process articulating with the antenna."
The solid, paired, branching cuticular invagination of the head capsule that is attached to the antenna and the mouthparts via muscles.
The paired apophysis that connects the posterior (ventral in prognathous head) and anterior (dorsal in prognathous head) walls of the head capsule and serves as site of isertion of atennal and mouthpart muscles.
tentorium
imiko
imiko
imiko
imiko
imiko
imiko
The solid, paired, branching cuticular invagination of the head capsule that is attached to the antenna and the mouthparts via muscles.
jgiron
2021-04-21
The paired apophysis that connects the posterior (ventral in prognathous head) and anterior (dorsal in prognathous head) walls of the head capsule and serves as site of isertion of atennal and mouthpart muscles.
imiko
2021-02-11
tentorium
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Tentorium: cephalic endoskeleton, usually composed of paired anterior, posterior and dorsal tentorial arms and a transverse tentorial bridge (corpotentorium)."
The insect cranial muscle that connects the tentorium and the antenna.
tentorio-antennal muscle
imiko
jgiron
jgiron
The insect cranial muscle that connects the tentorium and the antenna.
jgiron
2021-04-21
The cuticular depression that corresponds to an apophysis.
pit
imiko
imiko
The cuticular depression that corresponds to an apophysis.
imiko
2021-02-12
The tentorial pit that correspods to the anterior (dorsal in prognathous head) end of the tentorium.
anterior tentorial pit
imiko
imiko
jgiron
The tentorial pit that correspods to the anterior (dorsal in prognathous head) end of the tentorium.
imiko
2021-02-12
anterior tentorial pit
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Anterior tentorial pit (or groove): externally visible invagination area and origin of anterior tentorial arm; adjacent with dorsolateral clypeal margin."
The tentorial pit that correspods to the posterior (ventral in prognathous head) end of the tentorium.
posterior tetorial pit
imiko
imiko
jgiron
The tentorial pit that correspods to the posterior (ventral in prognathous head) end of the tentorium.
imiko
2021-02-12
posterior tetorial pit
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Posterior tentorial pit (or groove): externally visible invagination of posterior part of head capsule and origin of posterior tentorial arm; adjacent with foramen occipitale or gula."
The pit that correspods to the tentorium.
tentorial pit
imiko
imiko
The pit that correspods to the tentorium.
imiko
2021-02-12
Is the anatomical space encircled a sclerite
arthropod foramen
imiko
imiko
Is the anatomical space encircled a sclerite
jgiron
2021-02-19
The arthropod foramen of the head capsule that contains the antennifer and surrounds the scapus via the antenniferal-scapal conjunctiva.
antennal foramen
imiko
jgiron
imiko
jgiron
jgiron
The arthropod foramen of the head capsule that contains the antennifer and surrounds the scapus via the antenniferal-scapal conjunctiva.
jgiron
2021-04-21
The paired sclerite of the postabdomen that is attached to the abdominal tergite IX by the abdominal tergite IX-gonocoxa IX conjunctiva and is articulated with abdominal tergite IX.
second coxopodite
second gonocoxite
second valvifer
gonocoxa IX
jgiron
jgiron
imiko
jgiron
jgiron
The paired sclerite of the postabdomen that is attached to the abdominal tergite IX by the abdominal tergite IX-gonocoxa IX conjunctiva and is articulated with abdominal tergite IX.
imiko
2021-03-19
second coxopodite
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Coxopodite (=valvifer, gonocoxa, gonocoxite): short basal piece of ovipositor elements of female genital segments VIII and IX."
second gonocoxite
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Coxopodite (=valvifer, gonocoxa, gonocoxite): short basal piece of ovipositor elements of female genital segments VIII and IX."
second valvifer
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Coxopodite (=valvifer, gonocoxa, gonocoxite): short basal piece of ovipositor elements of female genital segments VIII and IX."
Is the conjunctiva of the postabdomen that connects the abdominal tergite IX and the gonocoxa IX.
abdominal tergite IX-gonocoxa IX conjunctiva
jgiron
jgiron
jgiron
jgiron
Is the conjunctiva of the postabdomen that connects the abdominal tergite IX and the gonocoxa IX.
imiko
2021-03-19
The protrusion on a sclerite that is elongated.
carina
The protrusion on a sclerite that is elongated.
starasov
2021-05-06
carina
???????
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
Is the sclerite of the insect maxilla that is attached to the stipes by the stipito-palpiferal conjunctiva and to the maxillary palpus by the palpifero-palpal conjunctiva.
palpifer
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
Is the sclerite of the insect maxilla that is attached to the stipes by the stipito-palpiferal conjunctiva and to the maxillary palpus by the palpifero-palpal conjunctiva.
jgiron
2021-02-17
palpifer
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Palpifer: small separate element of stipes, bears the maxillary palp."
The conjunctiva of the labium that connects the mentum and the prementum.
mental-premental conjunctiva
jgiron
jgiron
jgiron
jgiron
The conjunctiva of the labium that connects the mentum and the prementum.
jgiron
2021-02-17
Is the sclerite of the labium that is cmposed of the submentum and the mentum, which are connected by the submental-mental conjunctiva
postmentum
jgiron
jgiron
jgiron
jgiron
jgiron
Is the sclerite of the labium that is cmposed of the submentum and the mentum, which are connected by the submental-mental conjunctiva
jgiron
2021-02-17
postmentum
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Postmentum: posterior main element of labium, posteriorly adjacent with foramen occipitale in hexapods without gula or hypostomal bridge; often separated into two sclerites, the anterior mentum and the posterior submentum."
Is the sclerite of the labium that is anterior to the submentum and posterior to the prementum, and attached to the prementum by the mental-premental conjunctiva.
mentum
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
Is the sclerite of the labium that is anterior to the submentum and posterior to the prementum, and attached to the prementum by the mental-premental conjunctiva.
jgiron
2021-02-17
mentum
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Mentum: intermediate part of labium, anterior part of postmentum; bears the prementum at its distal edge."
Is the sclerite of the labium that is attached to the mentum by the submental-mental conjunctiva.
submentum
jgiron
jgiron
jgiron
jgiron
Is the sclerite of the labium that is attached to the mentum by the submental-mental conjunctiva.
jgiron
2021-02-17
submentum
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Submentum: posterior part of a divided postmentum."
Is the sclerite of the labium that is attached to the prementum by the premental-palpigeral conjunctiva and to the labial palpus by the palpigero-palpal conjunctiva.
palpiger
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
Is the sclerite of the labium that is attached to the prementum by the premental-palpigeral conjunctiva and to the labial palpus by the palpigero-palpal conjunctiva.
jgiron
2021-02-17
palpiger
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Palpiger: small separate element of prementum, bears the labial palp."
Is the conjunctiva of the head capsule that connects the antennifer and the scapus.
antenniferal-scapal conjunctiva
jgiron
jgiron
jgiron
jgiron
Is the conjunctiva of the head capsule that connects the antennifer and the scapus.
jgiron
2021-02-19
Is the conjunctiva of the antenna that connects a flagellomere and other flagellomere.
interflagellomeral conjunctiva
jgiron
jgiron
jgiron
jgiron
Is the conjunctiva of the antenna that connects a flagellomere and other flagellomere.
jgiron
2021-02-19
Is the conjunctiva of the insect maxilla that connects the stipes and the lacinia.
stipito-lacinial conjunctiva
jgiron
jgiron
jgiron
jgiron
Is the conjunctiva of the insect maxilla that connects the stipes and the lacinia.
jgiron
2021-02-19
Is the conjunctiva of the insect maxilla that connects the stipes and the palpifer.
stipito-palpiferal conjunctiva
jgiron
jgiron
jgiron
jgiron
Is the conjunctiva of the insect maxilla that connects the stipes and the palpifer.
jgiron
2021-02-19
Is the conjunctiva of the insect maxilla that connects the stipes and the galea.
stipito-galeal conjunctiva
jgiron
jgiron
jgiron
jgiron
Is the conjunctiva of the insect maxilla that connects the stipes and the galea.
jgiron
2021-02-19
Is the conjunctiva of the insect maxilla that connects the palpifer and the maxillary palpus.
palpifero-palpal conjunctiva
jgiron
jgiron
jgiron
jgiron
Is the conjunctiva of the insect maxilla that connects the palpifer and the maxillary palpus.
jgiron
2021-02-19
Is the conjunctiva of the labium that connects the submentum and the mentum.
submental-mental conjunctiva
jgiron
jgiron
jgiron
jgiron
Is the conjunctiva of the labium that connects the submentum and the mentum.
jgiron
2021-02-19
Is the conjunctiva of the labium that connects the prementum and the palpiger.
premental-palpigeral conjunctiva
jgiron
jgiron
jgiron
jgiron
Is the conjunctiva of the labium that connects the prementum and the palpiger.
jgiron
2021-02-19
Is the conjunctiva of the labium that connects the prementum and the paraglossa.
premental-paraglossal conjunctiva
jgiron
jgiron
jgiron
jgiron
Is the conjunctiva of the labium that connects the prementum and the paraglossa.
jgiron
2021-02-19
Is the conjunctiva of the labium that connects the prementum and the glossa.
premental-glossal conjunctiva
jgiron
jgiron
jgiron
jgiron
Is the conjunctiva of the labium that connects the prementum and the glossa.
jgiron
2021-02-19
Is the conjunctiva of the labium that connects the palpiger and the labial palpus.
palpigero-palpal conjunctiva
jgiron
jgiron
jgiron
jgiron
Is the conjunctiva of the labium that connects the palpiger and the labial palpus.
jgiron
2021-02-19
The conjunctiva of the insect maxilla that connects the clypeus and the labrum.
clypeo-labral conjunctiva
jgiron
jgiron
jgiron
The conjunctiva of the insect maxilla that connects the clypeus and the labrum.
jgiron
2021-02-19
Is the region of the head capsule that is anterior to the frons and is attached to the labrum by the clypeo-labral conjunctiva
clypeus
jgiron
jgiron
jgiron
jgiron
jgiron
Is the region of the head capsule that is anterior to the frons and is attached to the labrum by the clypeo-labral conjunctiva
jgiron
2021-02-19
clypeus
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Clypeus: anteroventral part of head capsule; primarily separated from frons by transverse frontoclypeal strengthening ridge between anterior tentorial pits; usually bearing the labrum at its distal margin."
The region of cuticle of the head capsule that is located posterior to the clypeus and delimited by the frontal suture.
frons
jgiron
jgiron
jgiron
jgiron
The region of cuticle of the head capsule that is located posterior to the clypeus and delimited by the frontal suture.
jgiron
2021-04-03
frons
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Frons: frontal part of head capsule, delimited by ecdysial lines (frontal sutures); often triangular and bearing unpaired (median) ocellus."
Is the ridge along the dorsal and lateral regions of the head capsule that is adjacent to the foramen occipitale.
postoccipital ridge
jgiron
jgiron
jgiron
Is the ridge along the dorsal and lateral regions of the head capsule that is adjacent to the foramen occipitale.
jgiron
2021-02-19
postoccipital ridge
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Postoccipital ridge: strengthening ridge enclosing the foramen occipitale dorsally and laterally; also serving as muscle attachment area."
Is the ridge of the head capsule surrounding the eye cuticle.
circumocular ridge
jgiron
jgiron
jgiron
Is the ridge of the head capsule surrounding the eye cuticle.
jgiron
2021-02-19
circumocular ridge
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Circumocular ridge: internal ridge enclosing compound eye."
Is the foramen of the head capsule that connects with the neck membrane and is divided by the tentorial bridge into alaforamen and neuroforamen.
foramen occipitale
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
Is the foramen of the head capsule that connects with the neck membrane and is divided by the tentorial bridge into alaforamen and neuroforamen.
jgiron
2021-02-24
foramen occipitale
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Foramen occipitale (=foramen magnum): posterior opening of head capsule; divided by tentorial bridge into alaforamen and neuroforamen."
Is the apophysis of the tentorium originating from each posterior tentorial arm.
corpotentorium
tentorial bridge
jgiron
jgiron
jgiron
Is the apophysis of the tentorium originating from each posterior tentorial arm.
jgiron
2021-02-24
corpotentorium
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Tentorial bridge (=corpotentorium): transverse element connecting posterior tentorial arms, often plate-like."
tentorial bridge
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Tentorial bridge (=corpotentorium): transverse element connecting posterior tentorial arms, often plate-like."
Is the dorsal region of the head capsule that surrounds the coronal suture, and is connected laterally to the genae.
vertex
jgiron
jgiron
jgiron
jgiron
Is the dorsal region of the head capsule that surrounds the coronal suture, and is connected laterally to the genae.
jgiron
2021-02-24
vertex
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Vertex: posterodorsal part of head capsule, usually medially divided by ecdysial line (coronal suture)."
Is the lateral region of the head capsule, connected dorsally to the sides of the vertex.
gena
jgiron
jgiron
jgiron
Is the lateral region of the head capsule, connected dorsally to the sides of the vertex.
jgiron
2021-02-24
gena
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Gena: lateral region of head capsule; not separated from vertex by a ridge or suture."
Is the lateral region of the head capsule that connects dorsally to the ventral side of the gena and ventrally to the mandible.
subgena
jgiron
jgiron
jgiron
Is the lateral region of the head capsule that connects dorsally to the ventral side of the gena and ventrally to the mandible.
jgiron
2021-02-24
subgena
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Subgena: narrow lateral region of head capsule, above external side of mandibular base, usually separated from gena by subgenal ridge."
The region of the cuticle of the head capsule that coincides with an ecdysial line.
suture
jgiron
jgiron
jgiron
The region of the cuticle of the head capsule that coincides with an ecdysial line.
jgiron
2021-04-21
suture
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Suture: ecdysial suture, zone of weakness."
The suture that surrounds the frons and is connected to the coronal suture.
frontal suture
jgiron
jgiron
jgiron
The suture that surrounds the frons and is connected to the coronal suture.
jgiron
2021-04-03
frontal suture
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Frontal suture: paired ecdysial sutures enclosing frons; anterior parts of epicranial suture."
The suture that is on the vertex and is connected to the coronal suture.
epicranial suture
coronal suture
jgiron
jgiron
jgiron
The suture that is on the vertex and is connected to the coronal suture.
jgiron
2021-04-03
epicranial suture
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
coronal suture
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Coronal suture: unpaired median ecdysial sutures dividing vertex; anteriorly continuous with frontal sutures."
Is the ridge of the head capsule comprising the posterior region of the subgenal ridge.
pleurostomal ridge
jgiron
jgiron
Is the ridge of the head capsule comprising the posterior region of the subgenal ridge.
jgiron
2021-02-24
pleurostomal ridge
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
[Pleurostomal ridge: anterior section of the subgenal ridge above the mandibular base. (p. 14)]
Is the ridge of the head capsule that separates the gena and the subgena.
subgenal ridge
jgiron
jgiron
jgiron
jgiron
Is the ridge of the head capsule that separates the gena and the subgena.
jgiron
2021-02-24
subgenal ridge
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Subgenal ridge: strengthening ridge separating gena from subgena."
Is the lateral region of the head capsule that is adjacent to the foramen occipitale
hypostomal bridge
jgiron
jgiron
jgiron
jgiron
Is the lateral region of the head capsule that is adjacent to the foramen occipitale
jgiron
2021-02-24
hypostomal bridge
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Hypostomal bridge: partial closure of foramen occipitale, formed by ventromedially adjacent extensions of lateral head capsule."
[posterior section of the subgenal ridge; p. 14]
Is the ridge of the head capsule that separates the clypeus and the frons.
frontoclypeal ridge
jgiron
jgiron
jgiron
jgiron
Is the ridge of the head capsule that separates the clypeus and the frons.
jgiron
2021-02-24
frontoclypeal ridge
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Frontoclypeal (strengthening) ridge (=frontoclypeal “suture”, epistomal “suture”): internal ridge separating clypeus from frons, between anterior tentorial pits."
Is the sclerite on the ventral region of the head capsule that is limited laterally by the gular ridges, posteriorly by the foramen occipitale and anteriorly by the submentum.
gula
jgiron
jgiron
jgiron
jgiron
jgiron
Is the sclerite on the ventral region of the head capsule that is limited laterally by the gular ridges, posteriorly by the foramen occipitale and anteriorly by the submentum.
jgiron
2021-02-24
gula
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Gula: sclerite partially closing foramen occipitale, formed by sclerotized region of ventral cervical membrane."
The ridges on the ventral region of the head capsule marking the sides of the gula.
gular ridges
jgiron
jgiron
jgiron
The ridges on the ventral region of the head capsule marking the sides of the gula.
jgiron
2021-02-24
gular ridges
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Gular ridges: lateral internal ridges enclosing the gula."
Is the apophysis of the tentorium that originates from each posterior tetorial pit.
posterior tentorial arm
jgiron
jgiron
jgiron
Is the apophysis of the tentorium that originates from each posterior tetorial pit.
jgiron
2021-02-24
posterior tentorial arm
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Posterior tentorial arm: paired posterior element of tentorium; originates at posterior tentorial pit."
Is the apophysis of the tentorium that is connected to an anterior tentorial pit.
anterior tentorial arm
jgiron
jgiron
jgiron
Is the apophysis of the tentorium that is connected to an anterior tentorial pit.
jgiron
2021-02-24
anterior tentorial arm
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Anterior tentorial arm: paired tentorial element anterior to tentorial bridge; originates at anterior tentorial pit."
Is the apophysis of the tentorium that is connected to an anterior tentorial arm.
dorsal tentorial arm
jgiron
jgiron
jgiron
Is the apophysis of the tentorium that is connected to an anterior tentorial arm.
jgiron
2021-02-24
dorsal tentorial arm
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Dorsal tentorial arm: paired dorsal element of tentorium, originating at anterior arm or connecting area of anterior and posterior arm; often connected with head capsule by fibrillae."
The arthropod foramen that is part of the foramen occipitale and is located above the tentorial bridge.
alaforamen
jgiron
jgiron
jgiron
The arthropod foramen that is part of the foramen occipitale and is located above the tentorial bridge.
jgiron
2021-04-03
alaforamen
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Alaforamen: part of foramen occipitale above tentorial bridge; passage of oesophagus and tracheal stems."
The arthropod foramen that is part of the foramen occipitale and located below the tentorial bridge.
neuroforamen
jgiron
jgiron
jgiron
The arthropod foramen that is part of the foramen occipitale and located below the tentorial bridge.
jgiron
2021-04-03
neuroforamen
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Neuroforamen: part of foramen occipitale below tentorial bridge; passage of cervical connectives between suboesophageal complex and prothoracic ganglion."
Is the posterior region of the head capsule that is continuous with the posterior region of the gena and is anterior to the postoccipital ridge.
postgena
jgiron
jgiron
jgiron
jgiron
Is the posterior region of the head capsule that is continuous with the posterior region of the gena and is anterior to the postoccipital ridge.
jgiron
2021-02-24
postgena
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Postgena: posterior genal region anterior to postoccipital ridge."
Is the region of the head capsule that is continuous with the postgena and adjacent to the foramen occipitale.
postgenal bridge
jgiron
jgiron
jgiron
jgiron
Is the region of the head capsule that is continuous with the postgena and adjacent to the foramen occipitale.
jgiron
2021-02-24
postgenal bridge
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Postgenal bridge: partial closure of foramen occipital formed by postgenal extensions."
Is the ridge of the head capsule that encircles the antennal foramen.
circumantennal ridge
jgiron
jgiron
jgiron
Is the ridge of the head capsule that encircles the antennal foramen.
jgiron
2021-02-24
circumantennal ridge
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"The antennal foramen is enclosed by a circumantennal ridge, which often bears a small articulatory process, the antennifer."
The posterior region of the head capsule that is adjacent to the posterior region of the vertex.
postocciput
jgiron
jgiron
jgiron
The posterior region of the head capsule that is adjacent to the posterior region of the vertex.
jgiron
2021-02-24
postocciput
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Postocciput: posteriormost head region."
Is the region of the head capsule that comprises the posterior region of the subgena.
hypostoma
jgiron
jgiron
Is the region of the head capsule that comprises the posterior region of the subgena.
jgiron
2021-02-24
hypostoma
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Hypostoma: posterior part of subgena."
Is the ridge composing the posterior region of the subgenal ridge.
hypostomal ridge
jgiron
jgiron
Is the ridge composing the posterior region of the subgenal ridge.
jgiron
2021-02-24
hypostomal ridge
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Hypostomal ridge: posterior part of subgenal ridge."
Is the ridge that runs along the posterior region of the head capsule.
occipital ridge
jgiron
jgiron
Is the ridge that runs along the posterior region of the head capsule.
jgiron
2021-02-24
occipital ridge
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Occipital ridge (=“occipital suture”): ridge on posterior head region; present in some groups, oblique and short or more or less parallel to postocciptal rigde (Orthoptera). No true segmental border."
Is the region of the cuticle comprising the posterior region of the clypeus.
postclypeus
jgiron
jgiron
Is the region of the cuticle comprising the posterior region of the clypeus.
jgiron
2021-02-24
postclypeus
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Postclypeus: sclerotized and pigmented proximal part of clypeus."
Is the region of the cuticle comprising the anterior region of the clypeus.
anteclypeus
jgiron
jgiron
Is the region of the cuticle comprising the anterior region of the clypeus.
jgiron
2021-02-24
anteclypeus
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Anteclypeus: transparent distal part of clypeus."
Is the region of the cuticle that is composed of the clypeus and the labrum.
clypeolabrum
jgiron
jgiron
jgiron
Is the region of the cuticle that is composed of the clypeus and the labrum.
jgiron
2021-02-24
clypeolabrum
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Clypeolabrum: area comprising the fused clypeus and labrum."
The sense organ of the insect head that is covered by the eye cuticle.
compound eye
jgiron
jgiron
jgiron
The sense organ of the insect head that is covered by the eye cuticle.
jgiron
2021-04-03
compound eye
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Compound eye: paired main light sense organs; almost always composed of numerous ommatidia."
The sense organ of the insect head that is covered by eye cuticle.
ocellus
jgiron
jgiron
jgiron
The sense organ of the insect head that is covered by eye cuticle.
jgiron
2021-04-03
ocellus
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Ocellus: relatively simple median eye with single cornea lens and always lacking a crystalline cone: three are probably present in the groundplan of Insecta, but reductions occur in many groups."
Are apophyses of the tentorium originating at each anterior tentorial arm.
laminatentoria
jgiron
jgiron
jgiron
Are apophyses of the tentorium originating at each anterior tentorial arm.
jgiron
2021-02-24
laminatentoria
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"In some groups an accessory bridge is formed by medially fused internally directed processes, the laminatentoria. This feature is sometimes erroneously referred to as “perforated corpotentorium”."
Is the region of cuticle of the insect abdomen that is posteriorly connected to the postabdomen.
preabdomen
jgiron
jgiron
jgiron
Is the region of cuticle of the insect abdomen that is posteriorly connected to the postabdomen.
jgiron
2021-03-05
preabdomen
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Preabdomen (=pregenital segments): anterior abdominal segments (I–VII)."
Is the region of cuticle of the insect abdomen that is anteriorly connected to the preabdomen.
postabdomen
jgiron
jgiron
jgiron
Is the region of cuticle of the insect abdomen that is anteriorly connected to the preabdomen.
jgiron
2021-03-05
postabdomen
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Postabdomen: posterior segments (VIII–XI) bearing genital appendages."
The sclerite of the insect abdomen that is dorsal and medial.
abdominal tergum
abdominal tergite
imiko
imiko
imiko
imiko
The sclerite of the insect abdomen that is dorsal and medial.
jgiron
2021-04-05
abdominal tergum
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Tergum: plate-like dorsal sclerite of abdominal segment."
abdominal tergite
Lawrence J, Ślipiński A (2013) 1 Australian beetles volume 1: morphology, classification and keys. CSIRO Publishing, 520 pp.
https://www.publish.csiro.au/book/6466/
"major plate of the abdominal tergum"
The sclerite of the insect abdomen that is ventral and medial.
sternum
abdominal sternite
jgiron
jgiron
jgiron
jgiron
The sclerite of the insect abdomen that is ventral and medial.
jgiron
2021-04-05
sternum
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Sternum: plate-like ventral sclerite of abdominal segment."
The conjunctiva of the insect abdomen that surrounds the spiracles.
pleural membrane
jgiron
jgiron
jgiron
The conjunctiva of the insect abdomen that surrounds the spiracles.
jgiron
2021-04-05
pleural membrane
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Pleural membrane: lateral unsclerotized part of abdominal segments, connecting tergum and sternum; usually bearing spiracles I–VIII."
The sclerite of the postabdomen that is attached to the posterior margin of the abdominal tergite X by the abdominal tergite X-epiproct conjunctiva.
proctiger
epiproct
jgiron
imiko
jgiron
imiko
jgiron
The sclerite of the postabdomen that is attached to the posterior margin of the abdominal tergite X by the abdominal tergite X-epiproct conjunctiva.
jgiron
2021-03-05
proctiger
Lawrence J, Ślipiński A (2013) 1 Australian beetles volume 1: morphology, classification and keys. CSIRO Publishing, 520 pp.
https://www.publish.csiro.au/book/6466/
[not defined]
epiproct
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Epiproct: unpaired dorsal element (tergum) of segment XI."
The paired sclerite of the insect abdomen that is attached to the lateral margin of the abdominal tergite X by the abdominal tergite X-paraproct conjunctiva.
paraproct
jgiron
jgiron
jgiron
jgiron
imiko
jgiron
The paired sclerite of the insect abdomen that is attached to the lateral margin of the abdominal tergite X by the abdominal tergite X-paraproct conjunctiva.
jgiron
2021-03-05
paraproct
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Paraproct: paired lateral element of segment XI."
The cuticular evagination of the postabdomen that is distal and attached to the parameres by the paramero-aedeagal conjunctiva and is connected to the endophallus.
insect penis
aedeagus
imiko
jgiron
imiko
jgiron
jgiron
jgiron
The cuticular evagination of the postabdomen that is distal and attached to the parameres by the paramero-aedeagal conjunctiva and is connected to the endophallus.
jgiron
2021-03-05
insect penis
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Penis: main element of the male copulatory apparatus."
aedeagus
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Aedeagus (penis is often used as a synonym): male copulatory organ."
The cuticular invagination of the postabdomen that is attached distally to the gonopore and basally to the aedeagus.
endophallus
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
The cuticular invagination of the postabdomen that is attached distally to the gonopore and basally to the aedeagus.
jgiron
2021-03-05
endophallus
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Endophallus: membranous extrusible internal part of aedeagus."
The paired cuticular evagination of the postabdomen that is attached to the phallobase by the phallobasal-parameral conjunctiva and to the aedeagus by the paramero-aedeagal conjunctiva.
paramere
imiko
jgiron
imiko
jgiron
jgiron
jgiron
jgiron
The paired cuticular evagination of the postabdomen that is attached to the phallobase by the phallobasal-parameral conjunctiva and to the aedeagus by the paramero-aedeagal conjunctiva.
jgiron
2021-03-05
paramere
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Parameres: paired lateral parts of aedeagus."
The region of cuticle of the postabdomen that is attached to the abdominal sternite IX by the abdominal sternite IX-phallobase conjunctiva and to the paramere by the phallobasal-parameral conjunctiva.
basal piece
phallobase
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
The region of cuticle of the postabdomen that is attached to the abdominal sternite IX by the abdominal sternite IX-phallobase conjunctiva and to the paramere by the phallobasal-parameral conjunctiva.
jgiron
2021-03-05
basal piece
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Phallobase (=basal piece): part of segment IX bearing copulatory organ."
phallobase
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Phallobase (=basal piece): part of segment IX bearing copulatory organ."
The region of the cuticle of the endophallus that is thicker.
endophallite
jgiron
jgiron
jgiron
The region of the cuticle of the endophallus that is thicker.
jgiron
2021-04-05
endophallite
Génier F (2019) Endophallites: a proposed neologism for naming the sclerotized elements of the insect endophallus (Arthropoda: Insecta). Annales de la Société entomologique de France (N.S.) 55: 482–484.
https://doi.org/10.1080/00379271.2019.1685907
"endophallite(s) refer to the sclerotized structures of the endophallus whether the structure be circular, flat, folded or spiniform."
The region of the cuticle in the postabdomen that is attached to the genital chamber.
bursa copulatrix
jgiron
jgiron
jgiron
The region of the cuticle in the postabdomen that is attached to the genital chamber.
jgiron
2021-04-05
bursa copulatrix
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Bursa copulatrix: evagination of the vagina, receives the copulatory organ."
The paired sclerite of the postabdomen that is attached to the abdominal sternite VII by the abdominal sternite VII-gonocoxa conjunctiva and is articulated with abdominal tergite IX. It is attached at the base of gonostylus VIII and adjacent to the gonopore.
first coxopodite
first gonocoxite
first valvifer
gonocoxa VIII
jgiron
jgiron
imiko
jgiron
jgiron
imiko
jgiron
The paired sclerite of the postabdomen that is attached to the abdominal sternite VII by the abdominal sternite VII-gonocoxa conjunctiva and is articulated with abdominal tergite IX. It is attached at the base of gonostylus VIII and adjacent to the gonopore.
jgiron
2021-03-05
first coxopodite
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Coxopodite (=valvifer, gonocoxa, gonocoxite): short basal piece of ovipositor elements of female genital segments VIII and IX."
first gonocoxite
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Coxopodite (=valvifer, gonocoxa, gonocoxite): short basal piece of ovipositor elements of female genital segments VIII and IX."
first valvifer
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Coxopodite (=valvifer, gonocoxa, gonocoxite): short basal piece of ovipositor elements of female genital segments VIII and IX."
gonocoxa VIII
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Coxopodite (=valvifer, gonocoxa, gonocoxite): short basal piece of ovipositor elements of female genital segments VIII and IX."
The region of the cuticle that is connected to the oviduct, the bursa copulatrix and the gonocoxa VIII, and is adjacent to the gonopore.
genital chamber
jgiron
jgiron
jgiron
jgiron
jgiron
The region of the cuticle that is connected to the oviduct, the bursa copulatrix and the gonocoxa VIII, and is adjacent to the gonopore.
jgiron
2021-03-05
genital chamber
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Genital chamber: cavity formed by an inflection of the body wall, receiving the common oviduct."
The appendage of the abdominal sternite VIII that is part of the ovipositor.
gonapophysis
jgiron
jgiron
jgiron
The appendage of the abdominal sternite VIII that is part of the ovipositor.
jgiron
2021-04-05
gonapophysis
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Gonapophysis (=valves or valvulae 1–3): distal piece of ovipositor elements of female genital segments VIII and IX, inserted on coxopodites, usually elongated."
The seta that is flattened.
sensillum placodeum
imiko
jgiron
The seta that is flattened.
jgiron
2021-04-05
sensillum placodeum
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Sensillum placodeum: flat sensillum with strongly modified plate-like seta."
The seta that is elongated.
trichobothrium
jgiron
jgiron
The seta that is elongated.
jgiron
2021-04-05
trichobothrium
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Trichobothrium: very long and fine sensillum, vibroreceptor."
The proximal apodemes of the aedeagus.
titillators
paraphyses
jgiron
jgiron
The proximal apodemes of the aedeagus.
jgiron
2021-04-05
titillators
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Paraphyses (=titillators): paired appendages of aedeagus."
paraphyses
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Paraphyses (=titillators): paired appendages of aedeagus."
The region of the cuticle thar is proximally attached to the gonopore.
ductus ejaculatorius
jgiron
jgiron
jgiron
The region of the cuticle thar is proximally attached to the gonopore.
jgiron
2021-04-05
ductus ejaculatorius
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Ductus ejaculatorius: unpaired ectodermal duct connecting vasa deferentia (i.e. vesiculae seminales) and aedeagus."
The anatomical space in the postabdomen that marks the opening of the reproductive system.
gonopore
jgiron
jgiron
The anatomical space in the postabdomen that marks the opening of the reproductive system.
jgiron
2021-04-21
gonopore
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Gonopore: external opening of the common oviduct."
2021-03-05
The region of the cuticle of the postabdomen that is paired and connected to the anterior region of the gonocoxa VIII.
gonostylus VIII
jgiron
jgiron
jgiron
jgiron
The region of the cuticle of the postabdomen that is paired and connected to the anterior region of the gonocoxa VIII.
jgiron
2021-03-05
gonostylus VIII
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Gonostyli: appendages of gonocoxae (usually only on coxopodite IX)"
The region of cuticle of the postabdomen that is distal to the genital chamber.
ovipositor
jgiron
jgiron
jgiron
The region of cuticle of the postabdomen that is distal to the genital chamber.
jgiron
2021-04-05
ovipositor
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Ovipositor: paired postabdominal apparatus (segments VIII and IX) primarily used for depositing eggs."
The region of the cuticle that is part of the oviduct and connected to the bursa copulatrix.
spermatheca
jgiron
jgiron
jgiron
The region of the cuticle that is part of the oviduct and connected to the bursa copulatrix.
jgiron
2021-04-05
spermatheca
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Spermatheca (=receptaculum seminis): unpaired or paired evagination of female genital tract; storage of sperm; connected by spermathecal duct (=ductus receptaculi) with vagina or bursa copulatrix."
The region of the cuticle that is part of the oviduct and attached to the spermatheca.
spermathecal gland
jgiron
jgiron
jgiron
The region of the cuticle that is part of the oviduct and attached to the spermatheca.
jgiron
2021-04-05
spermathecal gland
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Spermathecal gland: provides nourishment for spermatozoa stored in spermatheca."
The sulcus that coincides with the precoxal ridge.
precoxal suture
precoxal sulcus
jgiron
jgiron
The sulcus that coincides with the precoxal ridge.
jgiron
2021-04-09
precoxal suture
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Precoxal suture: suture separating katepisternum and preepisternum."
The cuticular protrusion of the pleuron that is connected lateraly to the notum.
fulcrum
pleural wing process
jgiron
jgiron
jgiron
The cuticular protrusion of the pleuron that is connected lateraly to the notum.
jgiron
2021-04-05
fulcrum
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Fulcrum (=pleural wing process): anterodorsal apex of the pleural ridge."
pleural wing process
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Fulcrum (=pleural wing process): anterodorsal apex of the pleural ridge."
The conjunctiva between the insect thorax and the insect abdomen that connects the posterior margin of the metanotum to the anterior margin of the abdominal tergite I.
metanoto-abdominal tergite I conjunctiva
jgiron
jgiron
jgiron
The conjunctiva between the insect thorax and the insect abdomen that connects the posterior margin of the metanotum to the anterior margin of the abdominal tergite I.
jgiron
2021-03-14
The region of the cuticle that is continuous with the genital chamber.
oviduct
jgiron
jgiron
The region of the cuticle that is continuous with the genital chamber.
jgiron
2021-03-14
oviduct
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Oviduct: female genital duct; originating as paired structures from ovarioles, uniting as common (median) oviduct."
Is the conjunctiva of the insect abdomen that joins the abdominal sternite VIII and the gonocoxa VIII.
abdominal sternite VII-gonocoxa VIII conjunctiva
jgiron
jgiron
jgiron
jgiron
Is the conjunctiva of the insect abdomen that joins the abdominal sternite VIII and the gonocoxa VIII.
jgiron
2021-03-14
Is the abdominal tergite of the preabdomen that is attached to the posterior margin of the abdominal tergite I by the abdominal tergite I-abdominal tergite II conjunctiva and to the anterior margin of the abdominal tergite III by the abdominal tergite II-abdominal tergite III conjunctiva.
abdominal tergite II
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
Is the abdominal tergite of the preabdomen that is attached to the posterior margin of the abdominal tergite I by the abdominal tergite I-abdominal tergite II conjunctiva and to the anterior margin of the abdominal tergite III by the abdominal tergite II-abdominal tergite III conjunctiva.
jgiron
2021-03-14
Is the conjunctiva of the insect abdomen that connects the abdominal tergite I and the abdominal tergite II.
abdominal tergite I-abdominal tergite II conjunctiva
jgiron
jgiron
jgiron
jgiron
Is the conjunctiva of the insect abdomen that connects the abdominal tergite I and the abdominal tergite II.
jgiron
2021-03-14
Is the abdominal tergite of the preabdomen that is attached to the posterior margin of the abdominal tergite II by the abdominal tergite II-abdominal tergite III conjunctiva and to the anterior margin of the abdominal tergite IV by the abdominal tergite III-abdominal tergite IV conjunctiva.
abdominal tergite III
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
Is the abdominal tergite of the preabdomen that is attached to the posterior margin of the abdominal tergite II by the abdominal tergite II-abdominal tergite III conjunctiva and to the anterior margin of the abdominal tergite IV by the abdominal tergite III-abdominal tergite IV conjunctiva.
jgiron
2021-03-14
Is the conjunctiva of the insect abdomen that connects the abdominal tergite II and the abdominal tergite III.
abdominal tergite II-abdominal tergite III conjunctiva
jgiron
jgiron
jgiron
jgiron
Is the conjunctiva of the insect abdomen that connects the abdominal tergite II and the abdominal tergite III.
jgiron
2021-03-14
Is the conjunctiva of the insect abdomen that connects the abdominal tergite III and the abdominal tergite IV.
abdominal tergite III-abdominal tergite IV conjunctiva
jgiron
jgiron
jgiron
jgiron
Is the conjunctiva of the insect abdomen that connects the abdominal tergite III and the abdominal tergite IV.
jgiron
2021-03-14
Is the abdominal tergite of the preabdomen that is attached to the posterior margin of the abdominal tergite III by the abdominal tergite III-abdominal tergite IV conjunctiva and to the anterior margin of the abdominal tergite V by the abdominal tergite IV-abdominal tergite V conjunctiva.
abdominal tergite IV
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
Is the abdominal tergite of the preabdomen that is attached to the posterior margin of the abdominal tergite III by the abdominal tergite III-abdominal tergite IV conjunctiva and to the anterior margin of the abdominal tergite V by the abdominal tergite IV-abdominal tergite V conjunctiva.
jgiron
2021-03-14
Is the abdominal tergite of the preabdomen that is attached to the posterior margin of the abdominal tergite IV by the abdominal tergite IV-abdominal tergite V conjunctiva and to the anterior margin of the abdominal tergite VI by the abdominal tergite V-abdominal tergite VI conjunctiva.
abdominal tergite V
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
Is the abdominal tergite of the preabdomen that is attached to the posterior margin of the abdominal tergite IV by the abdominal tergite IV-abdominal tergite V conjunctiva and to the anterior margin of the abdominal tergite VI by the abdominal tergite V-abdominal tergite VI conjunctiva.
jgiron
2021-03-14
Is the conjunctiva of the insect abdomen that connects the abdominal tergite IV and the abdominal tergite V.
abdominal tergite IV-abdominal tergite V conjunctiva
jgiron
jgiron
jgiron
jgiron
Is the conjunctiva of the insect abdomen that connects the abdominal tergite IV and the abdominal tergite V.
jgiron
2021-03-14
Is the abdominal tergite of the preabdomen that is attached to the posterior margin of the abdominal tergite V by the abdominal tergite V-abdominal tergite VI conjunctiva and to the anterior margin of the abdominal tergite VII by the abdominal tergite VI-abdominal tergite VII conjunctiva.
abdominal tergite VI
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
Is the abdominal tergite of the preabdomen that is attached to the posterior margin of the abdominal tergite V by the abdominal tergite V-abdominal tergite VI conjunctiva and to the anterior margin of the abdominal tergite VII by the abdominal tergite VI-abdominal tergite VII conjunctiva.
jgiron
2021-03-14
Is the conjunctiva of the insect abdomen that connects the abdominal tergite V and the abdominal tergite VI.
abdominal tergite V-abdominal tergite VI conjunctiva
jgiron
jgiron
jgiron
jgiron
Is the conjunctiva of the insect abdomen that connects the abdominal tergite V and the abdominal tergite VI.
jgiron
2021-03-14
Is the abdominal tergite of the preabdomen that is attached to the posterior margin of the abdominal tergite VI by the abdominal tergite VI-abdominal tergite VII conjunctiva and to the anterior margin of the abdominal tergite VIII by the abdominal tergite VII-abdominal tergite VIII conjunctiva.
abdominal tergite VII
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
Is the abdominal tergite of the preabdomen that is attached to the posterior margin of the abdominal tergite VI by the abdominal tergite VI-abdominal tergite VII conjunctiva and to the anterior margin of the abdominal tergite VIII by the abdominal tergite VII-abdominal tergite VIII conjunctiva.
jgiron
2021-03-14
Is the conjunctiva of the insect abdomen that connects the abdominal tergite VI and the abdominal tergite VII.
abdominal tergite VI-abdominal tergite VII conjunctiva
jgiron
jgiron
jgiron
jgiron
Is the conjunctiva of the insect abdomen that connects the abdominal tergite VI and the abdominal tergite VII.
jgiron
2021-03-14
Is the abdominal tergite of the postabdomen that is attached to the posterior margin of the abdominal tergite VII by the abdominal tergite VII-abdominal tergite VIII conjunctiva and to the anterior margin of the abdominal tergite IX by the abdominal tergite VIII-abdominal tergite IX conjunctiva.
abdominal tergite VIII
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
Is the abdominal tergite of the postabdomen that is attached to the posterior margin of the abdominal tergite VII by the abdominal tergite VII-abdominal tergite VIII conjunctiva and to the anterior margin of the abdominal tergite IX by the abdominal tergite VIII-abdominal tergite IX conjunctiva.
jgiron
2021-03-14
Is the conjunctiva of the insect abdomen that connects the abdominal tergite VII and the abdominal tergite VIII.
abdominal tergite VII-abdominal tergite VIII conjunctiva
jgiron
jgiron
jgiron
jgiron
Is the conjunctiva of the insect abdomen that connects the abdominal tergite VII and the abdominal tergite VIII.
jgiron
2021-03-14
The sclerite of the insect thorax or the insect abdomen that is on the lateral region of the notum.
paranota
laterotergite
jgiron
jgiron
jgiron
The sclerite of the insect thorax or the insect abdomen that is on the lateral region of the notum.
jgiron
2021-04-05
paranota
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Paranota (=laterotergites): dorsolateral tergal duplicatures."
laterotergite
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Laterotergite: separate lateral portion of abdominal tergum (only few groups)."
laterotergite
Lawrence J, Ślipiński A (2013) 1 Australian beetles volume 1: morphology, classification and keys. CSIRO Publishing, 520 pp.
https://www.publish.csiro.au/book/6466/
additional pair of sclerites flanking each tergite
The abdominal sternite of the preabdomen that is attached to the posterior margin of the metasternum by the metasterno-abdominal sternite I conjunctiva and to the anterior margin of the abdominal sternite II by the abdominal sternite I-abdominal sternite II conjunctiva.
abdominal sternite I
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
The abdominal sternite of the preabdomen that is attached to the posterior margin of the metasternum by the metasterno-abdominal sternite I conjunctiva and to the anterior margin of the abdominal sternite II by the abdominal sternite I-abdominal sternite II conjunctiva.
jgiron
2021-03-14
The conjunctiva of the metathorax that joins the metapleura and the metasternum.
metapleuro-metasternal conjunctiva
jgiron
jgiron
jgiron
jgiron
The conjunctiva of the metathorax that joins the metapleura and the metasternum.
jgiron
2021-04-09
The conjunctiva between the insect thorax and the insect abdomen that connects the posterior margin of the metasterum to the anterior margin of the abdominal sternite I.
metasterno-abdominal sternite I conjunctiva
jgiron
jgiron
jgiron
The conjunctiva between the insect thorax and the insect abdomen that connects the posterior margin of the metasterum to the anterior margin of the abdominal sternite I.
jgiron
2021-03-14
The conjunctiva of the insect abdomen that connects the abdominal sternite I and the abdominal sternite II.
abdominal sternite I-abdominal sternite II conjunctiva
jgiron
jgiron
jgiron
jgiron
The conjunctiva of the insect abdomen that connects the abdominal sternite I and the abdominal sternite II.
jgiron
2021-03-14
Is the abdominal tergite of the preabdomen that is attached to the posterior margin of the abdominal sternite I by the abdominal sternite I-abdominal sternite II conjunctiva and to the anterior margin of the abdominal sternite III by the abdominal sternite II-abdominal sternite III conjunctiva.
abdominal sternite II
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
Is the abdominal tergite of the preabdomen that is attached to the posterior margin of the abdominal sternite I by the abdominal sternite I-abdominal sternite II conjunctiva and to the anterior margin of the abdominal sternite III by the abdominal sternite II-abdominal sternite III conjunctiva.
jgiron
2021-03-14
Is the abdominal sternite of the preabdomen that is attached to the posterior margin of the abdominal sternite II by the abdominal sternite II-abdominal sternite III conjunctiva and to the anterior margin of the abdominal sternite IV by the abdominal sternite III-abdominal sternite IV conjunctiva.
abdominal sternite III
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
Is the abdominal sternite of the preabdomen that is attached to the posterior margin of the abdominal sternite II by the abdominal sternite II-abdominal sternite III conjunctiva and to the anterior margin of the abdominal sternite IV by the abdominal sternite III-abdominal sternite IV conjunctiva.
jgiron
2021-03-14
Is the abdominal sternite of the preabdomen that is attached to the posterior margin of the abdominal sternite III by the abdominal sternite III-abdominal sternite IV conjunctiva and to the anterior margin of the abdominal sternite V by the abdominal sternite IV-abdominal sternite V conjunctiva.
abdominal sternite IV
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
Is the abdominal sternite of the preabdomen that is attached to the posterior margin of the abdominal sternite III by the abdominal sternite III-abdominal sternite IV conjunctiva and to the anterior margin of the abdominal sternite V by the abdominal sternite IV-abdominal sternite V conjunctiva.
jgiron
2021-03-14
Is the abdominal sternite of the preabdomen that is attached to the posterior margin of the abdominal sternite IV by the abdominal sternite IV-abdominal sternite V conjunctiva and to the anterior margin of the abdominal sternite VI by the abdominal sternite V-abdominal sternite VI conjunctiva.
abdominal sternite V
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
Is the abdominal sternite of the preabdomen that is attached to the posterior margin of the abdominal sternite IV by the abdominal sternite IV-abdominal sternite V conjunctiva and to the anterior margin of the abdominal sternite VI by the abdominal sternite V-abdominal sternite VI conjunctiva.
jgiron
2021-03-14
Is the abdominal sternite of the preabdomen that is attached to the posterior margin of the abdominal sternite V by the abdominal sternite V-abdominal sternite VI conjunctiva and to the anterior margin of the abdominal sternite VII by the abdominal sternite VI-abdominal sternite VII conjunctiva.
abdominal sternite VI
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
Is the abdominal sternite of the preabdomen that is attached to the posterior margin of the abdominal sternite V by the abdominal sternite V-abdominal sternite VI conjunctiva and to the anterior margin of the abdominal sternite VII by the abdominal sternite VI-abdominal sternite VII conjunctiva.
jgiron
2021-03-14
Is the abdominal sternite of the preabdomen that is attached to the posterior margin of the abdominal sternite VI by the abdominal sternite VI-abdominal sternite VII conjunctiva and to the anterior margin of the abdominal sternite VIII by the abdominal sternite VII-abdominal sternite VIII conjunctiva.
abdominal sternite VII
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
Is the abdominal sternite of the preabdomen that is attached to the posterior margin of the abdominal sternite VI by the abdominal sternite VI-abdominal sternite VII conjunctiva and to the anterior margin of the abdominal sternite VIII by the abdominal sternite VII-abdominal sternite VIII conjunctiva.
jgiron
2021-03-14
The abdominal sternite of the postabdomen that is attached to the posterior margin of the abdominal sternite VII by the abdominal sternite VII-abdominal sternite VIII conjunctiva. In males it is attached to the anterior margin of the abdominal sternite IX by the abdominal sternite VIII-abdominal sternite IX conjunctiva. In females it is attached to the anterior margin of the gonocoxa.
abdominal sternite VIII
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
The abdominal sternite of the postabdomen that is attached to the posterior margin of the abdominal sternite VII by the abdominal sternite VII-abdominal sternite VIII conjunctiva. In males it is attached to the anterior margin of the abdominal sternite IX by the abdominal sternite VIII-abdominal sternite IX conjunctiva. In females it is attached to the anterior margin of the gonocoxa.
jgiron
2021-03-14
Is the conjunctiva of the insect abdomen that connects the abdominal sternite II and the abdominal sternite III.
abdominal sternite II-abdominal sternite III conjunctiva
jgiron
jgiron
jgiron
jgiron
Is the conjunctiva of the insect abdomen that connects the abdominal sternite II and the abdominal sternite III.
jgiron
2021-03-14
Is the conjunctiva of the insect abdomen that connects the abdominal sternite III and the abdominal sternite IV.
abdominal sternite III-abdominal sternite IV conjunctiva
jgiron
jgiron
jgiron
jgiron
Is the conjunctiva of the insect abdomen that connects the abdominal sternite III and the abdominal sternite IV.
jgiron
2021-03-14
Is the conjunctiva of the insect abdomen that connects the abdominal sternite IV and the abdominal sternite V.
abdominal sternite IV-abdominal sternite V conjunctiva
jgiron
jgiron
jgiron
jgiron
Is the conjunctiva of the insect abdomen that connects the abdominal sternite IV and the abdominal sternite V.
jgiron
2021-03-14
Is the conjunctiva of the insect abdomen that connects the abdominal sternite V and the abdominal sternite VI.
abdominal sternite V-abdominal sternite VI conjunctiva
jgiron
jgiron
jgiron
jgiron
Is the conjunctiva of the insect abdomen that connects the abdominal sternite V and the abdominal sternite VI.
jgiron
2021-03-14
Is the conjunctiva of the insect abdomen that connects the abdominal sternite VI and the abdominal sternite VII.
abdominal sternite VI-abdominal sternite VII conjunctiva
jgiron
jgiron
jgiron
jgiron
Is the conjunctiva of the insect abdomen that connects the abdominal sternite VI and the abdominal sternite VII.
jgiron
2021-03-14
Is the conjunctiva of the insect abdomen that connects the abdominal sternite VII and the abdominal sternite VIII.
abdominal sternite VII-abdominal sternite VIII conjunctiva
jgiron
jgiron
jgiron
jgiron
Is the conjunctiva of the insect abdomen that connects the abdominal sternite VII and the abdominal sternite VIII.
jgiron
2021-03-14
Is the abdominal tergite of the postabdomen that is attached to the posterior margin of the abdominal tergite VIII by the abdominal tergite VIII-abdominal tergite IX conjunctiva and to the anterior margin of the abdominal tergite X by the abdominal tergite IX-abdominal tergite X conjunctiva.
abdominal tergite IX
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
Is the abdominal tergite of the postabdomen that is attached to the posterior margin of the abdominal tergite VIII by the abdominal tergite VIII-abdominal tergite IX conjunctiva and to the anterior margin of the abdominal tergite X by the abdominal tergite IX-abdominal tergite X conjunctiva.
jgiron
2021-03-14
Is the abdominal tergite of the postabdomen that is attached to the posterior margin of the abdominal tergite IX by the abdominal tergite IX-abdominal tergite X conjunctiva and to the anterior margin of the epiproct and paraproct.
abdominal tergite X
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
Is the abdominal tergite of the postabdomen that is attached to the posterior margin of the abdominal tergite IX by the abdominal tergite IX-abdominal tergite X conjunctiva and to the anterior margin of the epiproct and paraproct.
jgiron
2021-03-14
Is the abdominal sternite of the postabdomen that is attached to the posterior margin of the abdominal sternite VIII by the abdominal sternite VIII-abdominal sternite IX conjunctiva and to the anterior margin of the abdominal sternite X by the abdominal sternite IX-abdominal sternite X conjunctiva.
abdominal sternite IX
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
Is the abdominal sternite of the postabdomen that is attached to the posterior margin of the abdominal sternite VIII by the abdominal sternite VIII-abdominal sternite IX conjunctiva and to the anterior margin of the abdominal sternite X by the abdominal sternite IX-abdominal sternite X conjunctiva.
jgiron
2021-03-14
Is the conjunctiva of the postabdomen that joins the abdominal tergite X and the epiproct.
abdominal tergite X-epiproct conjunctiva
jgiron
jgiron
jgiron
jgiron
Is the conjunctiva of the postabdomen that joins the abdominal tergite X and the epiproct.
jgiron
2021-03-14
Is the conjunctiva of the insect abdomen that connects the abdominal tergite VIII and the abdominal tergite IX.
abdominal tergite VIII-abdominal tergite IX conjunctiva
jgiron
jgiron
jgiron
jgiron
Is the conjunctiva of the insect abdomen that connects the abdominal tergite VIII and the abdominal tergite IX.
jgiron
2021-03-14
Is the conjunctiva of the insect abdomen that connects the abdominal tergite IX and the abdominal tergite X.
abdominal tergite IX-abdominal tergite X conjunctiva
jgiron
jgiron
jgiron
jgiron
Is the conjunctiva of the insect abdomen that connects the abdominal tergite IX and the abdominal tergite X.
jgiron
2021-03-14
Is the conjunctiva of the insect abdomen that connects the abdominal sternite VIII and the abdominal sternite IX.
abdominal sternite VIII-abdominal sternite IX conjunctiva
jgiron
jgiron
jgiron
jgiron
Is the conjunctiva of the insect abdomen that connects the abdominal sternite VIII and the abdominal sternite IX.
jgiron
2021-03-14
Is the conjunctiva of the insect abdomen that connects the abdominal sternite IX and the abdominal sternite X.
abdominal sternite IX-phallobase conjunctiva
jgiron
jgiron
jgiron
jgiron
Is the conjunctiva of the insect abdomen that connects the abdominal sternite IX and the abdominal sternite X.
jgiron
2021-03-14
Is the region of the cuticle of the insect thorax that is anteriorly connected to the head by the neck membrane, posteriorly connected to the mesothorax by the prothorax-mesothorax conjunctiva, and contains the pronotum, the propeluron, the prosternum and one pair of legs.
prothorax
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
Is the region of the cuticle of the insect thorax that is anteriorly connected to the head by the neck membrane, posteriorly connected to the mesothorax by the prothorax-mesothorax conjunctiva, and contains the pronotum, the propeluron, the prosternum and one pair of legs.
jgiron
2021-03-14
prothorax
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Prothorax: 1st thoracic segment, always completely wingless in extant hexapods."
The region of the cuticle of the pterothorax that bears mid legs and fore wings.
mesothorax
jgiron
jgiron
jgiron
jgiron
The region of the cuticle of the pterothorax that bears mid legs and fore wings.
jgiron
2021-04-05
mesothorax
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Mesothorax: 2nd thoracic segment, anterior segment of pterothorax; bearing forewings (groundplan of Pterygota)."
The region of the cuticle of the pterothorax that bears the hind legs and the hind wings.
metathorax
jgiron
jgiron
jgiron
jgiron
The region of the cuticle of the pterothorax that bears the hind legs and the hind wings.
jgiron
2021-04-05
metathorax
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Metathorax: 3rd thoracic segment, posterior segment of pterothorax; bearing hindwings (groundplan of Pterygota)."
The dorsal region of the cuticle of the insect thorax that is attached to the dorsal margin of the pleuron.
tergum
notum
jgiron
jgiron
jgiron
The dorsal region of the cuticle of the insect thorax that is attached to the dorsal margin of the pleuron.
jgiron
2021-04-05
tergum
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Tergum: dorsal wall of a thoracic (or abdominal) segment."
notum
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Notum: larger anterior part of tergum, composed of presutum, scutum and scutellum."
The region of the cuticle on the lateral region of the insect thorax that is attached to the notum and the sternum and is attached to the coxae by skeletal muscle tissue and the basal coxal conjunctiva.
pleuron
jgiron
jgiron
imiko
imiko
jgiron
jgiron
The region of the cuticle on the lateral region of the insect thorax that is attached to the notum and the sternum and is attached to the coxae by skeletal muscle tissue and the basal coxal conjunctiva.
jgiron
2021-04-05
pleuron
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Pleuron: lateral wall of thoracic segments, almost always divided by pleural ridge into anterior episternum and posterior epimeron."
The ventral region of the cuticle of the insect thorax that is attached to the ventral margin of the pleuron.
sternum
jgiron
jgiron
jgiron
The ventral region of the cuticle of the insect thorax that is attached to the ventral margin of the pleuron.
jgiron
2021-04-05
sternum
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Sternum: ventral wall of thoracic (or abdominal) segment, usually divided into presternum, basisternum, furcasternum and spinasternum in unspecialized hexapods; largely or completely invaginated in Holometabola (cryptosterny)."
The sclerite that is part of the pleuron.
pleurite
jgiron
jgiron
The sclerite that is part of the pleuron.
jgiron
2021-04-05
pleurite
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Pleurite: sclerotized element of pleuron."
The ridge between the epimeron and the episternum in either the mesothorax or the metathorax.
pleural ridge
jgiron
jgiron
jgiron
jgiron
The ridge between the epimeron and the episternum in either the mesothorax or the metathorax.
jgiron
2021-04-05
pleural ridge
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Pleural ridge: internal ridge, corresponding to externally visible pleural “suture”; separates episternum and epimeron; anterodorsally forming the pleural wing process and posteroventrally the pleuro-coxal joint."
The sclerite of the insect thorax that is part of the pleuron and anterior to the pleural ridge and attached to the anterior margin of the epimeron.
episternum
jgiron
jgiron
jgiron
jgiron
The sclerite of the insect thorax that is part of the pleuron and anterior to the pleural ridge and attached to the anterior margin of the epimeron.
jgiron
2021-04-05
episternum
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Episternum: part of pleuron anterior to pleural ridge."
The sclerite of the insect thorax that is part of the pleuron and posterior to the pleural ridge and attached to the posterior margin of the episternum.
epimeron
jgiron
jgiron
jgiron
jgiron
The sclerite of the insect thorax that is part of the pleuron and posterior to the pleural ridge and attached to the posterior margin of the episternum.
jgiron
2021-04-05
epimeron
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Epimeron: part of pleuron posterior to pleural ridge."
The sclerite that is located on the ventro-lateral region of the insect thorax and is attached to a coxa.
trochantin
jgiron
jgiron
jgiron
jgiron
The sclerite that is located on the ventro-lateral region of the insect thorax and is attached to a coxa.
jgiron
2021-04-05
trochantin
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Trochantin: small triangular or sickle-shaped ventral pleural sclerite; anteriorly articulating with coxa (trochantino-coxal joint)."
The part of the sternum that is attached to the anterior margin of the basisternum.
presternum
jgiron
jgiron
The part of the sternum that is attached to the anterior margin of the basisternum.
jgiron
2021-04-05
presternum
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Presternum: anteriormost part of sternum."
The part of the sternum that is attached to the posterior margin of the presternum and to the anterior margin of the furcasternum.
basisternum
jgiron
jgiron
jgiron
The part of the sternum that is attached to the posterior margin of the presternum and to the anterior margin of the furcasternum.
jgiron
2021-04-05
basisternum
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Basisternum: main part of sternum, between presternum and furcasternum."
The part of the sternum that is attached to the posterior margin of the basisternum and to the anterior margin of the spinasternum.
sternellum
furcasternum
jgiron
jgiron
jgiron
The part of the sternum that is attached to the posterior margin of the basisternum and to the anterior margin of the spinasternum.
jgiron
2021-04-05
sternellum
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Furcasternum (=sternellum): sternal element posterior to basisternum, area of origin of furca."
furcasternum
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Furcasternum (=sternellum): sternal element posterior to basisternum, area of origin of furca."
The part of the sternum that is attached to the posterior margin of the furcasternum and to the anterior margin of the poststernite.
spinasternum
jgiron
jgiron
jgiron
The part of the sternum that is attached to the posterior margin of the furcasternum and to the anterior margin of the poststernite.
jgiron
2021-04-05
spinasternum
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Spinasternum: small posterior sternal element, determining the posterior segmental border; area of origin of spina."
The part of the sternum that is attached to the posterior margin of the spinasternum.
poststernite
jgiron
jgiron
The part of the sternum that is attached to the posterior margin of the spinasternum.
jgiron
2021-04-05
poststernite
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Poststernite: posteriormost sternal element."
The sclerite that is surrounded by the neck membrane.
cervical sclerite
jgiron
jgiron
The sclerite that is surrounded by the neck membrane.
jgiron
2021-04-05
cervical sclerite
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Cervical sclerite: articulatory sclerite embedded in the cervical membrane."
The region of the cuticle on the lateral region of the prothorax that is attached to the pronotum and the prosternum, and is attached to the procoxa by the procoxal muscle and the basal procoxal conjunctiva.
propleuron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
The region of the cuticle on the lateral region of the prothorax that is attached to the pronotum and the prosternum, and is attached to the procoxa by the procoxal muscle and the basal procoxal conjunctiva.
jgiron
2021-04-21
The sclerite of the notum that is attached to the posterior margin of the scutellum.
postnotum
jgiron
jgiron
jgiron
The sclerite of the notum that is attached to the posterior margin of the scutellum.
jgiron
2021-04-05
postnotum
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Postnotum: smaller posterior part of tergum, forming internal intersegmental phragma; attachment area for dorsal indirect flight muscles."
The sclerite of the notum that is attached to the anterior margin of the scutum.
prescutum
jgiron
jgiron
jgiron
The sclerite of the notum that is attached to the anterior margin of the scutum.
jgiron
2021-04-05
prescutum
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Prescutum: anteriormost part of notum."
The sclerite of the notum that is attached to the posterior margin of the prescutum and to the anterior margin of the scutellum.
scutum
jgiron
jgiron
jgiron
jgiron
The sclerite of the notum that is attached to the posterior margin of the prescutum and to the anterior margin of the scutellum.
jgiron
2021-04-05
scutum
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Scutum: large anterior part of notum."
The sclerite of the notum that is attached to the posterior margin of the scutum.
scutellum
jgiron
jgiron
jgiron
The sclerite of the notum that is attached to the posterior margin of the scutum.
jgiron
2021-04-05
scutellum
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Scutellum: smaller posterior part of notum."
The sclerite that is on the lateral region of the notum and is adjacent to the wing.
alinotum
jgiron
jgiron
jgiron
The sclerite that is on the lateral region of the notum and is adjacent to the wing.
jgiron
2021-04-05
alinotum
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Alinotum: part of the notum connected with the wing base."
The sclerite of the pterothorax that is attached to some muscle.
prealare
prealar sclerite
jgiron
jgiron
jgiron
The sclerite of the pterothorax that is attached to some muscle.
jgiron
2021-04-21
prealare
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Prealare (=prealar sclerite): small attachment area of short direct flight muscles."
prealar sclerite
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Prealare (=prealar sclerite): small attachment area of short direct flight muscles."
The region of the cuticle of the dorso-lateral region of the pterothorax that is surrounded by the noto-pleural conjunctiva and articulated with the episternum.
prealar bridge
jgiron
jgiron
jgiron
jgiron
The region of the cuticle of the dorso-lateral region of the pterothorax that is surrounded by the noto-pleural conjunctiva and articulated with the episternum.
jgiron
2021-04-21
prealar bridge
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Prealar bridge: prescutal process, bent downwards and linked with episternum."
The region of the cuticle of the dorso-lateral region of the pterothorax that is surrounded by the noto-pleural conjunctiva and articulated with the epimeron.
postalar bridge
jgiron
jgiron
jgiron
jgiron
The region of the cuticle of the dorso-lateral region of the pterothorax that is surrounded by the noto-pleural conjunctiva and articulated with the epimeron.
jgiron
2021-04-21
postalar bridge
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Postalar bridge: lateral postnotal margin bent downwards and connected with the epimeron."
The sclerite of the insect thorax that is surrounded by the noto-pleural conjunctiva and is adjacent to the wing.
epipleurite
jgiron
jgiron
jgiron
jgiron
The sclerite of the insect thorax that is surrounded by the noto-pleural conjunctiva and is adjacent to the wing.
jgiron
2021-04-05
epipleurite
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Epipleurites: basalare and subalare."
The epipleurite that is adjacent to the anepisternum, is attached to the pleuron via muscle, is surrounded by the noto-pleural conjunctiva, and is anterior to the first axillary sclerite.
basalare
jgiron
imiko
imiko
imiko
jgiron
The epipleurite that is adjacent to the anepisternum, is attached to the pleuron via muscle, is surrounded by the noto-pleural conjunctiva, and is anterior to the first axillary sclerite.
jgiron
2021-04-09
basalare
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Basalare: sclerite associated with wing base, more or less distinctly separated from anepisternum; usually with internal muscle disc; attachment site of direct flight muscles."
The epipleurite that is adjacent to the notum, is attached to the coxa via muscle, is surrounded by the noto-pleural conjunctiva, and is posterior to the first axillary sclerite.
subalare
jgiron
imiko
imiko
imiko
jgiron
The epipleurite that is adjacent to the notum, is attached to the coxa via muscle, is surrounded by the noto-pleural conjunctiva, and is posterior to the first axillary sclerite.
jgiron
2021-04-09
subalare
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Subalare: sclerite associated with wing base, usually embedded in membrane between tergum and pleuron; attachment site of direct flight muscles."
The dorsal region of the episternum that is dorsal to the anapleural sulcus.
anepisternum
jgiron
jgiron
jgiron
The dorsal region of the episternum that is dorsal to the anapleural sulcus.
jgiron
2021-04-09
anepisternum
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Anepisternum: dorsal part of episternum, ventrally delimited by anapleural suture."
The region of the cuticle on the antero-ventral region of the episternum that is anterior to the anapleural sulcus.
preepisternum
jgiron
jgiron
jgiron
The region of the cuticle on the antero-ventral region of the episternum that is anterior to the anapleural sulcus.
jgiron
2021-04-09
preepisternum
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Preepisternum: anterior part of ventral episternal region; delimited from katepisternum by precoxal suture; largest part of ventrite in Holometabola."
The sulcus of the pleuron delimiting the dorsal region of the preepisternum and the ventral region of the anepisternum.
anapleural cleft
paracoxal suture
anapleural sulcus
jgiron
jgiron
jgiron
jgiron
The sulcus of the pleuron delimiting the dorsal region of the preepisternum and the ventral region of the anepisternum.
jgiron
2021-04-21
anapleural cleft
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Anapleural suture (=paracoxal suture): suture horizontally delimiting dorsal and ventral parts of episternum and (partially) epimeron; sometimes anteriorly widened and membranous (=anapleural cleft)."
paracoxal suture
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Anapleural suture (=paracoxal suture): suture horizontally delimiting dorsal and ventral parts of episternum and (partially) epimeron; sometimes anteriorly widened and membranous (=anapleural cleft)."
anapleural sulcus
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Anapleural suture (=paracoxal suture): suture horizontally delimiting dorsal and ventral parts of episternum and (partially) epimeron; sometimes anteriorly widened and membranous (=anapleural cleft)."
The anatomical line of weakness of the cuticle that allows molting and coincides with a suture.
molting line
ecdysial line
jgiron
jgiron
The anatomical line of weakness of the cuticle that allows molting and coincides with a suture.
jgiron
2021-04-21
molting line
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Molting lines (frontal and coronal sutures [=epicranial lines or sutures])"
The region of the cuticle on the postero-ventral region of the episternum that is posterior to the anapleural sulcus.
katepisternum
jgiron
jgiron
jgiron
The region of the cuticle on the postero-ventral region of the episternum that is posterior to the anapleural sulcus.
jgiron
2021-04-09
katepisternum
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Katepisternum: posterior part of ventral episternal region; separated from preepisternum by precoxal suture."
The region of the cuticle on the dorsal region of the epimeron.
anepimeron
jgiron
jgiron
The region of the cuticle on the dorsal region of the epimeron.
jgiron
2021-04-10
anepimeron
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Anepimeron: dorsal part of epimeron (present as separate element in some groups)."
The region of the cuticle on the ventral region of the epimeron.
katepimeron
jgiron
jgiron
The region of the cuticle on the ventral region of the epimeron.
jgiron
2021-04-10
katepimeron
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Katepimeron: ventral part of epimeron (present as separate element in some groups)."
The sclerite that is surrounded by the basal wing conjunctiva.
pteralia
axillary sclerite
jgiron
imiko
The sclerite that is surrounded by the basal wing conjunctiva.
jgiron
2021-04-10
pteralia
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Pteralia: small sclerites of wing base (axillary sclerites + plates)."
axillary sclerite
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Axillary sclerites (=axillaria, pteralia): small sclerites of wing base (usually 3); articulating with notal wing processes."
The ridge that is anterior to a coxa, demarcated by the anapleural sulcus.
precoxal ridge
jgiron
jgiron
jgiron
The ridge that is anterior to a coxa, demarcated by the anapleural sulcus.
jgiron
2021-04-09
precoxal ridge
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Precoxal ridge: mediolaterally directed ridge in front of coxa, corresponding with externally visible precoxal suture."
The sclerite attached to the spinasternum.
spina
jgiron
jgiron
The sclerite attached to the spinasternum.
jgiron
2021-04-10
spina
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Spina: smaller posterior endoskeletal element of thoracic segments, unpaired, arising on spinasternum."
The paired appendage of the postabdomen located between the epiproct and the paraproct.
cercus
jgiron
jgiron
jgiron
jgiron
jgiron
The paired appendage of the postabdomen located between the epiproct and the paraproct.
jgiron
2021-04-10
cercus
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Cerci: tactile appendages of segment XI, primarily multisegmented and tactile bearing setae."
The region of cuticle of the insect thorax that contains the mesothorax and the metathorax and bears the mid legs, the hind legs and the wings.
pterothorax
jgiron
jgiron
jgiron
jgiron
The region of cuticle of the insect thorax that contains the mesothorax and the metathorax and bears the mid legs, the hind legs and the wings.
jgiron
2021-04-05
pterothorax
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Pterothorax: 2nd and 3nd thoracic segments; bearing wings (groundplan of Pterygota), meso- and metathorax."
Is the conjunctiva of the postabdomen that joins the abdominal tergite X and each paraproct.
abdominal tergite X-paraproct conjunctiva
jgiron
jgiron
jgiron
jgiron
Is the conjunctiva of the postabdomen that joins the abdominal tergite X and each paraproct.
jgiron
2021-03-14
The segment of a leg attached to the distal margin of the coxa by the coxal-trochanteral conjunctiva and to the proximal margin of the femur by the trochantero-femoral conjunctiva.
trochanter
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
The segment of a leg attached to the distal margin of the coxa by the coxal-trochanteral conjunctiva and to the proximal margin of the femur by the trochantero-femoral conjunctiva.
jgiron
2021-03-18
trochanter
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Trochanter: 2nd element of leg, usually small and triangular."
The segment of the leg that is composed of tarsomeres connected to each other by intertarsomeral conjunctiva. The first tarsomere is connected to the distal margin of the tibia by the tibio-tarsal conjunctiva and last tarsomere is connected to the proximal margin of the pretarsus by the tarso-pretarsal conjunctiva.
tarsus
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
The segment of the leg that is composed of tarsomeres connected to each other by intertarsomeral conjunctiva. The first tarsomere is connected to the distal margin of the tibia by the tibio-tarsal conjunctiva and last tarsomere is connected to the proximal margin of the pretarsus by the tarso-pretarsal conjunctiva.
jgiron
tarsus
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Tarsus: 5th part of leg; undivided in entognathous orders, composed of 3–5 tarsomeres in most groups of Insecta."
The conjunctiva of the leg joining the distal margin of a coxa and the proximal margin of a femur.
coxal-trochanteral conjunctiva
imiko
jgiron
jgiron
jgiron
jgiron
The conjunctiva of the leg joining the distal margin of a coxa and the proximal margin of a femur.
jgiron
2021-03-14
The segment of a fore leg attached to the distal margin of the procoxa by the procoxal-protrochanteral conjunctiva and to the proximal margin of the profemur by the protrochantero-profemoral conjunctiva.
protrochanter
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
The segment of a fore leg attached to the distal margin of the procoxa by the procoxal-protrochanteral conjunctiva and to the proximal margin of the profemur by the protrochantero-profemoral conjunctiva.
jgiron
2021-03-18
The segment of a mid leg attached to the distal margin of the mesocoxa by the mesocoxal-mesotrochanteral conjunctiva and to the proximal margin of the mesofemur by the mesotrochantero-mesofemoral conjunctiva.
mesotrochanter
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
The segment of a mid leg attached to the distal margin of the mesocoxa by the mesocoxal-mesotrochanteral conjunctiva and to the proximal margin of the mesofemur by the mesotrochantero-mesofemoral conjunctiva.
jgiron
2021-03-18
The segment of a hind leg attached to the distal margin of the metacoxa by the metacoxal-metatrochanteral conjunctiva and to the proximal margin of the metafemur by the metatrochantero-metafemoral conjunctiva.
metatrochanter
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
The segment of a hind leg attached to the distal margin of the metacoxa by the metacoxal-metatrochanteral conjunctiva and to the proximal margin of the metafemur by the metatrochantero-metafemoral conjunctiva.
jgiron
2021-03-18
The conjunctiva that encircles the femur by joining the distal margin of the trochanter and the proximal margin of the femur.
trochantero-femoral conjunctiva
jgiron
jgiron
jgiron
jgiron
jgiron
The conjunctiva that encircles the femur by joining the distal margin of the trochanter and the proximal margin of the femur.
jgiron
2021-03-18
The conjunctiva that encircles the profemur by joining the distal margin of the protrochanter and the proximal margin of the profemur.
protrochantero-profemoral conjunctiva
jgiron
jgiron
jgiron
jgiron
jgiron
The conjunctiva that encircles the profemur by joining the distal margin of the protrochanter and the proximal margin of the profemur.
jgiron
2021-03-28
The conjunctiva that encircles the mesofemur by joining the distal margin of the mesotrochanter and the proximal margin of the mesofemur.
mesotrochantero-mesofemoral conjunctiva
jgiron
jgiron
jgiron
jgiron
jgiron
The conjunctiva that encircles the mesofemur by joining the distal margin of the mesotrochanter and the proximal margin of the mesofemur.
jgiron
2021-03-28
The conjunctiva that encircles the metafemur by joining the distal margin of the metatrochanter and the proximal margin of the metafemur.
metatrochantero-metafemoral conjunctiva
jgiron
jgiron
jgiron
jgiron
jgiron
The conjunctiva that encircles the metafemur by joining the distal margin of the metatrochanter and the proximal margin of the metafemur.
jgiron
2021-03-28
The conjunctiva that encircles the tibia by joining the distal margin of the femur and the proximal margin of the tibia.
femoro-tibial conjunctiva
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
The conjunctiva that encircles the tibia by joining the distal margin of the femur and the proximal margin of the tibia.
jgiron
2021-03-28
The conjunctiva that encircles the protibia by joining the distal margin of the profemur and the proximal margin of the protibia.
profemoro-protibial conjunctiva
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
The conjunctiva that encircles the protibia by joining the distal margin of the profemur and the proximal margin of the protibia.
jgiron
2021-03-28
The conjunctiva that encircles the mesotibia by joining the distal margin of the mesofemur and the proximal margin of the mesotibia.
mesofemoro-mesotibial conjunctiva
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
The conjunctiva that encircles the mesotibia by joining the distal margin of the mesofemur and the proximal margin of the mesotibia.
jgiron
2021-03-28
The conjunctiva that encircles the metatibia by joining the distal margin of the metafemur and the proximal margin of the metatibia.
metafemoro-metatibial conjunctiva
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
The conjunctiva that encircles the metatibia by joining the distal margin of the metafemur and the proximal margin of the metatibia.
jgiron
2021-03-28
The conjunctiva that encircles the tarsus by joining the distal margin of the tibia and the proximal margin of the tarsus.
tibio-tarsal conjunctiva
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
The conjunctiva that encircles the tarsus by joining the distal margin of the tibia and the proximal margin of the tarsus.
jgiron
2021-03-28
The conjunctiva that encircles the protarsus by joining the distal margin of the protibia and the proximal margin of the protarsus.
protibio-protarsal conjunctiva
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
The conjunctiva that encircles the protarsus by joining the distal margin of the protibia and the proximal margin of the protarsus.
jgiron
2021-03-28
The conjunctiva that encircles the mesotarsus by joining the distal margin of the mesotibia and the proximal margin of the mesotarsus.
mesotibio-mesotarsal conjunctiva
jgiron
The conjunctiva that encircles the mesotarsus by joining the distal margin of the mesotibia and the proximal margin of the mesotarsus.
jgiron
2021-03-28
The conjunctiva that encircles the metatarsus by joining the distal margin of the metatibia and the proximal margin of the metatarsus.
metatibio-metatarsal conjunctiva
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
The conjunctiva that encircles the metatarsus by joining the distal margin of the metatibia and the proximal margin of the metatarsus.
jgiron
2021-03-28
The region of the cuticle on the lateral region of the mesothorax that is attached to the mesonotum and the mesosternum, and is attached to the mesocoxa by the mesocoxal muscle and the basal mesocoxal conjunctiva.
mesopleuron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
The region of the cuticle on the lateral region of the mesothorax that is attached to the mesonotum and the mesosternum, and is attached to the mesocoxa by the mesocoxal muscle and the basal mesocoxal conjunctiva.
jgiron
2021-04-21
The conjunctiva that encircles the pretarsus by joining the distal margin of the distalmost tarsomere and the proximal margin of the pretarsus.
tarso-pretarsal conjunctiva
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
The conjunctiva that encircles the pretarsus by joining the distal margin of the distalmost tarsomere and the proximal margin of the pretarsus.
jgiron
2021-03-28
The segment of the leg that is composed of metatarsomeres connected to each other by intertarsomeral conjunctiva. The first metatarsomere is connected to the distal margin of the metatibia by the metatibio-metatarsal conjunctiva and the last metatarsomere is connected to the proximal margin of the metapretarsus by the metatarso-metapretarsal conjunctiva.
metatarsus
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
The segment of the leg that is composed of metatarsomeres connected to each other by intertarsomeral conjunctiva. The first metatarsomere is connected to the distal margin of the metatibia by the metatibio-metatarsal conjunctiva and the last metatarsomere is connected to the proximal margin of the metapretarsus by the metatarso-metapretarsal conjunctiva.
jgiron
2021-03-28
The segment of the mid leg that is composed of mesotarsomeres connected to each other by intertarsomeral conjunctiva. The first mesotarsomere is connected to the distal margin of the mesotibia by the mesotibio-mesotarsal conjunctiva and the last mesotarsomere is connected to the proximal margin of the mesopretarsus by the mesotarso-mesopretarsal conjunctiva.
mesotarsus
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
The segment of the mid leg that is composed of mesotarsomeres connected to each other by intertarsomeral conjunctiva. The first mesotarsomere is connected to the distal margin of the mesotibia by the mesotibio-mesotarsal conjunctiva and the last mesotarsomere is connected to the proximal margin of the mesopretarsus by the mesotarso-mesopretarsal conjunctiva.
jgiron
2021-03-28
The segment of the leg that is composed of protarsomeres connected to each other by intertarsomeral conjunctiva. The first protarsomere is connected to the distal margin of the protibia by the protibio-protarsal conjunctiva and the last protarsomere is connected to the proximal margin of the propretarsus by the protarso-propretarsal conjunctiva.
protarsus
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
jgiron
The segment of the leg that is composed of protarsomeres connected to each other by intertarsomeral conjunctiva. The first protarsomere is connected to the distal margin of the protibia by the protibio-protarsal conjunctiva and the last protarsomere is connected to the proximal margin of the propretarsus by the protarso-propretarsal conjunctiva.
jgiron
2021-03-28
The conjunctiva that encircles the propretarsus by joining the distal margin of the distalmost protarsomere and the proximal margin of the propretarsus.
protarso-propretarsal conjunctiva
jgiron
jgiron
jgiron
jgiron
jgiron
The conjunctiva that encircles the propretarsus by joining the distal margin of the distalmost protarsomere and the proximal margin of the propretarsus.
jgiron
2021-03-28
The conjunctiva that encircles the mesopretarsus by joining the distal margin of the distalmost mesotarsomere and the proximal margin of the mesopretarsus.
mesotarso-mesopretarsal conjunctiva
jgiron
jgiron
jgiron
jgiron
jgiron
The conjunctiva that encircles the mesopretarsus by joining the distal margin of the distalmost mesotarsomere and the proximal margin of the mesopretarsus.
jgiron
2021-03-28
The conjunctiva that encircles the metapretarsus by joining the distal margin of the distalmost metatarsomere and the proximal margin of the metapretarsus.
metatarso-metapretarsal conjunctiva
jgiron
jgiron
jgiron
jgiron
jgiron
The conjunctiva that encircles the metapretarsus by joining the distal margin of the distalmost metatarsomere and the proximal margin of the metapretarsus.
jgiron
2021-03-28
The appendage of the fore leg that is attached to the protarsus by the protarso-propretarsal conjunctiva.
propretarsus
jgiron
jgiron
jgiron
jgiron
The appendage of the fore leg that is attached to the protarsus by the protarso-propretarsal conjunctiva.
jgiron
2021-03-28
The appendage of the mid leg that is attached to the mesotarsus by the mesotarso-mesopretarsal conjunctiva.
mesopretarsus
jgiron
jgiron
jgiron
jgiron
The appendage of the mid leg that is attached to the mesotarsus by the mesotarso-mesopretarsal conjunctiva.
jgiron
2021-03-28
The appendage of the hind leg that is attached to the metatarsus by the metatarso-metapretarsal conjunctiva.
metapretarsus
jgiron
jgiron
jgiron
jgiron
The appendage of the hind leg that is attached to the metatarsus by the metatarso-metapretarsal conjunctiva.
jgiron
2021-03-28
The anatomical space on the postabdomen at the posterior margin of the digestive tract, connected to the epiproct and paraprocti.
anus
imiko
jgiron
jgiron
jgiron
imiko
The anatomical space on the postabdomen at the posterior margin of the digestive tract, connected to the epiproct and paraprocti.
jgiron
2021-04-10
The region of the cuticle of the postabdomen that is paired and connected to the anterior region of the gonocoxa IX.
gonostylus IX
jgiron
jgiron
jgiron
jgiron
The region of the cuticle of the postabdomen that is paired and connected to the anterior region of the gonocoxa IX.
jgiron
2021-03-28
Is the conjunctiva of the postabdomen that joins the parameres and the aedeagus.
paramero-aedeagal conjunctiva
jgiron
jgiron
jgiron
jgiron
Is the conjunctiva of the postabdomen that joins the parameres and the aedeagus.
jgiron
2021-03-28
The conjunctiva of the postabdomen that joins the phallobase and the parameres.
phallobasal-parameral conjunctiva
jgiron
jgiron
jgiron
jgiron
The conjunctiva of the postabdomen that joins the phallobase and the parameres.
jgiron
2021-03-28
The conjunctiva of the prothorax that joins the propleura and the prosternum.
propleuro-prosternal conjunctiva
imiko
jgiron
jgiron
jgiron
The conjunctiva of the prothorax that joins the propleura and the prosternum.
jgiron
2021-04-09
The conjunctiva of the pterothorax that surrounds the wing.
basal wing conjunctiva
imiko
imiko
jgiron
The conjunctiva of the pterothorax that surrounds the wing.
jgiron
2021-04-10
The thoracic muscle that attaches to the notum and to the trochantin.
For muscular terminology, tergum has been traditionally used instead of notum, even though "notum" is the prererred term to refer to the dorsal region of the cuticle of the insect thorax that is attached to the dorsal margin of the pleuron.
tergo-trochantinal muscle
imiko
jgiron
jgiron
The thoracic muscle that attaches to the notum and to the trochantin.
jgiron
2021-04-21
For muscular terminology, tergum has been traditionally used instead of notum, even though "notum" is the prererred term to refer to the dorsal region of the cuticle of the insect thorax that is attached to the dorsal margin of the pleuron.
jgiron
2021-04-09
The tergo-trochantinal muscle that is attached to the pronotum and the protrochantin.
pronoto-protrochantinal muscle
jgiron
jgiron
jgiron
The tergo-trochantinal muscle that is attached to the pronotum and the protrochantin.
jgiron
2021-04-09
The tergo-trochantinal muscle that is attached to the mesonotum and the mesotrochantin.
mesonoto-mesotrochantinal muscle
imiko
jgiron
jgiron
The tergo-trochantinal muscle that is attached to the mesonotum and the mesotrochantin.
jgiron
2021-04-09
The tergo-trochantinal muscle that is attached to the metanotum and the metatrochantin.
metanoto-metatrochantinal muscle
jgiron
jgiron
jgiron
The tergo-trochantinal muscle that is attached to the metanotum and the metatrochantin.
jgiron
2021-04-09
The thoracic muscle that extends between two nota (or terga).
tergo-tergal muscle
imiko
jgiron
The thoracic muscle that extends between two nota (or terga).
jgiron
2021-04-09
The thoracic muscle that extends between the pronotum and the mesonotum.
pronoto-mesonotal muscle
imiko
jgiron
jgiron
The thoracic muscle that extends between the pronotum and the mesonotum.
jgiron
2021-04-09
The thoracic muscle that extends between the mesonotum and the metanotum.
mesonoto-metanotal muscle
imiko
jgiron
jgiron
The thoracic muscle that extends between the mesonotum and the metanotum.
jgiron
2021-04-09
The thoracic muscle that extends between the notum (or tergum) and the coxa.
tergo-coxal muscle
imiko
jgiron
jgiron
The thoracic muscle that extends between the notum (or tergum) and the coxa.
jgiron
2021-04-09
The thoracic muscle that extends between the notum (or tergum) and the trochanter.
tergo-trochanteral muscle
imiko
jgiron
jgiron
The thoracic muscle that extends between the notum (or tergum) and the trochanter.
jgiron
2021-04-09
The thoracic muscle that attaches to the pleuron and to a coxa.
pleuro-coxal muscle
imiko
jgiron
jgiron
The thoracic muscle that attaches to the pleuron and to a coxa.
jgiron
2021-04-09
The thoracic muscle that is attached to a furca and to a coxa.
furco-coxal muscle
imiko
jgiron
jgiron
The thoracic muscle that is attached to a furca and to a coxa.
jgiron
2021-04-08
The thoracic muscle that is attached to a furca and to a trochanter.
furco-trochanteral muscle
imiko
jgiron
jgiron
The thoracic muscle that is attached to a furca and to a trochanter.
jgiron
2021-04-08
The thoracic muscle that extends between two furcae.
interfurcal muscle
imiko
jgiron
The thoracic muscle that extends between two furcae.
jgiron
2021-04-09
The thoracic muscle that extends between the profurca and the mesofurca.
profurco-mesofurcal muscle
imiko
jgiron
jgiron
The thoracic muscle that extends between the profurca and the mesofurca.
jgiron
2021-04-09
The thoracic muscle that extends between the mesofurca and the metafurca.
mesofurco-metafurcal muscle
imiko
jgiron
jgiron
The thoracic muscle that extends between the mesofurca and the metafurca.
jgiron
2021-04-09
The noto-pleural conjunctiva that joins the mesonotum and the mesopleuron.
mesonoto-mesopleural conjuntiva
imiko
jgiron
jgiron
The noto-pleural conjunctiva that joins the mesonotum and the mesopleuron.
jgiron
2021-04-09
The noto-pleural conjunctiva that joins the pronotum and the propleuron.
pronoto-propleural conjunctiva
imiko
jgiron
jgiron
The noto-pleural conjunctiva that joins the pronotum and the propleuron.
jgiron
2021-04-09
The noto-pleural conjunctiva that joins the metanotum and the metapleuron.
metanoto-metapleural conjunctiva
imiko
jgiron
jgiron
The noto-pleural conjunctiva that joins the metanotum and the metapleuron.
jgiron
2021-04-09
The conjunctiva of the insect thorax that joins the notum and the pleuron.
noto-pleural conjunctiva
imiko
jgiron
jgiron
jgiron
The conjunctiva of the insect thorax that joins the notum and the pleuron.
jgiron
2021-04-09
The axillary sclerite that is connected via muscle to the mesopleuron and is posterior to the first axillary sclerite.
third axillary sclerite
imiko
imiko
imiko
The axillary sclerite that is connected via muscle to the mesopleuron and is posterior to the first axillary sclerite.
jgiron
2021-04-10
The axillary sclerite that is on the ventral region of the basal wing conjunctiva.
ventral second axillary sclerite
imiko
imiko
The axillary sclerite that is on the ventral region of the basal wing conjunctiva.
jgiron
2021-04-10
The phragma of the metanotum that attaches to muscles attached to the mesonotum.
mesophragma
imiko
jgiron
jgiron
The phragma of the metanotum that attaches to muscles attached to the mesonotum.
jgiron
2021-04-09
The thoracic muscle that extends between the mesophragma and the abdominal tergite I.
mesophragmo-abdominal tergite I muscle
imiko
jgiron
jgiron
The thoracic muscle that extends between the mesophragma and the abdominal tergite I.
jgiron
2021-04-09
The thoracic muscle that extends between the metafurca and an abdominal sternite.
metafurco-abdominal sternite muscle
imiko
imiko
imiko
The thoracic muscle that extends between the metafurca and an abdominal sternite.
jgiron
2021-04-09
The phragma of the abdominal tergite I that attaches to muscles attached to the metanotum.
metaphragma
imiko
jgiron
jgiron
The phragma of the abdominal tergite I that attaches to muscles attached to the metanotum.
jgiron
2021-04-09
The conjunctiva of the insect thorax that joins the mesonotum and the metanotum.
mesonoto-metanotal conjunctiva
imiko
jgiron
jgiron
jgiron
The conjunctiva of the insect thorax that joins the mesonotum and the metanotum.
jgiron
2021-04-09
The conjunctiva of the mesothorax that joins the mesopleuron and the mesocoxa.
mesopleuro-mesocoxal conjunctiva
imiko
jgiron
jgiron
jgiron
The conjunctiva of the mesothorax that joins the mesopleuron and the mesocoxa.
jgiron
2021-04-09
The conjunctiva of the mesothorax that joins the mesopleura and the mesosternum.
mesopleuro-mesosternal conjunctiva
imiko
jgiron
jgiron
jgiron
The conjunctiva of the mesothorax that joins the mesopleura and the mesosternum.
jgiron
2021-04-09
The sclerite on the ventral region of the metathorax that bears the metafurca and is attached to the metapleuro-metasternal conjunctiva.
metasternum
jgiron
jgiron
jgiron
jgiron
The sclerite on the ventral region of the metathorax that bears the metafurca and is attached to the metapleuro-metasternal conjunctiva.
jgiron
2021-04-09
The conjunctiva of the mesothorax that joins the mesosternum and the mesocoxa.
mesosterno-mesocoxal conjunctiva
jgiron
jgiron
jgiron
jgiron
The conjunctiva of the mesothorax that joins the mesosternum and the mesocoxa.
jgiron
2021-04-09
entity
Entity
Julius Caesar
Verdi’s Requiem
the Second World War
your body mass index
BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
entity
Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
per discussion with Barry Smith
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
continuant
Continuant
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.
BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
continuant
Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
An entity that has temporal parts and that happens, unfolds or develops through time.
occurrent
ic
IndependentContinuant
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
the bottom right portion of a human torso
the interior of your mouth
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
independent continuant
b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
spatial region
An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
process
bfo
BFO:0000019
quality
quality
sdc
SpecificallyDependentContinuant
Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
of one-sided specifically dependent continuants: the mass of this tomato
of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
the disposition of this fish to decay
the function of this heart: to pump blood
the mutual dependence of proton donors and acceptors in chemical reactions [79
the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
the pink color of a medium rare piece of grilled filet mignon at its center
the role of being a doctor
the shape of this hole.
the smell of this portion of mozzarella
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.
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
specifically dependent continuant
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
per discussion with Barry Smith
(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
bfo
BFO:0000030
object
gdc
GenericallyDependentContinuant
The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
generically dependent continuant
b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
material
MaterialEntity
a flame
a forest fire
a human being
a hurricane
a photon
a puff of smoke
a sea wave
a tornado
an aggregate of human beings.
an energy wave
an epidemic
the undetached arm of a human being
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
bfo
BFO:0000040
material entity
material entity
A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
immaterial
ImmaterialEntity
BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10
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
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
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 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 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 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 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
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
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
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
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
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 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
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
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
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 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
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
organism or virus or viroid
biological entity
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
chebi_ontology
CHEBI:23367
molecular entity
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
fake:2
A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.
chebi_ontology
CHEBI:24431
chemical entity
Any substituent group or skeleton containing carbon.
chebi_ontology
CHEBI:33247
organic group
When two or more amino acids combine to form a peptide, the elements of water are removed, and what remains of each amino acid is called an amino-acid residue.
amino acid residue
protein residue
chebi_ontology
CHEBI:33708
amino-acid residue
When two or more amino acids combine to form a peptide, the elements of water are removed, and what remains of each amino acid is called an amino-acid residue.
Dummy:dummy
protein residue
PRO:DAN
A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by organyl groups.
chebi_ontology
CHEBI:50047
organic amino compound
A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
CALOHA:TS-2035
FMA:68646
GO:0005623
KUPO:0000002
VHOG:0001533
WBbt:0004017
XAO:0003012
cell
CL:0000000
The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).
cell
cell
A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
CARO:mah
A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment).
CARO:0000013
cell in vivo
cell
To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12).
native cell
A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment).
CARO:mah
A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina.
BTO:0000414
CALOHA:TS-2026
CARO:0000077
FBbt:00000124
FMA:66768
WBbt:0003672
epitheliocyte
cell
epithelial cell
A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina.
FB:ma
GOC:tfm
MESH:A11.436
An epithelial cell that is part of a duct.
cell
duct epithelial cell
An epithelial cell that is part of a duct.
https://orcid.org/0000-0001-5208-3432
A cell which moves among different tissues of the body, via blood, lymph, or other medium.
cell
circulating cell
A cell which moves among different tissues of the body, via blood, lymph, or other medium.
GOC:add
A somatic cell located in skeletal muscle.
BTO:0004392
CALOHA:TS-2158
FMA:9727
skeletal muscle cell
cell
cell of skeletal muscle
A somatic cell located in skeletal muscle.
GOC:tfm
A cell of the outer of the three germ layers of the embryo.
FMA:72549
ectoderm cell
cell
ectodermal cell
A cell of the outer of the three germ layers of the embryo.
MESH:A16.254.425.273
A cell of the inner of the three germ layers of the embryo.
FMA:72555
endoderm cell
cell
endodermal cell
A cell of the inner of the three germ layers of the embryo.
MESH:A16.254.425.407
A cell that lacks a nucleus.
FMA:68647
non-nucleated cell
cell
anucleate cell
A cell that lacks a nucleus.
FB:ma
A cell with a single nucleus.
cell
single nucleate cell
A cell with a single nucleus.
FB:ma
GOC:tfm
cell
binucleate cell
A cell with more than one nucleus.
AEO:0000203
WBbt:0008074
syncitium
syncytial cell
syncytium
cell
multinucleate cell
A cell with more than one nucleus.
FB:ma
cell
eukaryotic cell
cell
extraembryonic cell
An epithelial cell of the integument (the outer layer of an organism).
CL:1000396
BTO:0001470
CALOHA:TS-0283
FMA:62411
cell of epidermis
epithelial cell of skin
cell
epidermal cell
An epithelial cell of the integument (the outer layer of an organism).
Flybase:dsj
MA:ma
cell of epidermis
FMA:62411
epithelial cell of skin
FMA:62411
cell
animal cell
A cell whose primary function is to support other cell types.
BTO:0002315
cell
supportive cell
A cell whose primary function is to support other cell types.
FB:ma
GOC:tfm
A connective tissue cell found in bone.
adiehl
2011-11-16T04:28:16Z
cell
bone cell
true
A connective tissue cell found in bone.
GOC:add
GO_REF:0000034
An epithelial cell derived from endoderm.
tmeehan
2010-06-29T03:38:14Z
FMA:69075
cell
endo-epithelial cell
An epithelial cell derived from endoderm.
FMA:69075
GOC:tfm
An epithelial cell derived from ectoderm.
tmeehan
2010-06-29T03:38:22Z
FMA:69074
cell
ecto-epithelial cell
An epithelial cell derived from ectoderm.
FMA:69074
GOC:tfm
Epithelial cells derived from general body ectoderm and ectoderm placodes.
tmeehan
2010-08-26T08:31:08Z
FMA:70556
cell
general ecto-epithelial cell
Epithelial cells derived from general body ectoderm and ectoderm placodes.
GOC:tfm
A cell containing at least one nucleus.
tmeehan
2010-09-07T03:32:33Z
FMA:67513
cell
nucleate cell
A cell containing at least one nucleus.
GOC:tfm
An epithelial cell of the musculomembranous digestive tube extending from the mouth to the anus.
tmeehan
2010-09-08T09:26:53Z
cell
epithelial cell of alimentary canal
An epithelial cell of the musculomembranous digestive tube extending from the mouth to the anus.
GOC:tfm
ISBN:0721662544
An epithelial cell of a skin gland.
tmeehan
2010-09-14T12:00:07Z
FMA:70657
epithelial cell of gland of skin
cell
epithelial cell of skin gland
An epithelial cell of a skin gland.
GOC:tfm
A cell that is part of the nervous system.
tmeehan
2010-09-15T01:34:57Z
CALOHA:TS-2040
FMA:70333
cell
neural cell
A cell that is part of the nervous system.
GOC:tfm
ISBN:0618947256
A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone.
tmeehan
2010-09-15T03:01:54Z
CL:1000406
CALOHA:TS-2096
FMA:63875
cell
connective tissue cell
true
A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone.
GOC:tfm
ISBN:0618947256
A cell of the embryo.
tmeehan
2010-09-15T03:39:21Z
CALOHA:TS-0263
FMA:82840
FMA:82841
WBbt:0007028
cell
embryonic cell (metazoa)
A cell of the embryo.
FMA:0618947256
A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell).
tmeehan
2010-09-24T09:44:42Z
BTO:0001268
FMA:72300
WBbt:0008378
cell
somatic cell
A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell).
GOC:tfm
ISBN:0721662544
A cell located in the heart, including both muscle and non muscle cells.
tmeehan
2010-12-07T09:37:22Z
BTO:0001539
CALOHA:TS-0115
FMA:83808
FMA:84791
heart cell
cell
From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart.
cardiocyte
true
A cell located in the heart, including both muscle and non muscle cells.
GOC:tfm
A cell of the adventitial layer of ductal structures such as the uterer, defent duct, biliary duct, etc
tmeehan
2010-12-07T04:03:56Z
BTO:0002441
FMA:84639
cell
adventitial cell
A cell of the adventitial layer of ductal structures such as the uterer, defent duct, biliary duct, etc
GOC:tfm
Any cell in the retina, the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates.
PMID:10702418
cell
retinal cell
Any cell in the retina, the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates.
GOC:pr
Any native cell that is part of a cardiac septum.
TermGenie
2014-06-24T23:17:07Z
cell
CL:2000022
cardiac septum cell
Any native cell that is part of a cardiac septum.
GOC:TermGenie
A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.
molecular process
GO:0005554
molecular function
molecular_function
GO:0003674
Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.
Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.
molecular_function
A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.
GOC:pdt
catalytic activity
A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome).
The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
GO:0008372
NIF_Subcellular:sao1337158144
cell or subcellular entity
cellular component
cellular_component
subcellular entity
GO:0005575
Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. Note that when this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this.
Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
cellular_component
A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome).
GOC:pdt
NIF_Subcellular:sao1337158144
The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
GOC:go_curators
subcellular entity
NIF_Subcellular:nlx_subcell_100315
A component of a cell contained within (but not including) the plasma membrane. In eukaryotes it includes the nucleus and cytoplasm.
https://github.com/geneontology/go-ontology/issues/17776
Wikipedia:Intracellular
internal to cell
intracellular
protoplasm
cellular_component
nucleocytoplasm
protoplast
GO:0005622
intracellular anatomical structure
A component of a cell contained within (but not including) the plasma membrane. In eukaryotes it includes the nucleus and cytoplasm.
ISBN:0198506732
nucleocytoplasm
GOC:mah
protoplast
GOC:mah
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
NIF_Subcellular:sao1702920020
Wikipedia:Cell_nucleus
cell nucleus
horsetail nucleus
cellular_component
GO:0005634
nucleus
nucleus
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
GOC:go_curators
horsetail nucleus
GOC:al
GOC:mah
GOC:vw
PMID:15030757
The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
protein anabolism
biological_process
GO:0006412
translation
The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
GOC:go_curators
A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
jl
2012-09-19T15:05:24Z
GO:0000004
GO:0007582
GO:0044699
Wikipedia:Biological_process
biological process
physiological process
biological_process
single organism process
single-organism process
GO:0008150
Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this.
Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.
biological_process
A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
GOC:pdt
true
kinase activity
transferase activity
transferase activity, transferring phosphorus-containing groups
Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane.
NIF_Subcellular:sao1539965131
Wikipedia:Organelle
cellular_component
GO:0043226
organelle
Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane.
GOC:go_curators
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
NIF_Subcellular:sao414196390
membrane-enclosed organelle
cellular_component
GO:0043227
membrane-bounded organelle
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
GOC:go_curators
Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.
cellular_component
GO:0043229
intracellular organelle
Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.
GOC:go_curators
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
intracellular membrane-enclosed organelle
cellular_component
GO:0043231
intracellular membrane-bounded organelle
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
GOC:go_curators
cell part
A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.
kmv
2019-08-12T18:01:37Z
cellular_component
GO:0110165
cellular anatomical entity
A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.
GOC:kmv
data item
Data items include counts of things, analyte concentrations, and statistical summaries.
An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
JAR: datum -- well, this will be very tricky to define, but maybe some
information-like stuff that might be put into a computer and that is
meant, by someone, to denote and/or to be interpreted by some
process... I would include lists, tables, sentences... I think I might
defer to Barry, or to Brian Cantwell Smith
JAR: A data item is an approximately justified approximately true approximate belief
PERSON: Alan Ruttenberg
PERSON: Chris Stoeckert
PERSON: Jonathan Rees
data
data item
symbol
a serial number such as "12324X"
a stop sign
a written proper name such as "OBI"
An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.
20091104, MC: this needs work and will most probably change
2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154).
PERSON: James A. Overton
PERSON: Jonathan Rees
based on Oxford English Dictionary
symbol
information content entity
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
A generically dependent continuant that is about some thing.
2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).
information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907).
Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
PERSON: Chris Stoeckert
OBI_0000142
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 set
Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.
2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type
2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction.
person:Allyson Lister
person:Chris Stoeckert
OBI_0000042
group:OBI
data set
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
The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed.
A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry.
PERSON: Alan Ruttenberg
PERSON: Bill Hogan
PERSON: Bjoern Peters
PERSON: Melanie Courtot
CRID symbol
Original proposal from Bjoern, discussions at IAO calls
centrally registered identifier symbol
The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed.
An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs.
2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records').
Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation.
Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered.
PERSON: Alan Ruttenberg
PERSON: Bill Hogan
PERSON: Bjoern Peters
PERSON: Melanie Courtot
CRID
Original proposal from Bjoern, discussions at IAO calls
centrally registered identifier
PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles.
A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process.
PERSON: Alan Ruttenberg
PERSON: Bill Hogan
PERSON: Bjoern Peters
PERSON: Melanie Courtot
CRID registry
Original proposal from Bjoern, discussions at IAO calls
centrally registered identifier registry
identifier
An identifier is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity.
identifier
GC_ID:1
ncbi_taxonomy
all
root
all
GC_ID:1
ncbi_taxonomy
biota
cellular organisms
biota
GC_ID:1
PMID:23020233
PMID:30257078
eucaryotes
eukaryotes
ncbi_taxonomy
Eucarya
Eucaryotae
Eukarya
Eukaryotae
euk-
eukaryotes
NCBITaxon:2759
Eukaryota
eucaryotes
eukaryotes
Eucarya
Eucaryotae
Eukarya
Eukaryotae
euk-
PRO:DAN
eukaryotes
GC_ID:1
ncbi_taxonomy
Fungi/Metazoa group
opisthokonts
NCBITaxon:33154
Opisthokonta
Fungi/Metazoa group
opisthokonts
GC_ID:1
metazoans
multicellular animals
ncbi_taxonomy
Animalia
animals
metazoan-
NCBITaxon:33208
Metazoa
metazoans
multicellular animals
Animalia
animals
metazoan-
PRO:DAN
fruit fly
ncbi_taxonomy
NCBITaxon:7227
Drosophila melanogaster
fruit fly
obi
OBI:0100026
organism
A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
quality (PATO)
PATO:0000072
quality
PATO:0000001
quality
A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities
PATOC:GVG
A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
quality
PATO:0000051
morphology
A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
PATOC:GVG
A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc).
PATO:0001647
relational shape quality
quality
PATO:0000052
Shapes are invariant on size transformations. Shapes can be subdivided into 2D and 3D shapes, We can also make a distinction between shapes of complete self-connected objects, and shapes of parts of objects.
shape
A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc).
PATOC:GVG
quality
PATO:0000068
TODO: define this or obsolete it and move children somewhere else.
qualitative
A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average.
quality
PATO:0000069
deviation (from_normal)
A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average.
PATOC:GVG
A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude.
quality
PATO:0000117
size
A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude.
WordNet:WordNet
A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form.
PATO:0001452
conformation
relational structural quality
quality
PATO:0000141
structure
A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form.
PATOC:GVG
conformation
VT:1000738
A branchiness quality inhering in a bearer by virtue of the bearer's having branches.
ramified
ramiform
quality
PATO:0000402
branched
A branchiness quality inhering in a bearer by virtue of the bearer's having branches.
WordNet:WordNet
A shape quality inhering in a bearer by virtue of the bearer's being curled or wound (especially in concentric rings or spirals).
PATO:0001363
spiral
quality
helical
helicoid
helicoidal
helix-shaped
PATO:0000404
coiled
A shape quality inhering in a bearer by virtue of the bearer's being curled or wound (especially in concentric rings or spirals).
WordNet:WordNet
A quality inhering in a bearer by virtue of the bearer's having a horizontal surface without a slope, tilt, or curvature.
quality
plate-like
PATO:0000407
flat
A quality inhering in a bearer by virtue of the bearer's having a horizontal surface without a slope, tilt, or curvature.
web:http://www.merriam-webster.com/
A shape quality inhering in a bearer by virtue of the bearer's being such that every part of the surface or the circumference is equidistant from the center.
quality
round
rounded
PATO:0000411
circular
A shape quality inhering in a bearer by virtue of the bearer's being such that every part of the surface or the circumference is equidistant from the center.
thefreedictionary.com:thefreedictionary.com
A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average.
quality
average
PATO:0000461
normal
A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average.
PATOC:GVG
A size quality which is relatively high.
PATO:0001202
quality
big
enlarged
expanded
great
large
PATO:0000586
increased size
A size quality which is relatively high.
PATOC:GVG
A size quality which is relatively low.
hypoplasia
underdeveloped
quality
reduced
small
tiny
PATO:0000587
decreased size
A size quality which is relatively low.
PATOC:GVG
A thickness which is relatively high.
high thickness
stout
thickened
quality
thick
PATO:0000591
increased thickness
A thickness which is relatively high.
PATOC:GVG
A thickness which is relatively low.
low thickness
quality
slender
thin
PATO:0000592
decreased thickness
A thickness which is relatively low.
PATOC:GVG
A 1-D extent quality which is equal to the dimension through an object as opposed to its length or width.
quality
PATO:0000915
thickness
A 1-D extent quality which is equal to the dimension through an object as opposed to its length or width.
WordNet:WordNet
A shape quality inhering in a bearer by virtue of the bearer's having a sharp or tapered end or point.
apiculate
quality
PATO:0000944
sharpness
A shape quality inhering in a bearer by virtue of the bearer's having a sharp or tapered end or point.
PATOC:GVG
A spheroid quality inhering in a bearer by virtue of the bearer's being oval with two axes of symmetry, as produced by a conical section.
ellipse-shaped
ellipsoid
elliptical
quality
oval
ovoid
PATO:0000947
elliptic
A spheroid quality inhering in a bearer by virtue of the bearer's being oval with two axes of symmetry, as produced by a conical section.
PATOC:GVG
An optical quality which obtains by virtue of the ability of the bearer to absorb visible light.
quality
PATO:0000957
opacity
An optical quality which obtains by virtue of the ability of the bearer to absorb visible light.
PATOC:GVG
A optical quality inhering in a bearer by virtue of the bearer's lacking opacity.
clear
hyaline
quality
PATO:0000964
transparent
A optical quality inhering in a bearer by virtue of the bearer's lacking opacity.
PATOC:GVG
A structure quality inhering in a bearer by virtue of the bearer's disposition to admit the passage of gas or liquid through pores or interstices.
quality
PATO:0000973
porosity
A structure quality inhering in a bearer by virtue of the bearer's disposition to admit the passage of gas or liquid through pores or interstices.
PATOC:GVG
A porosity quality inhering in a bearer by virtue of the bearer's being capable of admitting the passage of gas or liquid through pores or interstices.
quality
PATO:0000984
porous
porous
A porosity quality inhering in a bearer by virtue of the bearer's being capable of admitting the passage of gas or liquid through pores or interstices.
PATOC:GVG
A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
PATO:0002079
Wikipedia:Physical_property
relational physical quality
quality
PATO:0001018
physical quality
A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
PATOC:GVG
A physical quality inhering in a bearer by virtue of the bearer's disposition to recover its size and shape after deformation in any way.
quality
PATO:0001031
elasticity
A physical quality inhering in a bearer by virtue of the bearer's disposition to recover its size and shape after deformation in any way.
merriam-webster:merriam-webster
A quality inhering in a bearer by virtue of the bearer's length being notably higher than its width.
quality
PATO:0001154
elongated
A quality inhering in a bearer by virtue of the bearer's length being notably higher than its width.
WordNet:WordNet
An elasticity quality inhering in a bearer by virtue of the bearer's ability to recover its size and shape after deformation in any way.
quality
PATO:0001171
elastic
An elasticity quality inhering in a bearer by virtue of the bearer's ability to recover its size and shape after deformation in any way.
merriam-webster:merriam-webster
linear
A quality which inheres in a continuant.
PATO:0001237
PATO:0001238
snap:Quality
monadic quality of a continuant
multiply inhering quality of a physical entity
quality of a continuant
quality of a single physical entity
quality of an object
quality of continuant
monadic quality of an object
monadic quality of continuant
quality
PATO:0001241
Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles.
physical object quality
A quality which inheres in a continuant.
PATOC:GVG
A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation.
quality
PATO:0001291
electromagnetic (EM) radiation quality
A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation.
Wikipedia:http://en.wikipedia.org/wiki/Electromagnetic_radiation
An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light.
quality
PATO:0001300
optical quality
An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light.
PATOC:GVG
A shape quality that obtains by virtue of the bearer having inward facing edges; having a surface or boundary that curves or bulges outward, as the exterior of a sphere.
quality
PATO:0001355
convex
A shape quality that obtains by virtue of the bearer having inward facing edges; having a surface or boundary that curves or bulges outward, as the exterior of a sphere.
PATOC:GVG
A shape quality inhering in a colony by virtue of the bearer's appearing above the medium surface with terraced edges.
quality
PATO:0001369
raised
A shape quality inhering in a colony by virtue of the bearer's appearing above the medium surface with terraced edges.
PATOC:GVG
A monadic quality of continuant that exists at the cellular level of organisation.
quality
PATO:0001396
cellular quality
A monadic quality of continuant that exists at the cellular level of organisation.
PATOC:GVG
A cellular quality inhering in a bearer by virtue of bearer's number of nuclei.
quality
PATO:0001404
nucleate quality
A cellular quality inhering in a bearer by virtue of bearer's number of nuclei.
PATOC:GVG
A nucleate quality inhering in a bearer by virtue of the bearer's having no nucleus.
quality
PATO:0001405
anucleate
A nucleate quality inhering in a bearer by virtue of the bearer's having no nucleus.
Biology-online:Biology-online
A nucleate quality inhering in a bearer by virtue of the bearer's having two nuclei.
quality
PATO:0001406
binucleate
A nucleate quality inhering in a bearer by virtue of the bearer's having two nuclei.
Biology-online:Biology-online
A nucleate quality inhering in a bearer by virtue of the bearer's having one nucleus.
quality
PATO:0001407
mononucleate
A nucleate quality inhering in a bearer by virtue of the bearer's having one nucleus.
Biology-online:Biology-online
A shape quality inhering in a bearer by virtue of the bearer's terminating in a point or edge.
quality
PATO:0001419
sharp
A shape quality inhering in a bearer by virtue of the bearer's terminating in a point or edge.
PATOC:GVG
A shape quality inhering in a bearer by virtue of the bearer's being gradually narrower or thinner toward one end.
taper
quality
PATO:0001500
tapered
A shape quality inhering in a bearer by virtue of the bearer's being gradually narrower or thinner toward one end.
WordNet:WordNet
A physical quality inhering in a bearer by virtue of the bearer's disposition to being turned, bowed, or twisted without breaking.
quality
PATO:0001543
flexibility
A physical quality inhering in a bearer by virtue of the bearer's disposition to being turned, bowed, or twisted without breaking.
merriam-webster:merriam-webster
A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity characterized by particles arranged such that their shape and volume are relatively stable.
solidity
quality
PATO:0001546
quality of a solid
A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity characterized by particles arranged such that their shape and volume are relatively stable.
Chemistry:http://chemistry.about.com/od/chemistryglossary/a/soliddefinition.htm
A surface shape quality inhering in a bearer by virtue of the bearer's exhibiting a degree of bending.
quality
PATO:0001591
curvature
A surface shape quality inhering in a bearer by virtue of the bearer's exhibiting a degree of bending.
WordNet:WordNet
A size quality inhering in an bearer by virtue of the bearer's extension in one dimension.
1-D size
quality
PATO:0001708
1-D extent
A size quality inhering in an bearer by virtue of the bearer's extension in one dimension.
PATOC:GVG
A quality that inheres in an bearer by virtue of how that bearer interacts with radiation.
quality
PATO:0001739
radiation quality
A quality that inheres in an bearer by virtue of how that bearer interacts with radiation.
PATOC:GVG
A shape quality in which a portion of the outermost boundary of an entity folds in space such that a portion that was originally convex is now concave.
quality
PATO:0001748
invaginated
A shape quality in which a portion of the outermost boundary of an entity folds in space such that a portion that was originally convex is now concave.
PATOC:GVG
A shape quality inhering in a bearer by virtue of the bearer's being wound in a continuous series of loops.
quality
PATO:0001794
coiling
A shape quality inhering in a bearer by virtue of the bearer's being wound in a continuous series of loops.
Online_Dictionary:Online_Dictionary
A coiling which is relatively high.
high coiling
quality
PATO:0001795
increased coiling
A coiling which is relatively high.
PATOC:GVG
A coiling which is relatively low.
low coiling
quality
PATO:0001796
decreased coiling
A coiling which is relatively low.
PATOC:GVG
A shape quality in a bearer by virtue of the bearer's curving inward.
quality
PATO:0001857
concave
A shape quality in a bearer by virtue of the bearer's curving inward.
WordNet:WordNet
A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section.
PATO:0001203
rod-like
rod-shaped
tubulate
quality
PATO:0001873
cylindrical
A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section.
PATOC:MAH
A nucleate quality inhering in a bearer by virtue of the bearer's having more than one nucleus.
quality
PATO:0001908
multinucleate
A nucleate quality inhering in a bearer by virtue of the bearer's having more than one nucleus.
PATOC:GVG
An organismal quality inhering in a bearer by virtue of the bearer's consisting cells.
quality
PATO:0001992
cellularity
An organismal quality inhering in a bearer by virtue of the bearer's consisting cells.
PATOC:GVG
A cellularity quality inhering in a bearer by virtue of the bearer's consisting of more than one cell.
quality
PATO:0001993
multicellular
A cellularity quality inhering in a bearer by virtue of the bearer's consisting of more than one cell.
PATOC:GVG
A quality that inheres in an entire organism or part of an organism.
quality
PATO:0001995
organismal quality
A quality that inheres in an entire organism or part of an organism.
PATOC:CJM
Surface shape that refers to the inward or outward curvature of the surface.
quality
PATO:0002005
concavity
Surface shape that refers to the inward or outward curvature of the surface.
PATOC:MAH
A shape that inheres in a 2 dimensional entity, such as a cross section or projection of a 3 dimensional entity.
quality
2-D projection
cross-sectional
PATO:0002006
2-D shape
A shape that inheres in a 2 dimensional entity, such as a cross section or projection of a 3 dimensional entity.
PATOC:CJM
A complete three dimensional shape in which for every line connecting pair of points on the object is within the object. Or: a shape lacking cavities. Contrast: concave.
Image:http://upload.wikimedia.org/wikipedia/commons/0/06/Convex_polygon_illustration1.png
quality
PATO:0002007
Use this term or an is_a child of this term when the entire shape of the object is known.
convex 3-D shape
A complete three dimensional shape in which for every line connecting pair of points on the object is within the object. Or: a shape lacking cavities. Contrast: concave.
PATOC:CJM
A shape quality inhering in a bearer by virtue of the degree to which there are subdivisions or offshoots in a bearer entity.
quality
PATO:0002009
branchiness
A shape quality inhering in a bearer by virtue of the degree to which there are subdivisions or offshoots in a bearer entity.
PATOC:MAH
A structural quality that inheres in a bearer by virtue of the bearer's containing hollow areas.
quality
PATO:0002014
structure, cavities
A structural quality that inheres in a bearer by virtue of the bearer's containing hollow areas.
PATOC:GVG
A convex 3-D shape quality inhering in a bearer by virtue of the bearer's resembling a cone (a 3-D shape with a round cross section that tapers).
Image:http://upload.wikimedia.org/wikipedia/commons/d/d2/Cone_3d.png
cone-shaped
quality
PATO:0002021
conical
A convex 3-D shape quality inhering in a bearer by virtue of the bearer's resembling a cone (a 3-D shape with a round cross section that tapers).
Wikipedia:http://en.wikipedia.org/wiki/Cone_(geometry)
A quality inhering in a bearer by virtue of the bearer's having an empty space or cavity within.
George Gkoutos
2009-09-18T02:19:20Z
quality
PATO:0002078
hollow
A quality inhering in a bearer by virtue of the bearer's having an empty space or cavity within.
url:http://www.merriam-webster.com/dictionary/hollow
A quality inhering in a bearer by virtue of its constitution.
George Gkoutos
2010-03-15T04:35:27Z
quality
PATO:0002198
quality of a substance
A quality inhering in a bearer by virtue of its constitution.
PATOC:GVG
A quality inhering in a bearer that is shaped in the form of a fan.
george
2010-07-09T01:43:42Z
fan-like
quality
PATO:0002219
fan-shaped
A quality inhering in a bearer that is shaped in the form of a fan.
thefreedictionary:http://www.thefreedictionary.com/fan-shaped
A tapered shape quality inhering in a bearer by virtue of the bearer's tapering gradually to a sharp point.
george
2010-07-15T09:03:18Z
quality
PATO:0002228
acuminate
A tapered shape quality inhering in a bearer by virtue of the bearer's tapering gradually to a sharp point.
url:http://www.thefreedictionary.com/acuminate
A quality inhering in a bearer by virtue of the bearer's surface becoming more extended in a plane.
george
2010-08-16T03:59:34Z
quality
compressed
PATO:0002254
Becoming flat but not necessarily completely flat.
flattened
A quality inhering in a bearer by virtue of the bearer's surface becoming more extended in a plane.
PATOC:CVS
A shape that inheres in a 3 dimensional entity.
george
2010-10-05T12:31:16Z
quality
PATO:0002266
3-D shape
A shape that inheres in a 3 dimensional entity.
PATOC:OREGON
An elasticity which is relatively high.
George Gkoutos
2011-03-30T11:50:21Z
quality
PATO:0002287
increased elasticity
An elasticity which is relatively high.
PATOC:GVG
An elasticity which is relatively low.
George Gkoutos
2011-03-30T11:50:39Z
quality
PATO:0002288
decreased elasticity
An elasticity which is relatively low.
PATOC:GVG
A quality that has a value that is increased compared to normal or average.
George Gkoutos
2011-06-16T06:39:43Z
quality
PATO:0002300
increased quality
A quality that has a value that is increased compared to normal or average.
PATOC:GVG
A quality that has a value that is decreased compared to normal or average.
George Gkoutos
2011-06-16T06:40:15Z
quality
PATO:0002301
decreased quality
A quality that has a value that is decreased compared to normal or average.
PATOC:GVG
A quality of an object that has a value that is decreased compared to normal or average.
George Gkoutos
2011-06-16T06:51:54Z
quality
PATO:0002303
decreased object quality
A quality of an object that has a value that is decreased compared to normal or average.
PATOC:GVG
A quality of an object that has a value that is increased compared to normal or average.
George Gkoutos
2011-06-16T06:54:01Z
quality
PATO:0002305
increased object quality
A quality of an object that has a value that is increased compared to normal or average.
PATOC:GVG
A shape constituting a transition between a rectangle and a circle; a closed curve, of which the circle and ellipse are special cases, whose parametric equation is x = a.cos2/rt, y = b.cos2/rt
George Gkoutos
2011-10-12T12:45:16Z
Lamé curve
quality
PATO:0002318
superelliptic
A shape constituting a transition between a rectangle and a circle; a closed curve, of which the circle and ellipse are special cases, whose parametric equation is x = a.cos2/rt, y = b.cos2/rt
wiktionary:superellipse
A nucleate quality inhering in a bearer by virtue of the bearer's having one or more nucleus.
gkoutos
2013-10-21T05:44:34Z
quality
PATO:0002505
nucleated
A nucleate quality inhering in a bearer by virtue of the bearer's having one or more nucleus.
PATOC:GVG
A shape quality inhering in a bearer by virtue of the bearer's having a shape like a ring (a circular shape enclosing a space).
wasila.dahdul
2014-08-12T12:01:56Z
annular
ring-shaped
quality
PATO:0002539
ring shaped
A shape quality inhering in a bearer by virtue of the bearer's having a shape like a ring (a circular shape enclosing a space).
PATOC:WD
An increase in porosity.
quality
PATO:0015024
increased porosity
An increase in porosity.
https://github.com/pato-ontology/pato/issues/110
An decrease in porosity.
quality
PATO:0015025
decreased porosity
An decrease in porosity.
https://github.com/pato-ontology/pato/issues/110
An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.
natural protein
native protein
protein
PR:000000001
The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB].
protein
An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.
PRO:DAN
PRO:WCB
natural protein
PRO:DAN
native protein
IEDB:BP
An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds.
peptide
polypeptide
protein
PR:000018263
Category=external.
amino acid chain
An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds.
PRO:DAN
PRO:JSG
peptide
PRO:DAN
polypeptide
PRO:DAN
A protein that is encoded in the genome of Drosophila melanogaster.
fruit fly protein
protein
PR:000029060
Drosophila melanogaster protein
A protein that is encoded in the genome of Drosophila melanogaster.
PRO:DAN
fruit fly protein
PRO:DAN
A protein that is encoded in the genome of some Eukaryota.
Eukaryota protein
protein
PR:000036194
eukaryotic protein
A protein that is encoded in the genome of some Eukaryota.
PRO:DAN
Eukaryota protein
PRO:DAN
A protein that is a translation product of the resilin gene in fruit fly.
UniProtKB:Q9V7U0
fly-resilin
protein
CG15920
resilin
PR:Q9V7U0
Category=organism-gene.
pro-resilin (fruit fly)
A protein that is a translation product of the resilin gene in fruit fly.
PRO:DNx
UniProtKB:Q9V7U0
fly-resilin
PRO:DNx
CG15920
UniProtKB:Q9V7U0
resilin
UniProtKB:Q9V7U0
A material entity consisting of multiple components that are causally integrated.
May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43
Chris Mungall
http://www.jbiomedsem.com/content/4/1/43
system
protein-coding
sequence
SO:0000010
protein_coding
An extent of biological sequence.
located_sequence_feature
sequence feature
sequence
located sequence feature
SO:0000110
sequence_feature
An extent of biological sequence.
SO:ke
A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions.
sequence
SO:0000704
gene
A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions.
SO:immuno_workshop
protein coding gene
sequence
SO:0001217
protein_coding_gene
An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity.
uberon
UBERON:0000000
processual entity
An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity.
span:ProcessualEntity
A layer of dense irregular connective tissue that lines organs and supports the mucosa, as well as joins the mucosa to the bulk of underlying smooth muscle. [WP,unvetted].
submucosal
BTO:0002107
FMA:85391
FMA:85392
NCIT:C13167
UMLS:C0225344
organ submucosa
region of submucosa
submucosa of organ
submucosa of region of organ
uberon
submucous layer
tela submucosa
tunica submucosa
UBERON:0000009
submucosa
http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png
http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png
A layer of dense irregular connective tissue that lines organs and supports the mucosa, as well as joins the mucosa to the bulk of underlying smooth muscle. [WP,unvetted].
UMLS:C0225344
ncithesaurus:Submucosa
organ submucosa
FMA:85391
region of submucosa
FMA:85392
submucosa of organ
FMA:85391
submucosa of region of organ
FMA:85392
submucous layer
BTO:0002107
tela submucosa
BTO:0002107
A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands.
Nervous structures including ganglia outside of the central nervous system. Kimmel et al, 1995.[TAO]
Part of nervous system in which nerves extend throughout the body outside of the brain and spinal cord.[AAO]
The peripheral nervous system (PNS) is the part of the nervous system connected to the CNS which contains cranial nerves III - XII, spinal, peripheral and autonomic nerves. (CUMBO)
(...) specific vertebrate traits within the chordate phylum such as skeletal tissues, PNS, and spectacular head and brain development, are linked to the NC (neural crest) and its derivatives.[well established][VHOG]
PNS
AAO:0000429
BAMS:PNS
BILA:0000081
BIRNLEX:1111
BTO:0001028
CALOHA:TS-0808
EFO:0000891
EHDAA2:0001445
EHDAA:2893
EMAPA:16665
EV:0100335
FBbt:00005098
FMA:9903
GAID:715
MA:0000218
MAT:0000338
MESH:D017933
MIAA:0000338
NCIT:C12465
TAO:0000142
UMLS:C0206417
UMLS:C1305921
VHOG:0000399
XAO:0000178
ZFA:0000142
pars peripherica
systema nervosum periphericum
uberon
UBERON:0000010
peripheral nervous system
http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png
cjm
A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands.
GO:0007422
Nervous structures including ganglia outside of the central nervous system. Kimmel et al, 1995.[TAO]
2012-08-14
TAO:0000142
TAO
ZFIN:curator
Part of nervous system in which nerves extend throughout the body outside of the brain and spinal cord.[AAO]
2012-06-20
AAO:0000429
AAO
AAO:BJB
The peripheral nervous system (PNS) is the part of the nervous system connected to the CNS which contains cranial nerves III - XII, spinal, peripheral and autonomic nerves. (CUMBO)
(...) specific vertebrate traits within the chordate phylum such as skeletal tissues, PNS, and spectacular head and brain development, are linked to the NC (neural crest) and its derivatives.[well established][VHOG]
2012-09-17
VHOG:0000399
VHOG
DOI:10.1007/978-0-387-46954-6_6 Dupin E, Creuzet S, Le Douarin NM, The contribution of the neural crest to the vertebrate body. Advances in experimental medicine and biology (2006)
PNS
UMLS:C0206417
BIRNLEX:1111
UMLS:C0206417
ncithesaurus:Peripheral_Nervous_System
UMLS:C1305921
BIRNLEX:1111
pars peripherica
FMA:9903
FMA:TA
systema nervosum periphericum
FMA:9903
FMA:TA
Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis.
Note the distinction between the entire skin of the body, of which there is only 1 in an organism, and zones of skin, of which there can be many. Examples: skin of knee
(...) it is well-established that neural crest cells contribute to both the dermal skeleton (craniofacial bone, teeth, and the caudal fin rays of teleosts) and the integument, including craniofacial dermis and all pigment cells outside the retina (...).[well established][VHOG]
we assume that mouse, HOG and GAID all mean zone of skin when they say skin. We also choose skin as an exact synonym, as it is more intuitive
EHDAA2:0001844
EHDAA:6530
EMAPA:17525
EV:0100152
FMA:86166
GAID:933
MA:0000151
MAT:0000284
MESH:D012867
MIAA:0000284
OpenCyc:Mx4rvVjX3ZwpEbGdrcN5Y29ycA
VHOG:0000860
portion of skin
region of skin
skin
skin region
skin zone
uberon
UBERON:0000014
zone of skin
http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg
http://upload.wikimedia.org/wikipedia/commons/e/e8/HumanSkinDiagram.jpg
FMA
Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis.
(...) it is well-established that neural crest cells contribute to both the dermal skeleton (craniofacial bone, teeth, and the caudal fin rays of teleosts) and the integument, including craniofacial dermis and all pigment cells outside the retina (...).[well established][VHOG]
2012-09-17
VHOG:0000860
VHOG
DOI:10.1111/j.1469-7580.2008.01043.x Vickaryous MK, Sire JY, The integumentary skeleton of tetrapods: origin, evolution, and development. J Anat (2009)
skin
MA:0000151
A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures.
AEO:0000192
CARO:0000010
FMA:50705
anatomical boundary
uberon
UBERON:0000015
Except in the case of abstracted fiat boundaries such as the midline plane of an organism, all 2D anatomical entities have a 3 dimensional projection. For example, the surface of the shell of a muscle has a distinct shape that projects into the third dimension. Note that boundaries are 2D structures. They have no thickness - and so can not be sites of gene expression or gene product localisation. For this, use boundary region terms.
non-material anatomical boundary
CARO
A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures.
CARO:0000010
anatomical boundary
CARO:0000010
An organ of sight that includes the camera-type eyeball and supporting structures such as the lacrimal apparatus, the conjunctiva, the eyelid.
A cavitated compound organ that transduces light waves into neural signals.[TAO]
The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]
FMA distinguishes Eye (subdivision of face) which has its parts an Eyeball (organ), as well as other structures, and the orbit of skull. MA includes eyelid, conjunctiva and lacrimal apparatus as part of MA:eye - consistent with FMA - so we can infer that MA:eye is more like FMA:eye than FMA:eyeball. For other AOs this distinction is less meaningful - e.g. ZFA has no eyelid; XAO has no eyelid, but it has conjuctiva, which is considered part of the xao:eye. GO considers eyelid development part of eye development. See also notes on optic nerve - XAO, AAO and BTO consider this part of the eye. MA considers the eye muscles part of the eye, whereas FMA has a class 'orbital content' for this
eye
AAO:0010340
BIRNLEX:1169
BTO:0004688
EHDAA2:0000484
EHDAA:936
EMAPA:16198
FMA:54448
MA:0000261
NCIT:C12401
OpenCyc:Mx8Ngx4rwKSh9pwpEbGdrcN5Y29ycB4rvVil5pwpEbGdrcN5Y29ycB4rvViTvpwpEbGdrcN5Y29ycA
TAO:0000107
UMLS:C0015392
UMLS:C1280202
VHOG:0000275
XAO:0000179
ZFA:0000107
regio orbitalis
vertebrate eye
uberon
camera-type eye plus associated structures
eyes
orbital part of face
orbital region
UBERON:0000019
camera-type eye
definitional
An organ of sight that includes the camera-type eyeball and supporting structures such as the lacrimal apparatus, the conjunctiva, the eyelid.
GO:0043010
A cavitated compound organ that transduces light waves into neural signals.[TAO]
2012-08-14
TAO:0000107
TAO
TAO:wd
The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]
2012-09-17
VHOG:0000275
VHOG
DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)
FMA distinguishes Eye (subdivision of face) which has its parts an Eyeball (organ), as well as other structures, and the orbit of skull. MA includes eyelid, conjunctiva and lacrimal apparatus as part of MA:eye - consistent with FMA - so we can infer that MA:eye is more like FMA:eye than FMA:eyeball. For other AOs this distinction is less meaningful - e.g. ZFA has no eyelid; XAO has no eyelid, but it has conjuctiva, which is considered part of the xao:eye. GO considers eyelid development part of eye development. See also notes on optic nerve - XAO, AAO and BTO consider this part of the eye. MA considers the eye muscles part of the eye, whereas FMA has a class 'orbital content' for this
FMA
eye
FMA:54448
UMLS:C0015392
BIRNLEX:1169
UMLS:C0015392
ncithesaurus:Eye
UMLS:C1280202
BIRNLEX:1169
regio orbitalis
FMA:54448
FMA:TA
eyes
TAO:0000107
orbital part of face
FMA:54448
orbital region
FMA:54448
An organ that is capable of transducing sensory stimulus to the nervous system.
AEO:0000094
BSA:0000121
BTO:0000202
CALOHA:TS-2043
EHDAA2:0001824
EHDAA:500
EMAPA:35955
FBbt:00005155
GAID:63
HAO:0000930
MA:0000017
MESH:D012679
NCIT:C33224
UMLS:C0935626
VHOG:0001407
WBbt:0006929
organ of sense organ system
organ of sensory organ system
organ of sensory system
sense organ system organ
sensory organ
sensory organ system organ
sensory system organ
sensillum
uberon
Sinnesorgan
sensor
UBERON:0000020
sense organ
http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png
An organ that is capable of transducing sensory stimulus to the nervous system.
UMLS:C0935626
ncithesaurus:Organ_of_the_Special_Sense
organ of sense organ system
OBOL:accepted
organ of sensory organ system
OBOL:accepted
organ of sensory system
OBOL:accepted
sense organ system organ
OBOL:automatic
sensory organ system organ
OBOL:automatic
sensory system organ
OBOL:accepted
sensillum
WBbt:0006929
Sinnesorgan
BTO:0000202
Any hollow cylindrical anatomical structure containing a lumen through which substances are transported.
not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts)
tubular
galen:Tube
anatomical tube
duct
uberon
UBERON:0000025
tube
Any hollow cylindrical anatomical structure containing a lumen through which substances are transported.
A thin layer of loose connective tissue which lies beneath the epithelium and together with the epithelium constitutes the mucosa[WP]. The lamina propria contains capillaries and a central lacteal (lymph vessel) in the small intestine, as well as lymphoid tissue. Lamina propria also contains glands with the ducts opening on to the mucosal epithelium, that secrete mucus and serous secretions.
BTO:0002330
FMA:62517
NCIT:C32918
UMLS:C1179187
lamina propria mucosa
lamina propria mucosae
uberon
tunica propria
UBERON:0000030
lamina propria
GI:Organization.svg
A thin layer of loose connective tissue which lies beneath the epithelium and together with the epithelium constitutes the mucosa[WP]. The lamina propria contains capillaries and a central lacteal (lymph vessel) in the small intestine, as well as lymphoid tissue. Lamina propria also contains glands with the ducts opening on to the mucosal epithelium, that secrete mucus and serous secretions.
UMLS:C1179187
ncithesaurus:Lamina_Propria
tunica propria
BTO:0002330
The head is the anterior-most division of the body [GO].
Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO]
Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO]
Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG]
AAO:0010335
AEO:0000106
BILA:0000115
BIRNLEX:1230
BTO:0000282
CALOHA:TS-0436
EFO:0000964
EHDAA2:0003106
EMAPA:31858
FBbt:00000004
FMA:7154
GAID:61
HAO:0000397
MA:0000023
MAT:0000294
MESH:D006257
MIAA:0000294
NCIT:C12419
OpenCyc:Mx4rEOLm4rgPEdmAAAACs6hRjg
OpenCyc:Mx4rvVi6YJwpEbGdrcN5Y29ycA
SPD:0000016
TAO:0001114
TGMA:0000002
UMLS:C0018670
VHOG:0001644
WBbt:0005739
XAO:0003024
ZFA:0001114
galen:Head
head (volume)
adult head
uberon
cephalic area
UBERON:0000033
head
The head is the anterior-most division of the body [GO].
GO:0060322
Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO]
2012-06-20
AAO:0010335
AAO
AAO:BJB
Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO]
2012-08-14
TAO:0001114
TAO
ZFIN:curator
Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG]
2012-09-17
VHOG:0001644
VHOG
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.82
UMLS:C0018670
BIRNLEX:1230
UMLS:C0018670
ncithesaurus:Head
head (volume)
FMA:7154
cephalic area
SPD:0000016
multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer.
A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO]
a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP]
in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA.
FMA:9581
GAID:19
MESH:D012704
NCIT:C13169
TAO:0005425
UMLS:C0036760
ZFA:0005425
tunica serosa
wall of serous sac
uberon
serosa
UBERON:0000042
serous membrane
http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png
http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png
multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer.
A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO]
2012-08-14
TAO:0005425
TAO
a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP]
in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA.
FMA
UMLS:C0036760
ncithesaurus:Serosa
tunica serosa
FMA:9581
wall of serous sac
FMA:9581
serosa
Dense regular connective tissue that connects muscle to bone[VSAO].
Dense regular connective tissue that connects muscle to bone.[VSAO]
Phylogenetically, tendinous tissue first appears in the invertebrate chordate Branchiostoma as myosepta. This two-dimensional array of collagen fibers is highly organized, with fibers running along two primary axes. In hagfish the first linear tendons appear and the myosepta have developed specialized regions with unidirectional fiber orientation - a linear tendon within the flat sheet of myoseptum.[well established][VHOG]
in FMA, tendon is an organ component that with parts dense-irregular-connective-tissue of tendon and dense-irregular-connective-tissue of tendon sheath; we follow VSAO in making it a subtype of the former. In VSAO tendons connect muscle to bone; in WP the def states integument (e.g. auricular muscles) - but JB confirms this is not actually tendon but aponeurosis
AEO:0000091
BTO:0001356
CALOHA:TS-1021
EHDAA2:0003091
EMAPA:35854
EV:0100149
FMA:9721
GAID:276
MA:0000115
MESH:D013710
NCIT:C13045
OpenCyc:Mx4rvVjefJwpEbGdrcN5Y29ycA
UMLS:C0039508
VHOG:0001286
VSAO:0000073
XAO:0000173
ZFA:0005647
galen:Tendon
uberon
sinew
tendo
UBERON:0000043
tendon
http://upload.wikimedia.org/wikipedia/commons/3/3c/Achilles-tendon.jpg
VSAO
OG
Dense regular connective tissue that connects muscle to bone[VSAO].
GO_REF:0000034
VSAO:0000073
Dense regular connective tissue that connects muscle to bone.[VSAO]
2012-08-14
VSAO:0000073
VSAO
PSPUB:0000170
Phylogenetically, tendinous tissue first appears in the invertebrate chordate Branchiostoma as myosepta. This two-dimensional array of collagen fibers is highly organized, with fibers running along two primary axes. In hagfish the first linear tendons appear and the myosepta have developed specialized regions with unidirectional fiber orientation - a linear tendon within the flat sheet of myoseptum.[well established][VHOG]
2012-09-17
VHOG:0001286
VHOG
DOI:10.1016/S1095-6433(02)00241-6 Summers AP, Koob TJ, The evolution of tendon - morphology and material properties. Comparative Biochemistry and Physiology-Part A: Molecular and Integrative Physiology (2002)
in FMA, tendon is an organ component that with parts dense-irregular-connective-tissue of tendon and dense-irregular-connective-tissue of tendon sheath; we follow VSAO in making it a subtype of the former. In VSAO tendons connect muscle to bone; in WP the def states integument (e.g. auricular muscles) - but JB confirms this is not actually tendon but aponeurosis
FMA
UMLS:C0039508
ncithesaurus:Tendon
sinew
tendo
An eye with one concave chamber. Note that 'simple' does not imply a reduced level of complexity or acuity.
TGMA:0000729
uberon
UBERON:0000047
simple eye
An eye with one concave chamber. Note that 'simple' does not imply a reduced level of complexity or acuity.
A tubular structure that contains, conveys body fluid, such as blood or lymph.
uberon
UBERON:0000055
vessel
A tubular structure that contains, conveys body fluid, such as blood or lymph.
A tubular structure that transports secreted or excreted substances.
A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171].
Most ducts, but not all, are exocrine gland ducts. Some ontologies classify structures such as the oviduct here.
AAO:0011123
FBbt:00100314
FMA:30320
NCIT:C12948
TAO:0005171
UMLS:C0687028
XAO:0004000
ZFA:0005171
galen:Duct
anatomical duct
exocrine duct
exocrine gland duct
uberon
ducts
UBERON:0000058
duct
A tubular structure that transports secreted or excreted substances.
A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171].
ZFA:0005171
UMLS:C0687028
ncithesaurus:Duct
ducts
XAO:0004000
Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers.
in FMA, serosa is a wall
UBERON:0009915
wall
EMAPA:25036
FMA:82482
galen:Wall
wall of organ
uberon
organ wall
UBERON:0000060
anatomical wall
Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers.
FMA:82482
in FMA, serosa is a wall
FMA
wall of organ
FMA:82482
organ wall
FMA:82482
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
AAO:0010825
AEO:0000003
BILA:0000003
CARO:0000003
EHDAA2:0003003
EMAPA:0
FBbt:00007001
FMA:305751
FMA:67135
GAID:781
HAO:0000003
MA:0003000
MESH:D000825
TAO:0000037
TGMA:0001823
VHOG:0001759
XAO:0003000
ZFA:0000037
biological structure
connected biological structure
uberon
UBERON:0000061
anatomical structure
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
CARO:0000003
connected biological structure
CARO:0000003
Anatomical structure that performs a specific function or group of functions [WP].
Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4
BIRNLEX:4
CARO:0020004
EFO:0000634
EMAPA:35949
ENVO:01000162
FMA:67498
MA:0003001
NCIT:C13018
OpenCyc:Mx4rv5XMb5wpEbGdrcN5Y29ycA
OpenCyc:Mx4rwP3iWpwpEbGdrcN5Y29ycA
UMLS:C0178784
WBbt:0003760
uberon
anatomical unit
body organ
element
UBERON:0000062
organ
Anatomical structure that performs a specific function or group of functions [WP].
Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
GO:0048513
UMLS:C0178784
ncithesaurus:Organ
element
A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity.
FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction
Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball.
Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal.
FMA:86140
uberon
organ region with fixed fiat boundary
organ segment
segment of organ
UBERON:0000063
organ subunit
A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity.
Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball.
FMA:86140
3
Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal.
FMA:86140
1
organ region with fixed fiat boundary
FMA:86140
organ segment
FMA:86140
segment of organ
FMA:86140
A multicellular structure that is a part of an organ.
currently defined in a very broad sense, may be replaced by more specific classes in the future
AAO:0011124
BIRNLEX:16
EFO:0000635
FMA:82472
cardinal organ part
uberon
regional part of organ
UBERON:0000064
organ part
A multicellular structure that is a part of an organ.
cardinal organ part
FMA:82472
regional part of organ
BIRNLEX:16
The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage.
adult stage
BTO:0001043
BilaDO:0000004
EFO:0001272
FBdv:00005369
WBls:0000041
XtroDO:0000084
fully formed animal stage
juvenile-adult stage
uberon
UBERON:0000066
fully formed stage
https://github.com/obophenotype/uberon/issues/566
The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage.
A life cycle stage that starts with fertilization and ends with the fully formed embryo.
BilaDO:0000002
EV:0300001
FBdv:00005289
FMA:72652
HsapDv:0000002
MmusDv:0000002
OGES:000000
OGES:000022
WBls:0000003
WBls:0000092
WBls:0000102
XAO:1000012
embryonic stage
uberon
embryogenesis
UBERON:0000068
embryo stage
A life cycle stage that starts with fertilization and ends with the fully formed embryo.
End of the life of an organism.
ncit:Death is an outcome
XAO:0000437
XtroDO:0000085
uberon
death
UBERON:0000071
death stage
End of the life of an organism.
XAO:0000437
ncit:Death is an outcome
ncit
Any part or collection of parts of the central or peripheral nervous system. Parts may span both CNS and PNS.
Melissa Haendel
2009-06-18T09:00:04Z
BIRNLEX:1157
NCIT:C13040
UMLS:C1518256
part of nervous system
uberon
UBERON:0000073
regional part of nervous system
Any part or collection of parts of the central or peripheral nervous system. Parts may span both CNS and PNS.
BIRNLEX:1157
UMLS:C1518256
ncithesaurus:Nervous_System_Part
part of nervous system
BIRNLEX:1157
Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism.
UBERON:0010322
FMA:85544
NCIT:C34076
UMLS:C1519343
galen:ComplexSkeletalStructure
skeletal system subdivision
uberon
skeletal system part
UBERON:0000075
subdivision of skeletal system
cjm
Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism.
UBERONREF:0000003
UMLS:C1519343
ncithesaurus:Skeletal_System_Part
skeletal system subdivision
FMA:85544
The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm.
merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube)
(or external ectoderm) forms the following structures: Skin Epithelium of the mouth and nasal cavity saliavary glands, and glands of mouth and nasal cavity Enamel - as a side note dentin and dental pulp are formed from ectomesenchyme which is derived from ectoderm Epithelium of pineal and pituitary glands Lens and cornea of the eye Apical ectodermal ridge inducing development of the limb buds of the embryo. Sensory receptors in epidermis
EHDAA2:0001968
EHDAA:1494
EHDAA:350
EHDAA:4784
EHDAA:4790
EHDAA:4796
EHDAA:7860
EMAPA:16096
FMA:87656
NCIT:C34309
UMLS:C1515087
surface (external) ectoderm
surface ectoderm
uberon
UBERON:0000076
external ectoderm
http://upload.wikimedia.org/wikipedia/commons/1/1d/Ectoderm.png
EHDAA2
EHDAA2
The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm.
MGI:anna
MP:0012532
UMLS:C1515087
ncithesaurus:Surface_Ectoderm
surface ectoderm
MP:0012532
An anatomical structure that develops from the endoderm and the mesoderm.
Grouping term for query purposes. Notes that the developmental relationships are being refined such that most structures should develop in whole from at most one layer, but may have contributions from multiple
uberon
UBERON:0000077
mixed endoderm/mesoderm-derived structure
An anatomical structure that develops from the endoderm and the mesoderm.
An anatomical structure that develops from the ectoderm, mesoderm and endoderm.
Grouping term for query purposes. Notes that the developmental relationships are being refined such that most structures should develop in whole from at most one layer, but may have contributions from multiple
uberon
UBERON:0000078
mixed ectoderm/mesoderm/endoderm-derived structure
An anatomical structure that develops from the ectoderm, mesoderm and endoderm.
stage succeeding embryo, including mature structure
In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)
BilaDO:0000003
OGES:000010
OGES:000014
OGES:000024
WBls:0000022
WBls:0000093
WBls:0000103
postembryonic stage
post-hatching stage
uberon
postembryonic
UBERON:0000092
post-embryonic stage
https://github.com/obophenotype/uberon/issues/344
stage succeeding embryo, including mature structure
Nonparenchymatous organ that primarily consists of dense connective tissue organized into a sheet which interconnects two or more organs, separates two or more body spaces from one another, or surrounds an organ or body part. Examples: interosseous membrane of forearm, obturator membrane, tympanic membrane, fibrous pericardium, fascia lata, dura mater. [FMA]
cjm
2009-07-30T05:19:13Z
membrane
FMA:7145
membrane of organ
uberon
UBERON:0000094
membrane organ
FMA-def
Nonparenchymatous organ that primarily consists of dense connective tissue organized into a sheet which interconnects two or more organs, separates two or more body spaces from one another, or surrounds an organ or body part. Examples: interosseous membrane of forearm, obturator membrane, tympanic membrane, fibrous pericardium, fascia lata, dura mater. [FMA]
FMA:7145
An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism.
FBdv:00000000
HsapDv:0000001
MmusDv:0000001
OGES:000011
ncithesaurus:Life
entire life cycle
entire lifespan
life
lifespan
uberon
UBERON:0000104
life cycle
https://github.com/obophenotype/uberon/issues/532
An entire span of an organism's life, commencing with the zygote stage and ending in the death of the organism.
A spatiotemporal region encompassing some part of the life cycle of an organism.
this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here
the WBls class 'all stages' belongs here as it is the superclass of other WBls stages
we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage
BILS:0000105
EFO:0000399
FBdv:00007012
FMA:24120
HsapDv:0000000
MmusDv:0000000
OlatDv:0000010
PdumDv:0000090
WBls:0000002
XAO:1000000
ZFS:0000000
ZFS:0100000
ncithesaurus:Developmental_Stage
developmental stage
stage
uberon
UBERON:0000105
life cycle stage
A spatiotemporal region encompassing some part of the life cycle of an organism.
A stage at which the organism is a single cell produced by means of sexual reproduction.
As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]
BILS:0000106
BilaDO:0000005
EFO:0001322
EHDAA:27
FBdv:00005288
NCIT:C12601
PdumDv:0000100
VHOG:0000745
XAO:1000001
ZFS:0000001
1-cell stage
fertilized egg stage
one cell stage
uberon
fertilized egg stage
one-cell stage
zygote
zygotum
UBERON:0000106
zygote stage
A stage at which the organism is a single cell produced by means of sexual reproduction.
As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]
2012-09-17
VHOG:0000745
VHOG
ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107
fertilized egg stage
BTO:0000854
one-cell stage
VHOG:0000745
zygote
VHOG:0000745
zygotum
The first few specialized divisions of an activated animal egg; Stage consisting of division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. The different cells derived from cleavage are called blastomeres and form a compact mass called the morula. Cleavage ends with the formation of the blastula.
BILS:0000107
BilaDO:0000006
EFO:0001290
FBdv:00000054
MESH:A16.254.270
MmusDv:0000004
OGES:000015
OGES:000020
PdumDv:0000200
XAO:1000004
ZFS:0000046
uberon
UBERON:0000107
cleavage stage
The first few specialized divisions of an activated animal egg; Stage consisting of division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. The different cells derived from cleavage are called blastomeres and form a compact mass called the morula. Cleavage ends with the formation of the blastula.
GO:0040016
An early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence.
consider adding a preceding stage 'morula stage' as part of cleavage
BILS:0000108
BilaDO:0000007
EFO:0001282
HsapDv:0000006
MmusDv:0000007
OGES:000003
OGES:000016
OGES:000021
OpenCyc:Mx4rEetFnKP2EdqAAAACs4vPlg
WBls:0000005
XAO:1000003
ZFS:0000045
uberon
UBERON:0000108
blastula stage
http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png
An early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence.
A stage defined by complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm.
BILS:0000109
BilaDO:0000008
EFO:0001296
FBdv:00005317
HsapDv:0000010
MmusDv:0000013
OGES:000004
OGES:000019
WBls:0000010
XAO:1000005
ZFS:0000047
uberon
blastocystis trilaminaris stage
trilaminar blastocyst stage
trilaminar blastoderm stage
trilaminar disk stage
trilaminar germ stage
trilaminar stage
UBERON:0000109
gastrula stage
BILS
A stage defined by complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm.
GO:0007369
blastocystis trilaminaris stage
trilaminar blastocyst stage
trilaminar blastoderm stage
trilaminar disk stage
trilaminar germ stage
trilaminar stage
Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system.
BILS:0000110
BilaDO:0000009
HsapDv:0000012
MmusDv:0000017
XAO:1000006
uberon
UBERON:0000110
neurula stage
https://github.com/obophenotype/uberon/issues/343
Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system.
GO:0001841
A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism.
BILS:0000111
BilaDO:0000010
HsapDv:0000015
MmusDv:0000018
OGES:000005
OGES:000032
uberon
segmentation stage
UBERON:0000111
organogenesis stage
https://github.com/obophenotype/uberon/issues/533
A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism.
uberon
UBERON:0000153
anterior region of body
lexical
uberon
UBERON:0000154
posterior region of body
lexical
Anatomical conduit that connects two adjacent body spaces (or a body space with the space surrounding the organism)[FMA,modified].
in FMA, this is an anatomical conduit *space*, rather than anatomical conduit
anatomical ostium
ostium
FMA:3724
anatomical orifice
hilum
uberon
UBERON:0000161
orifice
Anatomical conduit that connects two adjacent body spaces (or a body space with the space surrounding the organism)[FMA,modified].
FMA:3724
in FMA, this is an anatomical conduit *space*, rather than anatomical conduit
FMA
anatomical ostium
FMA:3724
anatomical orifice
FMA:3724
The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks).
Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO]
Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG]
oral
some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives
in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips
AAO:0010355
BTO:0001090
BTO:0004698
CALOHA:TS-1315
EFO:0000825
EHDAA2:0001326
EHDAA:542
EMAPA:16262
FBbt:00003126
FMA:49184
GAID:75
MA:0000341
MA:0002474
MAT:0000038
MESH:D009055
MIAA:0000038
OpenCyc:Mx4rvVidh5wpEbGdrcN5Y29ycA
TADS:0000040
TAO:0000547
TAO:0000590
TGMA:0000131
VHOG:0000280
VHOG:0000812
XAO:0003029
ZFA:0000547
ZFA:0000590
galen:Mouth
regio oralis
adult mouth
uberon
cavital oralis
cavitas oris
cavum oris
mouth cavity
oral region
oral vestibule
rima oris
stoma
stomatodaeum
trophic apparatus
vestibule of mouth
vestibulum oris
UBERON:0000165
mouth
https://github.com/obophenotype/uberon/issues/661
http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg
the mouth contains structures such as jaw skeleton that may not strictly be considered tract parts
exceptions in some taxa
The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks).
Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO]
2012-06-20
AAO:0010355
AAO
AAO:BJB
Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG]
2012-09-17
VHOG:0000812
VHOG
DOI:10.1038/nature07309 Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008)
in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips
FMA
regio oralis
BTO:0004698
regio oralis
FMA:49184
FMA:TA
cavital oralis
cavitas oris
BTO:0001090
cavum oris
BTO:0001090
mouth cavity
BTO:0001090
oral region
EHDAA2:0001326
oral vestibule
BTO:0001090
rima oris
BTO:0001090
stomatodaeum
VHOG:0000812
trophic apparatus
vestibule of mouth
BTO:0001090
vestibulum oris
BTO:0001090
The orifice that connects the mouth to the exterior of the body.
(...) mouth development is very similar in protostomes and 'basal' deuterostomes, whereas the chordate mouth seems to develop at a new position. Recent data for echinoderms and hemichordates further suggest that this change in mouth position may result from change in the influence of a conserved ectodermal patterning system on mouth development. It has been suggested that the mouths of vertebrates and urochordates may constitute a 'new' mouth.[well established][VHOG]
FMA:59806
oral fissure
oral orifice
uberon
mouth
oral part of face
UBERON:0000166
oral opening
FMA
The orifice that connects the mouth to the exterior of the body.
(...) mouth development is very similar in protostomes and 'basal' deuterostomes, whereas the chordate mouth seems to develop at a new position. Recent data for echinoderms and hemichordates further suggest that this change in mouth position may result from change in the influence of a conserved ectodermal patterning system on mouth development. It has been suggested that the mouths of vertebrates and urochordates may constitute a 'new' mouth.[well established][VHOG]
2012-09-17
VHOG:0000280
VHOG
DOI:10.1016/j.semcdb.2007.06.002 Christiaen L, Jaszczyszyn Y, Kerfant M, Kanob S, Thermes V, Joly JS, Evolutionary modification of mouth position in deuterostomes. Seminars in Cell and Developmental Biology (2007)
oral fissure
FMA:59806
oral orifice
FMA:59806
mouth
Anatomical cavity at the start of the digestive tract that that is enclosed by the mouth. The boundaries and contents vary depending on the species. In vertebrates, the boundaries are the oral opening, the cheeks, the palate and (if present) the palatoglossal arch - if this is not present then the mouth and pharynx form the oropharyngeal cavity. The buccal cavity contains the teeth, tongue and palate (when present)
Anatomical cavity bounded anteriorly by the mouth and posteriorly by the derivatives of the branchial arches.[AAO]
The cavity of the mouth, bounded by the jaw bones and associated structures (muscles and mucosa). [TFD][VHOG]
Echinoderms, hemichordates, and chordates are called deuterostomes because the mouth arises not from the blastopore but from a second invagination at the anterior end of the larva that pushes in to connect with the archenteron.[well established][VHOG]
AAO:0000053
AAO:0000960
BSA:0000107
CALOHA:TS-1315
EFO:0001975
EHDAA2:0001324
EHDAA:6970
EMAPA:17411
EMAPA:18399
EV:0100057
FMA:20292
HAO:0000669
NCIT:C12421
TAO:0001027
TGMA:0000102
UMLS:C0226896
VHOG:0000188
WBbt:0005255
XAO:0000126
ZFA:0001027
buccal cavity
cavity of mouth
uberon
bucca
UBERON:0000167
oral cavity
Anatomical cavity at the start of the digestive tract that that is enclosed by the mouth. The boundaries and contents vary depending on the species. In vertebrates, the boundaries are the oral opening, the cheeks, the palate and (if present) the palatoglossal arch - if this is not present then the mouth and pharynx form the oropharyngeal cavity. The buccal cavity contains the teeth, tongue and palate (when present)
ISBN:0073040584
Anatomical cavity bounded anteriorly by the mouth and posteriorly by the derivatives of the branchial arches.[AAO]
2012-06-20
AAO:0000960
AAO
AAO:EJS
The cavity of the mouth, bounded by the jaw bones and associated structures (muscles and mucosa). [TFD][VHOG]
2012-09-17
VHOG:0000188
VHOG
Echinoderms, hemichordates, and chordates are called deuterostomes because the mouth arises not from the blastopore but from a second invagination at the anterior end of the larva that pushes in to connect with the archenteron.[well established][VHOG]
2012-09-17
VHOG:0000188
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.32
UMLS:C0226896
ncithesaurus:Oral_Cavity
buccal cavity
FMA:20292
ISBN:0073040584
A fluid that is composed of blood plasma and erythrocytes.
This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid.
A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO]
Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]
relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]
Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG]
AAO:0000046
BTO:0000089
CALOHA:TS-0079
EFO:0000296
EHDAA2:0000176
EHDAA:418
EMAPA:16332
ENVO:02000027
EV:0100047
FMA:9670
GAID:965
MA:0000059
MESH:D001769
MIAA:0000315
NCIT:C12434
OpenCyc:Mx4rvVjI8JwpEbGdrcN5Y29ycA
TAO:0000007
UMLS:C0005767
VHOG:0000224
XAO:0000124
ZFA:0000007
galen:Blood
portion of blood
vertebrate blood
uberon
whole blood
UBERON:0000178
blood
Bgee:AN
A fluid that is composed of blood plasma and erythrocytes.
FMA:9670
A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO]
2012-08-14
TAO:0000007
TAO
ZFIN:curator
Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]
2012-06-20
AAO:0000046
AAO
AAO:LAP
relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]
2012-06-20
AAO:0000046
AAO
Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG]
2012-09-17
VHOG:0000224
VHOG
DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual review of cell and developmental biology (2006)
UMLS:C0005767
ncithesaurus:Blood
whole blood
BTO:0000089
Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs.
cjm
2009-04-08T04:38:19Z
CARO:0000081
uberon
blood or blood analog
circulating fluid
UBERON:0000179
haemolymphatic fluid
Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs.
A layer of membrane around a tendon. It has 2 layers: synovial sheath + fibrous tendon sheath
TODO - add layer relations. 'tendon sheath' GAT in FMA.
BTO:0000051
FMA:45087
FMA:76715
NCIT:C96299
UMLS:C0224856
synovial tendon sheath
uberon
vagina tendinis
UBERON:0000304
tendon sheath
A layer of membrane around a tendon. It has 2 layers: synovial sheath + fibrous tendon sheath
UMLS:C0224856
ncithesaurus:Tendon_Sheath
synovial tendon sheath
FMA:45087
vagina tendinis
Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence.
TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula
UBERON:0007011
BILA:0000059
BTO:0000128
GAID:1294
MESH:A16.254.270.274
OGEM:000006
OpenCyc:Mx4rEetFnKP2EdqAAAACs4vPlg
blastula embryo
uberon
blastosphere
UBERON:0000307
blastula
http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png
Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence.
blastula embryo
BILA:0000059
blastosphere
The wall of the digestive tract. This encompasses all parts of the digestive tract with the exception of the lumen (cavity).
We model the digestive tract as consisting of two parts: the wall and the lumen.
BTO:0000547
FMA:45653
digestive tract wall
wall of digestive tract
wall of gut
uberon
wall of alimentary tract
UBERON:0000328
gut wall
The wall of the digestive tract. This encompasses all parts of the digestive tract with the exception of the lumen (cavity).
wall of gut
FMA:45653
A lining of mostly endodermal origin, covered in epithelium, which is involved in absorption and secretion. They line various body cavities that are exposed to the external environment and internal organs. It is at several places continuous with skin: at the nostrils, the lips, the ears, the genital area, and the anus. The sticky, thick fluid secreted by the mucous membranes and gland is termed mucus. The term mucous membrane refers to where they are found in the body and not every mucous membrane secretes mucus[WP]
mucosal
FMA has mucosa vs region of mucosa; these are subtypes of Mucosa: Mucosa of gallbladder, tongue, .... The following are subtypes of Region of mucosa: Mucosa of zone of stomach, trachea, bronchus, dorsum of tongue.... Depends on whether the covered area is an organ or organ component. Uberon does not regard organ vs organ component as crucial distinction and thus collapses these into a single class deliberately
AEO:0000199
BTO:0000886
CALOHA:TS-2031
EHDAA2_RETIRED:0003234
EV:0100382
FMA:85355
FMA:85358
GAID:297
MESH:D009092
NCIT:C13166
OpenCyc:Mx4rvmKNOpwpEbGdrcN5Y29ycA
UMLS:C0026724
galen:Mucosa
mucosa of organ
mucosa of organ part
mucosal region
mucous membrane
organ mucosa
uberon
region of mucosa
tunica mucosa
UBERON:0000344
mucosa
http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png
http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png
A lining of mostly endodermal origin, covered in epithelium, which is involved in absorption and secretion. They line various body cavities that are exposed to the external environment and internal organs. It is at several places continuous with skin: at the nostrils, the lips, the ears, the genital area, and the anus. The sticky, thick fluid secreted by the mucous membranes and gland is termed mucus. The term mucous membrane refers to where they are found in the body and not every mucous membrane secretes mucus[WP]
FMA has mucosa vs region of mucosa; these are subtypes of Mucosa: Mucosa of gallbladder, tongue, .... The following are subtypes of Region of mucosa: Mucosa of zone of stomach, trachea, bronchus, dorsum of tongue.... Depends on whether the covered area is an organ or organ component. Uberon does not regard organ vs organ component as crucial distinction and thus collapses these into a single class deliberately
FMA
UMLS:C0026724
ncithesaurus:Mucosa
mucosa of organ
FMA:85355
mucosa of organ part
FMA:85358
mucosal region
FMA:85358
mucous membrane
FMA:85355
organ mucosa
FMA:85355
region of mucosa
FMA:85358
tunica mucosa
tunica mucosa
BTO:0000886
A mucosa that is part of a pharynx [Automatically generated definition].
UBERON:0003344
BTO:0001047
EMAPA:26957
FMA:55031
MA:0003143
mucosa of organ of pharynx
mucosa of pharynx
mucous membrane of pharynx
organ mucosa of pharynx
pharynx mucosa
pharynx mucosa of organ
pharynx mucous membrane
pharynx organ mucosa
tunica mucosa pharyngea
tunica mucosa pharyngis
uberon
mucous membrane of the pharynx
UBERON:0000355
pharyngeal mucosa
A mucosa that is part of a pharynx [Automatically generated definition].
OBOL:automatic
mucosa of organ of pharynx
OBOL:automatic
mucosa of pharynx
OBOL:automatic
mucous membrane of pharynx
FMA:55031
mucous membrane of pharynx
OBOL:automatic
organ mucosa of pharynx
OBOL:automatic
pharynx mucosa
OBOL:automatic
pharynx mucosa of organ
OBOL:automatic
pharynx mucous membrane
OBOL:automatic
pharynx organ mucosa
OBOL:automatic
tunica mucosa pharyngea
FMA:55031
FMA:TA
mucous membrane of the pharynx
BTO:0001047
The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified].
consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77
Anatomical system that consists of the muscles of the body.[VSAO]
we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA
AAO:0000307
BILA:0000088
BTO:0001369
BTO:0001485
EFO:0000801
EMAPA:35578
FBbt:00005069
FMA:72954
MA:0002888
MAT:0000025
MIAA:0000025
VSAO:0000033
XAO:0004042
muscle system
muscle system of body
muscular system
musculature system
set of all muscles
set of muscles of body
vertebrate muscular system
uberon
muskelsystem
UBERON:0000383
musculature of body
The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified].
VSAO:0000033
Anatomical system that consists of the muscles of the body.[VSAO]
2012-08-14
VSAO:0000033
VSAO
VSAO:curator
we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA
MA
muscular system
FMA:72954
musculature system
BILA:0000088
set of all muscles
FMA:72954
set of muscles of body
FMA:72954
vertebrate muscular system
BTO:0001369
muskelsystem
BTO:0001485
Tissue that surrounds the lens nucleus
BTO:0001632
CALOHA:TS-0542
FMA:58970
MESH:A09.371.509.225
cortex of lens
uberon
UBERON:0000389
lens cortex
Tissue that surrounds the lens nucleus
cortex of lens
FMA:58970
The core of the crystalline lens, surrounded by the cortex.
BTO:0001633
FMA:58971
MESH:A09.371.509.670
nucleus of lens
uberon
UBERON:0000390
lens nucleus
The core of the crystalline lens, surrounded by the cortex.
BTO:0001633
nucleus of lens
FMA:58971
A gland in which the principal secretory cells are serous secreting cells.
glands that secrete watery albuminous material that often contains enzymes[MP:0008052].
BTO:0001837
EMAPA:37950
FMA:62889
uberon
UBERON:0000409
serous gland
http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray1021.png
A gland in which the principal secretory cells are serous secreting cells.
glands that secrete watery albuminous material that often contains enzymes[MP:0008052].
MP:0008052
EMAPA:37950
MA:th
An anatomical wall that is part of an artery [Automatically generated definition].
BTO:0002009
FMA:14155
galen:ArterialWall
arterial wall
wall of artery
uberon
UBERON:0000415
artery wall
An anatomical wall that is part of an artery [Automatically generated definition].
OBOL:automatic
arterial wall
FMA:14155
wall of artery
FMA:14155
A portion of organism substance that is produced by exocrine glands.
BTO has two distunct classes, with exocrine glandular secretion a subtype of secretion - however, all examples in BTO directly under secretion appear to be exocrine gland secretions
UBERON:0006540
secretion
AEO:0001005
BTO:0002977
BTO:0002979
EMAPA:36535
FMA:9675
MA:0002504
MESH:D012634
NCIT:C34062
UMLS:C1516992
galen:Secretion
bodily secretion
exocrine gland fluid/secretion
secreted substance
uberon
exocrine gland fluid
exocrine gland fluid or secretion
exocrine gland secretion
external secretion
UBERON:0000456
secretion of exocrine gland
A portion of organism substance that is produced by exocrine glands.
BTO has two distunct classes, with exocrine glandular secretion a subtype of secretion - however, all examples in BTO directly under secretion appear to be exocrine gland secretions
BTO
secretion
FMA:9675
UMLS:C1516992
ncithesaurus:Exocrine_Gland_Fluid_or_Secretion
bodily secretion
MESH:D012634
exocrine gland fluid/secretion
MA:0002504
external secretion
BTO:0002977
Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.
AAO:0010839
AEO:0000004
BILA:0000004
CALOHA:TS-2101
CARO:0000004
EHDAA2:0003004
EMAPA:35178
FBbt:00007019
FMA:9669
HAO:0000004
MA:0002450
NCIT:C13236
SPD:0000008
TAO:0001487
TGMA:0001824
VHOG:0001726
XAO:0004001
ZFA:0001487
galen:BodySubstance
body fluid or substance
body substance
organism substance
portion of body substance
portion of organism substance
uberon
UBERON:0000463
organism substance
this relationship may be too strong and may be weakened in future
Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.
body fluid or substance
MA:0002450
body substance
FMA:9669
organism substance
CARO:0000004
portion of body substance
FMA:9669
portion of organism substance
ZFA:0001487
Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures.
lumen
space
AAO:0010110
AEO:0000005
BILA:0000005
CARO:0000005
EHDAA2:0003005
FBbt:00007017
FMA:5897
HAO:0000005
NCIT:C94478
TAO:0001668
TGMA:0001825
UMLS:C0524461
VHOG:0001728
XAO:0003190
ZFA:0001643
lumen space
uberon
anatomical spaces
UBERON:0000464
anatomical space
Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures.
UMLS:C0524461
ncithesaurus:Lumen_Space
anatomical spaces
ZFA:0001643
Anatomical entity that has mass.
AAO:0010264
AEO:0000006
BILA:0000006
CARO:0000006
EHDAA2:0003006
FBbt:00007016
FMA:67165
HAO:0000006
TAO:0001836
TGMA:0001826
VHOG:0001721
uberon
UBERON:0000465
material anatomical entity
Anatomical entity that has mass.
Anatomical entity that has no mass.
AAO:0010265
AEO:0000007
BILA:0000007
CARO:0000007
EHDAA2:0003007
FBbt:00007015
FMA:67112
HAO:0000007
TAO:0001835
TGMA:0001827
VHOG:0001727
immaterial physical anatomical entity
uberon
UBERON:0000466
immaterial anatomical entity
Anatomical entity that has no mass.
immaterial physical anatomical entity
FMA:67112
Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function.
system
AAO:0000007
AEO:0000011
BILA:0000011
BIRNLEX:14
BSA:0000049
CALOHA:TS-2088
CARO:0000011
EHDAA2:0003011
EHDAA:392
EMAPA:16103
EV:0100000
FBbt:00004856
FMA:7149
HAO:0000011
MA:0000003
NCIT:C12919
OpenCyc:Mx4rCWM0QCtDEdyAAADggVbxzQ
TAO:0001439
TGMA:0001831
UMLS:C0460002
VHOG:0001725
WBbt:0005746
WBbt:0005763
XAO:0003002
ZFA:0001439
galen:AnatomicalSystem
body system
connected anatomical system
organ system
uberon
anatomical systems
UBERON:0000467
anatomical system
Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function.
CARO:0000011
system
GO:0048731
UMLS:C0460002
ncithesaurus:Organ_System
body system
BIRNLEX:14
connected anatomical system
CARO:0000011
anatomical systems
ZFA:0001439
Anatomical structure that is an individual member of a species and consists of more than one cell.
TODO - split body and mc organism? body continues after death stage
organismal
organism
AAO:0010026
AEO:0000191
BILA:0000012
BIRNLEX:18
BSA:0000038
BTO:0000042
CARO:0000012
EFO:0002906
EHDAA2:0003103
EHDAA2:0003191
EHDAA:1
EMAPA:25765
EV:0100016
FBbt:00000001
FMA:256135
HAO:0000012
NCIT:C13041
TADS:0000001
TAO:0001094
TGMA:0001832
VHOG:0000671
WBbt:0007833
XAO:0003004
ZFA:0001094
galen:Organism
ncithesaurus:Whole_Organism
multi-cellular organism
animal
uberon
Koerper
body
whole body
whole organism
UBERON:0000468
multicellular organism
Anatomical structure that is an individual member of a species and consists of more than one cell.
CARO:0000012
organism
FBbt:00000001
VHOG:0000671
WBbt:0007833
multi-cellular organism
CARO:0000012
animal
BTO:0000042
Koerper
BTO:0001489
body
AEO:0000103
BIRNLEX:18
FMA:256135
NCIT:C13041
whole body
BTO:0001489
whole organism
FBbt:00000001
Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument.
Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency
AAO:0010053
AEO:0000032
BILA:0000032
BIRNLEX:7
CALOHA:TS-2084
CARO:0000032
EFO:0000808
EHDAA2:0003032
EMAPA:36031
FBbt:00007009
FMA:7153
HAO:0000032
MA:0002433
MAT:0000293
MESH:D001829
MIAA:0000293
NCIT:C32221
OpenCyc:Mx4rvViAHJwpEbGdrcN5Y29ycA
TAO:0001308
TGMA:0001840
UMLS:C0229962
VHOG:0001758
XAO:0003013
ZFA:0001308
galen:BodyPart
anatomic region
uberon
body part
body region
cardinal body part
UBERON:0000475
organism subdivision
CARO
Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument.
CARO:0000032
CARO:DOS
UMLS:C0229962
ncithesaurus:Body_Part
anatomic region
MA:0002433
body region
FMA:7153
cardinal body part
FMA:7153
Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue.
AAO:0010268
AEO:0000040
BILA:0000040
CARO:0000040
EHDAA2:0003040
FBbt:00007013
FMA:63863
HAO:0000040
TAO:0000382
TGMA:0001841
XAO:0003162
ZFA:0000382
uberon
acellular anatomical structures
UBERON:0000476
acellular anatomical structure
CARO
Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue.
acellular anatomical structures
ZFA:0000382
Anatomical group that has its parts adjacent to one another.
Will be obsoleted in CARO v2 [https://github.com/obophenotype/caro/issues/3]
AAO:0010009
AEO:0000041
BILA:0000041
CARO:0000041
EHDAA2:0003041
FBbt:00007277
FMA:49443
HAO:0000041
TADS:0000605
TAO:0001478
TGMA:0001842
VHOG:0001737
XAO:0003160
ZFA:0001478
uberon
UBERON:0000477
anatomical cluster
Anatomical group that has its parts adjacent to one another.
A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis.
AAO:0010020
AEO:0000042
BILA:0000042
CALOHA:TS-2119
CARO:0000042
EHDAA2:0003042
EHDAA:46
FBbt:00005835
FMA:85537
HAO:0000042
NCIT:C34055
TAO:0000020
TGMA:0001843
UMLS:C1282438
VHOG:0000292
XAO:0004005
ZFA:0000020
extra-embryonic structure
uberon
extraembryonic structures
extraembryonic tissue
UBERON:0000478
see also conceptus extraembryonic component in EHDAA2.
extraembryonic structure
A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis.
CARO:DOS
UMLS:C1282438
ncithesaurus:Extraembryonic_Structure
extraembryonic structures
ZFA:0000020
Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.
changed label and definition to reflect CARO2
AAO:0000607
AAO:0010054
AEO:0000043
BILA:0000043
BIRNLEX:19
CALOHA:TS-2090
CARO:0000043
EHDAA2:0003043
EMAPA:35868
FBbt:00007003
FMA:9637
HAO:0000043
MA:0003002
MESH:D014024
NCIT:C12801
TAO:0001477
TGMA:0001844
UMLS:C0040300
VHOG:0001757
WBbt:0005729
XAO:0003040
ZFA:0001477
galen:Tissue
portion of tissue
tissue portion
simple tissue
uberon
UBERON:0000479
tissue
CARO
Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.
CARO:0000043
UMLS:C0040300
ncithesaurus:Tissue
portion of tissue
CARO:0000043
simple tissue
AEO:0000043
Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types.
AAO:0010048
AEO:0000055
BILA:0000055
CARO:0000055
EHDAA2:0003055
FBbt:00007010
HAO:0000055
TAO:0001488
TGMA:0001847
VHOG:0001762
XAO:0003037
ZFA:0001488
uberon
multi-tissue structures
UBERON:0000481
multi-tissue structure
CARO
Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types.
CARO:0000055
multi-tissue structures
ZFA:0001488
Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO].
The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG]
epithelial
AAO:0000144
AAO:0010055
AEO:0000066
BILA:0000066
BTO:0000416
CALOHA:TS-0288
CARO:0000066
EHDAA2:0003066
EMAPA:32738
FBbt:00007005
FMA:9639
GAID:402
HAO:0000066
MA:0003060
MESH:D004848
NCIT:C12710
TAO:0001486
UMLS:C0014609
VHOG:0000387
XAO:0003045
ZFA:0001486
epithelial tissue
portion of epithelium
uberon
UBERON:0000483
epithelium
Tkanka:nablonkowa.png
Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO].
The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG]
2012-09-17
VHOG:0000387
VHOG
ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.59
UMLS:C0014609
ncithesaurus:Epithelium
portion of epithelium
FMA:9639
Unilaminar epithelium that consists of a single layer of cuboidal cells.
needs to be synchronized with CL - there is no distinct cuboidal cell in CL
AAO:0010064
AEO:0000067
BILA:0000067
CARO:0000067
EHDAA2:0003067
FMA:45566
HAO:0000067
NCIT:C33553
TAO:0001497
UMLS:C0836134
XAO:0004009
ZFA:0001497
epithelium simplex cuboideum
uberon
simple cuboidal epithelia
UBERON:0000484
simple cuboidal epithelium
http://upload.wikimedia.org/wikipedia/commons/d/d0/Gray1133.png
Unilaminar epithelium that consists of a single layer of cuboidal cells.
UMLS:C0836134
ncithesaurus:Simple_Cuboidal_Epithelium
simple cuboidal epithelia
ZFA:0001497
Epithelium which consists of more than one layer of epithelial cells that may or may not be in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, ciliated stratified columnar epithelium.[FMA]
Epithelium that consists of more than one layer of epithelial cells.[CARO]
AAO:0010059
AEO:0000069
BILA:0000069
BTO:0002074
CARO:0000069
EHDAA2:0003069
FMA:45562
HAO:0000069
NCIT:C33622
TAO:0001494
UMLS:C0682575
XAO:0004006
ZFA:0001494
stratified epithelium
uberon
laminated epithelium
UBERON:0000486
multilaminar epithelium
Epithelium which consists of more than one layer of epithelial cells that may or may not be in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, ciliated stratified columnar epithelium.[FMA]
FMA:FMA
Epithelium that consists of more than one layer of epithelial cells.[CARO]
2012-06-20
CARO:0000069
CARO
FMA:45562
UMLS:C0682575
ncithesaurus:Stratified_Epithelium
laminated epithelium
BTO:0002074
Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA]
Unilaminar epithelium that consists of a single layer of squamous cells.[CARO]
AAO:0010066
AEO:0000070
BILA:0000070
BTO:0002073
CARO:0000070
EHDAA2:0003070
FMA:45565
HAO:0000070
NCIT:C13178
TAO:0001498
UMLS:C0836133
XAO:0004010
ZFA:0001498
epithelium simplex squamosum
uberon
simple squamous epithelia
UBERON:0000487
simple squamous epithelium
Illu:epithelium.jpg
Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA]
FMA:45565
Unilaminar epithelium that consists of a single layer of squamous cells.[CARO]
2012-06-20
CARO:0000070
CARO
FMA:45565
UMLS:C0836133
ncithesaurus:Simple_Squamous_Epithelium
simple squamous epithelia
ZFA:0001498
Epithelium that consists of epithelial cells not arranged in one ore more layers.
AAO:0010057
AEO:0000071
BILA:0000071
CARO:0000071
EHDAA2:0003071
FMA:61741
HAO:0000071
TAO:0001493
XAO:0004004
ZFA:0001493
heterogenous epithelium
uberon
atypical epithelia
UBERON:0000488
atypical epithelium
Epithelium that consists of epithelial cells not arranged in one ore more layers.
atypical epithelia
ZFA:0001493
Compound organ that contains one or more macroscopic anatomical spaces.
this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future
AAO:0010016
AEO:0000072
BILA:0000072
CARO:0000072
EHDAA2:0003072
FMA:55671
HAO:0000072
TAO:0001490
TGMA:0001857
VHOG:0001730
XAO:0003165
ZFA:0001490
cavitated organ
uberon
cavitated compound organs
UBERON:0000489
cavitated compound organ
Compound organ that contains one or more macroscopic anatomical spaces.
cavitated organ
FMA:55671
cavitated compound organs
ZFA:0001490
Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA]
consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable
Epithelium that consists of a single layer of epithelial cells.[CARO]
AAO:0010062
AEO:0000073
BILA:0000073
BTO:0002073
CARO:0000073
EHDAA2:0003073
FMA:45561
HAO:0000073
NCIT:C33554
TAO:0001495
UMLS:C0682574
XAO:0004007
ZFA:0001495
simple epithelium
uberon
unilaminar epithelia
UBERON:0000490
unilaminar epithelium
Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA]
FMA:45561
Epithelium that consists of a single layer of epithelial cells.[CARO]
2012-06-20
CARO:0000073
CARO
FMA:45561
UMLS:C0682574
ncithesaurus:Simple_Epithelium
simple epithelium
FMA:45561
unilaminar epithelia
ZFA:0001495
Subdivision of trunk that lies between the head and the abdomen.
note that we use the slightly verbose term 'thoracic segment of trunk' to avoid confusuon with insect thorax. todo - taxonomic constraints. Also, in FMA 'thorax' is a synonym for chest
EMAPA:35862
FMA:259209
MA:0000022
thorax
uberon
anterior subdivision of trunk
upper body
upper trunk
UBERON:0000915
thoracic segment of trunk
FMA
Subdivision of trunk that lies between the head and the abdomen.
thorax
MA:0000022
upper trunk
FMA:259209
Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
embryonic
Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo
AAO:0011035
AEO:0000169
BILA:0000056
BSA:0000039
BTO:0000379
CALOHA:TS-0229
EFO:0001367
EHDAA2:0000002
EHDAA2_RETIRED:0003236
EHDAA:38
EMAPA:16039
FBbt:00000052
FMA:69068
GAID:963
MAT:0000226
MESH:D004622
MIAA:0000019
NCIT:C28147
OGEM:000001
OpenCyc:Mx4rwP1ceZwpEbGdrcN5Y29ycA
UMLS:C0013935
VHOG:0001766
XAO:0000113
ZFA:0000103
embryonic organism
uberon
developing organism
developmental tissue
UBERON:0000922
embryo
https://github.com/obophenotype/uberon/issues/503
Wrinkledfrog:embryos.jpg
Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
BTO:0000379
FB:FBrf0039741
FB:FBrf0041814
GO:0009790
Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo
ZFA
UMLS:C0013935
ncithesaurus:Embryo
embryonic organism
BILA:0000056
developing organism
BILA:0000056
A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm.
The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]
embryonic tissue
AAO:0000480
BILA:0000035
BTO:0000556
EMAPA:36033
FBbt:00000110
FMA:69069
GAID:1303
MESH:A16.254.425
NCIT:C12950
NCIT:C54105
TAO:0001122
UMLS:C0920502
UMLS:C1708239
VHOG:0001223
XAO:0003011
ZFA:0001122
germinal layer
primary germ layer
uberon
embryonic germ layer
embryonic germ layers
UBERON:0000923
Classically the germ layers are ectoderm, mesoderm and endoderm. Alternatively: primary = ectoderm, endoderm; secondary=mesoderm; tertiary=dorsal mesoderm, NC[https://github.com/obophenotype/uberon/wiki/The-neural-crest]
germ layer
A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm.
The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]
2012-09-17
VHOG:0001223
VHOG
ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722
embryonic tissue
FMA:69069
UMLS:C0920502
ncithesaurus:Embryonic_Tissue
UMLS:C1708239
ncithesaurus:Germinal_Layer
germinal layer
ncithesaurus:Germinal_Layer
primary germ layer
GO:0001704
ZFA:0001122
Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue.
Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO]
The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]
ectodermal
AAO:0000137
BILA:0000036
BTO:0000315
CALOHA:TS-0216
EFO:0000414
EHDAA2:0000428
EMAPA:16069
EV:0100003
FBbt:00000111
FMA:69070
GAID:1304
MAT:0000155
MAT:0000173
MESH:A16.254.425.273
MIAA:0000173
NCIT:C12703
TAO:0000016
UMLS:C0013574
VHOG:0000153
XAO:0000001
ZFA:0000016
embryonic ectoderm
uberon
UBERON:0000924
ectoderm
http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png
Bgee:AN
Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue.
Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO]
2012-06-20
AAO:0000137
AAO
AAO:EJS
The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]
2012-09-17
VHOG:0000153
VHOG
ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722
UMLS:C0013574
ncithesaurus:Ectoderm
embryonic ectoderm
VHOG:0000153
Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut.
The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]
endodermal
AAO:0000139
BILA:0000038
BTO:0000800
CALOHA:TS-0273
EFO:0002545
EHDAA2:0000436
EMAPA:16062
EV:0100005
FBbt:00000125
FMA:69071
GAID:1305
MAT:0000175
MESH:A16.254.425.407
MIAA:0000175
NCIT:C12706
TAO:0000017
UMLS:C0014144
VHOG:0000154
XAO:0000090
ZFA:0000017
uberon
entoderm
UBERON:0000925
endoderm
http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png
http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png
Bgee:AN
Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut.
The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]
2012-09-17
VHOG:0000154
VHOG
ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722
UMLS:C0014144
ncithesaurus:Endoderm
entoderm
The middle germ layer of the embryo, between the endoderm and ectoderm.
Primary germ layer that is the middle of the embryonic germ layers.[AAO]
The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]
mesodermal
sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates
UBERON:0003263
AAO:0000304
BILA:0000037
BTO:0000839
CALOHA:TS-0623
EFO:0001981
EHDAA2:0001128
EHDAA:124
EHDAA:160
EHDAA:183
EMAPA:16083
EV:0100006
FBbt:00000126
FMA:69072
GAID:522
MAT:0000174
MESH:A16.254.425.660
MIAA:0000174
NCIT:C12750
TAO:0000041
UMLS:C0025485
VHOG:0000152
XAO:0000050
ZFA:0000041
uberon
embryonic mesoderm
entire mesoderm
mesodermal mantle
UBERON:0000926
mesoderm
http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png
sometimes not considered primary
Bgee:AN
The middle germ layer of the embryo, between the endoderm and ectoderm.
Primary germ layer that is the middle of the embryonic germ layers.[AAO]
2012-06-20
AAO:0000304
AAO
AAO:EJS
The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]
2012-09-17
VHOG:0000152
VHOG
ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722
sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates
UMLS:C0025485
ncithesaurus:Mesoderm
embryonic mesoderm
VHOG:0000152
entire mesoderm
Anterior part of the embryonic digestive tract that develops into a mouth. The stomodeum includes as parts an invagination of the ectoderm and the stomodeal cavity.
consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence
Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO]
the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx
stomodeal
This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity.
stomodeal-hypophyseal primordium
BTO:0004224
EHDAA2:0001929
EMAPA:16263
FBbt:00000439
FMA:295846
NCIT:C34306
TAO:0001290
TGMA:0000135
UMLS:C1514977
XAO:0000269
ZFA:0001290
mouth primordium
primitive oral cavity
stomatodeum
stomodaeum
uberon
mouth pit
oral ectoderm
oral pit
UBERON:0000930
stomodeum
http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png
Anterior part of the embryonic digestive tract that develops into a mouth. The stomodeum includes as parts an invagination of the ectoderm and the stomodeal cavity.
Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO]
2012-08-14
TAO:0001290
TAO
ZFIN:curator
the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx
MP:0012522
NCBITaxon:40674
stomodeal-hypophyseal primordium
XAO:0000269
UMLS:C1514977
ncithesaurus:Stomodeum
mouth primordium
XAO:0000269
primitive oral cavity
stomatodeum
mouth pit
EMAPA:16263
oral ectoderm
ZFA:0001290
ZFIN:ZDB-PUB-100726-23
oral pit
EMAPA:16263
A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ.
Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO]
Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO]
relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO]
As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG]
cardiac
AAO:0010210
BILA:0000020
BTO:0000562
CALOHA:TS-0445
EFO:0000815
EHDAA2:0000738
EHDAA:420
EMAPA:16105
EV:0100018
FMA:7088
GAID:174
MA:0000072
MAT:0000036
MESH:D006321
MIAA:0000036
NCIT:C12727
OpenCyc:Mx4rvVjvDpwpEbGdrcN5Y29ycA
TAO:0000114
UMLS:C0018787
VHOG:0000276
XAO:0000064
ZFA:0000114
galen:Heart
chambered heart
vertebrate heart
branchial heart
uberon
Herz@de
cardium
UBERON:0000948
Taxon notes:" the ascidian tube-like heart lacks chambers....The ascidian heart is formed after metamorphosis as a simple tube-like structure with a single-layered myoepithelium that is continuous with a single-layered pericar- dial wall. It lacks chambers and endocardium.... The innovation of the chambered heart was a key event in vertebrate evolution, because the chambered heart generates one-way blood flow with high pressure, a critical requirement for the efficient blood supply of large-body vertebrates... all extant vertebrates have hearts with two or more chambers (Moorman and Christoffels 2003)" DOI:10.1101/gad.1485706
heart
MA
A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ.
Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO]
2012-08-14
TAO:0000114
TAO
ZFIN:curator
Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO]
2012-06-20
AAO:0010210
AAO
AAO:BJB
relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO]
2012-06-20
AAO:0010210
AAO
As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG]
2012-09-17
VHOG:0000276
VHOG
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481
UMLS:C0018787
ncithesaurus:Heart
chambered heart
branchial heart
Herz@de
BTO:0000562
cardium
EMAPA:16105
The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP].
requires review for applicability to invertebrate structures, e.g. synganglion
Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO]
Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO]
The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO)
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG]
AAO:0010478
ABA:Brain
BAMS:Br
BAMS:Brain
BILA:0000135
BIRNLEX:796
BTO:0000142
CALOHA:TS-0095
DHBA:10155
EFO:0000302
EHDAA2:0000183
EHDAA:2641
EHDAA:6485
EMAPA:16894
EV:0100164
FBbt:00005095
FMA:50801
GAID:571
HBA:4005
MA:0000168
MAT:0000098
MBA:8
MBA:997
MESH:D001921
MIAA:0000098
NCIT:C12439
OpenCyc:Mx4rvVjT65wpEbGdrcN5Y29ycA
PBA:3999
TAO:0000008
UMLS:C0006104
UMLS:C1269537
VHOG:0000157
XAO:0000010
ZFA:0000008
galen:Brain
http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=21
uberon
encephalon
suprasegmental levels of nervous system
suprasegmental structures
synganglion
the brain
UBERON:0000955
brain
GO
FMA
Bgee:AN
The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP].
Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO]
2012-08-14
TAO:0000008
TAO
ZFIN:curator
Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO]
2012-06-20
AAO:0010478
AAO
AAO:BJB
The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO)
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG]
2012-09-17
VHOG:0000157
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165
UMLS:C0006104
BIRNLEX:796
UMLS:C0006104
ncithesaurus:Brain
UMLS:C1269537
BIRNLEX:796
http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=21
BIRNLEX:796
encephalon
BTO:0000142
suprasegmental levels of nervous system
NeuroNames:21
suprasegmental structures
NeuroNames:21
the brain
NeuroNames:21
the transparent anterior portion of the fibrous coat of the eye that serves as the chief refractory structure
corneal
Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals. In fish, and aquatic vertebrates in general, the cornea plays no role in focusing light, since it has virtually the same refractive index as water
AAO:0010344
BTO:0000286
CALOHA:TS-0171
EFO:0000377
EHDAA2:0000316
EHDAA:10199
EMAPA:17161
EV:0100341
FMA:58238
GAID:892
MA:0000266
MESH:D003315
NCIT:C12342
OpenCyc:Mx4rvViBa5wpEbGdrcN5Y29ycA
TAO:0000640
UMLS:C0010031
VHOG:0000164
XAO:0000180
ZFA:0000640
cornea of camera-type eye
uberon
corneas
tunica cornea
UBERON:0000964
cornea
http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg
XAO
MA
MA
FMA-isa
definitional
the transparent anterior portion of the fibrous coat of the eye that serves as the chief refractory structure
ISBN:0-683-40008-8
MESH:A09.371.060.217
MP:0001312
UMLS:C0010031
ncithesaurus:Cornea
cornea of camera-type eye
GO:0061303
corneas
ZFA:0000640
Transparent part of camera-type eye that helps to refract light to be focused on the retina.
The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]
This class excludes compound eye corneal lenses.
AAO:0010348
BTO:0000723
CALOHA:TS-0545
EHDAA:9057
EMAPA:17838
EV:0100343
FMA:58241
MA:0000275
MAT:0000141
MESH:A09.371.509
MIAA:0000141
NCIT:C12743
OpenCyc:Mx4rvVj0fZwpEbGdrcN5Y29ycA
RETIRED_EHDAA2:0000975
TAO:0000035
UMLS:C0023317
VHOG:0000169
XAO:0000008
ZFA:0000035
camera-type eye lens
eye lens
lens
lens crystallina
uberon
crystalline lens
lenses
ocular lens
UBERON:0000965
The lens is avascular and nourished by diffusion from the aqueous and vitreous
lens of camera-type eye
Transparent part of camera-type eye that helps to refract light to be focused on the retina.
The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]
2012-09-17
VHOG:0000169
VHOG
DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)
UMLS:C0023317
ncithesaurus:Crystalline_Lens
camera-type eye lens
GO:0002088
eye lens
lens
lens crystallina
crystalline lens
BTO:0000723
lenses
ZFA:0000035
ocular lens
BTO:0000723
The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates.
The portion of the eye developing from the optic primordium and including the neural retina and the retinal pigment layer. Kimmel et al, 1995.[TAO]
The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]
retinal
AAO:0010352
BAMS:R
BIRNLEX:1153
BTO:0001175
CALOHA:TS-0865
EFO:0000832
EHDAA2:0001627
EHDAA:4757
EMAPA:17168
EV:0100348
FMA:58301
GAID:755
MA:0000276
MAT:0000142
MBA:304325711
MESH:D012160
MIAA:0000142
NCIT:C12343
NIFSTD_RETIRED:birnlex_1156
OpenCyc:Mx4rvViTfpwpEbGdrcN5Y29ycA
TAO:0000152
UMLS:C0035298
UMLS:C1278894
VHOG:0000229
XAO:0000009
ZFA:0000152
inner layer of eyeball
retina of camera-type eye
tunica interna of eyeball
uberon
Netzhaut
retinas
UBERON:0000966
Currently this class encompasses only verteberate AOs but could in theory also include cephalopod - we may want to make a more specific class for vertebrate retina. note that this class excludes ommatidial retinas, as the retina must be part of an eyeball. Use the parent class photoreceptor array / light-sensitive tissue for arthropods
retina
http://upload.wikimedia.org/wikipedia/commons/e/ed/Human_eye_cross-sectional_view_grayscale.png
EHDAA2
The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates.
ZFIN:curator
The portion of the eye developing from the optic primordium and including the neural retina and the retinal pigment layer. Kimmel et al, 1995.[TAO]
2012-08-14
TAO:0000152
TAO
ZFIN:curator
The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]
2012-09-17
VHOG:0000229
VHOG
DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)
UMLS:C0035298
BIRNLEX:1153
UMLS:C0035298
ncithesaurus:Retina
UMLS:C1278894
BIRNLEX:1153
retina of camera-type eye
GO:0060041
Netzhaut
BTO:0001175
retinas
ZFA:0000152
An organ that detects light.
This class encompasses a variety of light-detecting structures from different phyla with no implication of homology, from the compound insect eye to the vertebrate camera-type eye (distinct classes are provided for each)
ocular
optic
Note that whilst this is classified as an organ, it is in fact more of a unit composed of different structures: in Drosophila, it includes the interommatidial bristle as a part; we consider here the vertebrate eye to include the eyeball/eye proper as a part, with the eye having as parts (when present): eyelids, conjuctiva,
BILA:0000017
BTO:0000439
CALOHA:TS-0309
EFO:0000827
EV:0100336
FBbt:00005162
GAID:69
MAT:0000140
MESH:D005123
MIAA:0000140
OpenCyc:Mx4rvViTvpwpEbGdrcN5Y29ycA
uberon
light-detecting organ
visual apparatus
UBERON:0000970
eye
An organ that detects light.
visual apparatus
EV:0100336
An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column.
true necks are considered to be present when the pectoral girdle is separate from the skull - Tiktaalik is the earliest known fish to have a true neck.
cervical
AEO:0000108
BTO:0000420
CALOHA:TS-2045
EFO:0000967
EHDAA2:0003108
EMAPA:35587
FMA:7155
GAID:86
MA:0000024
MAT:0000297
MESH:D009333
MIAA:0000297
NCIT:C13063
OpenCyc:Mx4rvVjLF5wpEbGdrcN5Y29ycA
UMLS:C0027530
galen:Neck
uberon
collum
neck (volume)
UBERON:0000974
neck
Female:neck.jpg
An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column.
ISBN:9780674021839
UMLS:C0027530
ncithesaurus:Neck
collum
neck (volume)
FMA:7155
Anatomical cluster that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO].
Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO]
Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO]
articulation
joint
AEO:0000182
BTO:0001686
CALOHA:TS-2023
EFO:0000948
EMAPA:35456
FMA:7490
GAID:102
MA:0000319
MAT:0000188
MESH:D007596
MIAA:0000188
NCIT:C13044
OpenCyc:Mx4rvVjjdpwpEbGdrcN5Y29ycA
RETIRED_EHDAA2:0003182
TAO:0000367
UMLS:C0022417
VHOG:0001276
VSAO:0000101
XAO:0000171
ZFA:0001596
galen:Joint
uberon
articular joint
joints
UBERON:0000982
skeletal joint
Anatomical cluster that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO].
GO_REF:0000034
VSAO:0000101
Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO]
2012-08-14
VSAO:0000101
VSAO
PSPUB:0000170
Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO]
2012-08-14
TAO:0000367
TAO
TAO:pem
articulation
VSAO:0000101
joint
FMA:7490
VSAO:0000101
UMLS:C0022417
ncithesaurus:Joint
articular joint
BTO:0001686
joints
ZFA:0001596
Anatomical system that has as its parts the organs concerned with reproduction.
consider splitting genitalia from reproductive system
Anatomical system which consists of organs and tissues associated with sexual reproduction of the organism.[AAO]
Arguably, one of the most important aspects of urbilaterian organogenesis would have been gonadogenesis, since Urbilateria must have successfully generated gametes and developed a strategy for extrusion and fertilization, in order to be the ancestor of all living Bilateria.[well established][VHOG]
AAO:0010258
BILA:0000103
BTO:0000081
CALOHA:TS-1318
EFO:0000809
EHDAA2:0001603
EHDAA:5923
EMAPA:17381
EV:0100100
FBbt:00004857
FMA:7160
GAID:363
HAO:0000374
HAO:0000895
MA:0000326
MIAA:0000305
NCIT:C12841
OpenCyc:Mx4rvVja4ZwpEbGdrcN5Y29ycA
TAO:0000632
UMLS:C1261210
VHOG:0000182
WBbt:0005747
XAO:0000142
ZFA:0000632
uberon
Geschlechtsorgan
animal reproductive system
genital system
genital tract
genitalia
organa genitalia
reproductive tissue
reproductive tract
systemata genitalia
UBERON:0000990
reproductive system
http://upload.wikimedia.org/wikipedia/commons/5/52/Penis.svg
Anatomical system that has as its parts the organs concerned with reproduction.
Anatomical system which consists of organs and tissues associated with sexual reproduction of the organism.[AAO]
2012-06-20
AAO:0010258
AAO
AAO:BJB
Arguably, one of the most important aspects of urbilaterian organogenesis would have been gonadogenesis, since Urbilateria must have successfully generated gametes and developed a strategy for extrusion and fertilization, in order to be the ancestor of all living Bilateria.[well established][VHOG]
2012-09-17
VHOG:0000182
VHOG
PMID:21672850 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across Bilateria. Integrative and Comparative Biology (2007)
UMLS:C1261210
ncithesaurus:Reproductive_System
Geschlechtsorgan
BTO:0000081
animal reproductive system
BTO:0000081
genitalia
organa genitalia
BTO:0000081
reproductive tissue
BTO:0000081
systemata genitalia
Reproductive organ that produces and releases eggs (ovary) or sperm (testis).
Anatomical structure which produces gametes as well as certain sex hormones controlled by the pituitary gonadotropins.[AAO]
The part of the reproductive system that produces and releases eggs (ovary) or sperm (testis).[TAO]
Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved.[uncertain][VHOG]
gonadal
FMA xref is a 'general anatomical term'
AAO:0000213
BILA:0000123
BSA:0000079
BTO:0000534
EMAPA:17383
FBbt:00004858
FMA:18250
GAID:368
HAO:0000379
MA:0002420
MESH:D006066
NCIT:C12725
OpenCyc:Mx4rwQvdiZwpEbGdrcN5Y29ycA
TAO:0000413
UMLS:C0018067
VHOG:0000397
WBbt:0005175
XAO:0003146
ZFA:0000413
gonada
uberon
gonads
UBERON:0000991
gonad
Reproductive organ that produces and releases eggs (ovary) or sperm (testis).
ISBN:0140512888
ZFA:0000413
ZFIN:curator
Anatomical structure which produces gametes as well as certain sex hormones controlled by the pituitary gonadotropins.[AAO]
2012-06-20
AAO:0000213
AAO
AAO:BJB
The part of the reproductive system that produces and releases eggs (ovary) or sperm (testis).[TAO]
2012-08-14
TAO:0000413
TAO
ZFIN:curator
Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved.[uncertain][VHOG]
2012-09-17
VHOG:0000397
VHOG
DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T, Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009)
FMA xref is a 'general anatomical term'
FMA
UMLS:C0018067
ncithesaurus:Gonad
gonads
ZFA:0000413
A cuticular covering that is composed primarily of chitin. The main structural component of arthropod cuticle is a polysaccharide, chitin, composed of N-acetylglucosamine units, together with proteins and lipids[WP].
TODO - split from exoskeleton? Also: See above sf item to see if this belongs in GO
UBERON:FBbt_00004970
exoskeleton
EFO:0000944
FBbt:00004970
HAO:0000240
MAT:0000150
MIAA:0000150
OpenCyc:Mx4rvVkBTJwpEbGdrcN5Y29ycA
cuticle
uberon
arthropod cuticle
arthropod exoskeleton
insect cuticle
UBERON:0001001
chitin-based cuticle
A cuticular covering that is composed primarily of chitin. The main structural component of arthropod cuticle is a polysaccharide, chitin, composed of N-acetylglucosamine units, together with proteins and lipids[WP].
cuticle
FBbt:00004970
arthropod exoskeleton
tough but flexible, non-mineral outer coverings of an organism, or parts of an organism, that provide protection. Cuticles are non-homologous, differing in their origin, structure and chemical composition[WP].
TODO - check cuticle vs exoskeleton. Note that GO has a very generic definition of cuticle. See also arthropod-anatomy ontology. Note in ncit Cuticle is a plant part
cuticular
BTO:0001600
uberon
cuticula
cuticular exoskeleton
UBERON:0001002
cuticle
tough but flexible, non-mineral outer coverings of an organism, or parts of an organism, that provide protection. Cuticles are non-homologous, differing in their origin, structure and chemical composition[WP].
cuticula
BTO:0001600
The outer epithelial layer of the skin that is superficial to the dermis.
A cellular, multilayered epithelium derived from the ectoderm. Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. Le Guellec et al, 2004.[TAO]
The outer epithelial layer of the external integument of the body that is derived from the embryonic epiblast.[AAO]
relationship loss: subclass external integument structures (AAO:0000961)[AAO]
(...) outer epithelia in all metazoan animals are homologous. (...) The ancestor of all metazoans likely had an epidermis with a basal extracellular matrix (ECM), an apical extracellular glycocalyx, and one cilium with a striated rootlet per cell.[well established][VHOG]
epidermal
Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. In terrestrial vertebrates the epidermis often forms an outer keratinized or cornified layer, the stratum corneum. Interaction between the epideris and dermis gives rise to feathers (birds), hair and mammary glands (mammals), teeth and scales (placoid: chondrichthyans; cosmoids, ganoid, cycloid in bony fishes).
epidermis
skin
AAO:0000143
BTO:0000404
CALOHA:TS-0283
EFO:0000954
EMAPA:17528
EV:0100153
FMA:70596
GAID:932
MA:0000153
MAT:0000154
MESH:D004817
MIAA:0000154
NCIT:C12708
TAO:0000105
UMLS:C0014520
VHOG:0000077
XAO:0000028
ZFA:0000105
vertebrate epidermis
uberon
UBERON:0001003
skin epidermis
The outer epithelial layer of the skin that is superficial to the dermis.
ISBN:0073040584
A cellular, multilayered epithelium derived from the ectoderm. Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. Le Guellec et al, 2004.[TAO]
2012-08-14
TAO:0000105
TAO
ZFIN:curator
The outer epithelial layer of the external integument of the body that is derived from the embryonic epiblast.[AAO]
2012-06-20
AAO:0000143
AAO
AAO:BJB
relationship loss: subclass external integument structures (AAO:0000961)[AAO]
2012-06-20
AAO:0000143
AAO
(...) outer epithelia in all metazoan animals are homologous. (...) The ancestor of all metazoans likely had an epidermis with a basal extracellular matrix (ECM), an apical extracellular glycocalyx, and one cilium with a striated rootlet per cell.[well established][VHOG]
2012-09-17
VHOG:0000077
VHOG
ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.71-72
UMLS:C0014520
ncithesaurus:Epidermis
Functional system which consists of structures involved in respiration.
The anatomical system in which the exchange of oxygen and carbon dioxide between the organism and its environment.[AAO]
There is no doubt that the primitive pattern of vertebrate air-breathing is the buccal pulse pump found in actinopterygian fishes.[well established][VHOG]
AAO:0000541
BTO:0000203
CALOHA:TS-1319
EFO:0000804
EHDAA2:0001604
EHDAA:2203
EMAPA:16727
EV:0100036
FMA:7158
GAID:78
MA:0000327
MAT:0000030
MESH:D012137
MIAA:0000030
NCIT:C12779
OpenCyc:Mx4rvVjzFJwpEbGdrcN5Y29ycA
TAO:0000272
UMLS:C0035237
VHOG:0000202
XAO:0000117
ZFA:0000272
apparatus respiratorius
respiratory system
uberon
Atmungssystem
apparatus respiratorius
systema respiratorium
UBERON:0001004
respiratory system
http://upload.wikimedia.org/wikipedia/commons/5/5e/Respiratory_system_complete_en.svg
Functional system which consists of structures involved in respiration.
The anatomical system in which the exchange of oxygen and carbon dioxide between the organism and its environment.[AAO]
2012-06-20
AAO:0000541
AAO
AAO:BJB
There is no doubt that the primitive pattern of vertebrate air-breathing is the buccal pulse pump found in actinopterygian fishes.[well established][VHOG]
2012-09-17
VHOG:0000202
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.599 and Figure 18-23
UMLS:C0035237
ncithesaurus:Respiratory_System
Atmungssystem
BTO:0000203
apparatus respiratorius
BTO:0000203
systema respiratorium
Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes.
An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO]
digestive
many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class
AAO:0000129
BILA:0000082
BTO:0000058
CALOHA:TS-1293
EFO:0000793
EV:0100056
FBbt:00005055
FMA:7152
GAID:278
MA:0002431
MAT:0000018
MESH:D004064
MIAA:0000018
TADS:0000170
TAO:0000339
WBbt:0005748
XAO:0000125
ZFA:0000339
galen:DigestiveSystem
ncithesaurus:Digestive_System
uberon
alimentary system
alimentary tract
gastrointestinal system
gut
UBERON:0001007
digestive system
Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes.
FB:gg
NLM:alimentary+system
An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO]
2012-06-20
AAO:0000129
AAO
AAO:BJB
many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class
MA
organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP].
the cardiovascular system and the lymphatic system are parts of the circulatory system
Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO]
We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG]
AAO:0000959
CALOHA:TS-2103
FBbt:00005057
OpenCyc:Mx4rvVjzG5wpEbGdrcN5Y29ycA
VHOG:0001248
uberon
systema cardiovasculare
UBERON:0001009
circulatory system
http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg
organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP].
WBbt coelomocyte currently classified as circulating cell
Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO]
2012-06-20
AAO:0000959
AAO
AAO:BJB
We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG]
2012-09-17
VHOG:0001248
VHOG
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.493
systema cardiovasculare
Portion of connective tissue composed of adipocytes enmeshed in areolar tissue
Connective tissue in which fat is stored.[TAO]
Tissue that contains adipocytes, used for cushioning, thermal insulation, lubrication (primarily in the pericardium) and energy storage.[AAO]
relationship loss: subclass connective tissue proper (AAO:0000099)[AAO]
Adipose tissue is unique to vertebrates. It is found in mostmammals, birds, reptiles and amphibians, and a variety is found in some species of fish. Furthermore, in insects the fat body found in larvae as well as in adults shares some homology with adipose tissue.[well established][VHOG]
adipose
In humans, adipose tissue is located beneath the skin (subcutaneous fat), around internal organs (visceral fat), in bone marrow (yellow bone marrow) and in breast tissue. Adipose tissue is found in specific locations, which are referred to as adipose depots. Adipose tissue contains several cell types, with the highest percentage of cells being adipocytes, which contain fat droplets. Other cell types include fibroblasts, macrophages, and endothelial cells. Adipose tissue contains many small blood vessels.; Mice have eight major adipose depots, four of which are within the abdominal cavity. The paired gonadal depots are attached to the uterus and ovaries in females and the epididymis and testes in males; the paired retroperitoneal depots are found along the dorsal wall of the abdomen, surrounding the kidney, and, when massive, extend into the pelvis. The mesenteric depot forms a glue-like web that supports the intestines, and the omental depot, which originates near the stomach and spleen, and, when massive, extends into the ventral abdomen.
in FMA this is dense irregular connective tissue
AAO:0000001
AEO:000020
BTO:0001487
CALOHA:TS-0013
EFO:0000790
EHDAA2:0003120
EMAPA:35112
EV:0100381
FMA:20110
GAID:920
MA:0000009
MAT:0000015
MESH:D000273
MIAA:0000015
NCIT:C12472
OpenCyc:Mx4rvVjc_ZwpEbGdrcN5Y29ycA
TAO:0002134
UMLS:C0001527
VHOG:0001284
XAO:0003049
ZFA:0005345
galen:FattyTissue
fat
fat tissue
fatty tissue
uberon
adipose
bodyfat
fatty depot
UBERON:0001013
adipose tissue
FMA
Portion of connective tissue composed of adipocytes enmeshed in areolar tissue
MESH:A10.165.114
MGI:cwg
MP:0000003
Connective tissue in which fat is stored.[TAO]
2012-08-14
TAO:0002134
TAO
ZFIN:curator
Tissue that contains adipocytes, used for cushioning, thermal insulation, lubrication (primarily in the pericardium) and energy storage.[AAO]
2012-06-20
AAO:0000001
AAO
AAO:LAP
relationship loss: subclass connective tissue proper (AAO:0000099)[AAO]
2012-06-20
AAO:0000001
AAO
Adipose tissue is unique to vertebrates. It is found in mostmammals, birds, reptiles and amphibians, and a variety is found in some species of fish. Furthermore, in insects the fat body found in larvae as well as in adults shares some homology with adipose tissue.[well established][VHOG]
2012-09-17
VHOG:0001284
VHOG
DOI:10.1017/S0029665107005423 Haugen F, Drevon CA, The interplay between nutrients and the adipose tissue. The Proceedings of the Nutrition Society (2007)
in FMA this is dense irregular connective tissue
FMA
UMLS:C0001527
ncithesaurus:Adipose_Tissue
fat
MA:0000009
adipose
BTO:0001487
bodyfat
BTO:0001487
A subdivision of the muscular system corresponding to a subdisivision of an organism.
In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here.
AAO:0011066
BTO:0000887
EFO:0001949
EMAPA:32715
EMAPA:35577
FMA:32558
MA:0000165
NCIT:C13056
OpenCyc:Mx4rvVjmr5wpEbGdrcN5Y29ycA
TAO:0000548
UMLS:C0026845
VSAO:0005038
WBbt:0005737
ZFA:0000548
muscle group
muscles set
musculature
musculi
set of muscles
set of skeletal muscles
uberon
muscle system
muscles
musculature system
UBERON:0001015
musculature
http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png
A subdivision of the muscular system corresponding to a subdisivision of an organism.
In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here.
FMA
UMLS:C0026845
ncithesaurus:Muscle
musculi
FMA:32558
FMA:TA
set of muscles
FMA:32558
set of skeletal muscles
MA:0000165
The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO].
A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO]
Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]
Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]
nervous
neural
AAO:0000324
BILA:0000079
BIRNLEX:844
BTO:0001484
CALOHA:TS-1313
EFO:0000802
EHDAA2:0001246
EHDAA:826
EMAPA:16469
EV:0100162
FBbt:00005093
FMA:7157
GAID:466
MA:0000016
MAT:0000026
MESH:D009420
MIAA:0000026
NCIT:C12755
OpenCyc:Mx4rvViT_pwpEbGdrcN5Y29ycA
TAO:0000396
UMLS:C0027763
VHOG:0000402
WBbt:0005735
XAO:0000177
ZFA:0000396
neurological system
nerve net
uberon
systema nervosum
UBERON:0001016
nervous system
http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg
http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png
Bgee:AN
The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO].
BIRNLEX:844
ISBN:0-14-051288-8
ISBN:3110148986
NLM:nervous+system
WB:rynl
ZFIN:curator
A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO]
2012-08-14
TAO:0000396
TAO
ZFIN:curator
Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]
2012-06-20
AAO:0000324
AAO
AAO:BJB
Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]
2012-09-17
VHOG:0000402
VHOG
ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.117
UMLS:C0027763
ncithesaurus:Nervous_System
neurological system
GO:0050877
nerve net
systema nervosum
The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord.
Part of the nervous system which includes the brain and spinal cord.[AAO]
The brain and spinal cord. Kimmel et al, 1995.[TAO]
The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO).
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG]
AAO:0000090
BAMS:CNS
BILA:0000080
BIRNLEX:1099
BTO:0000227
CALOHA:TS-0150
EFO:0000908
EHDAA2:0000225
EHDAA:828
EMAPA:16470
EMAPA:16754
EV:0100163
FBbt:00005094
FMA:55675
GAID:570
MA:0000167
MAT:0000457
MESH:D002490
NCIT:C12438
OpenCyc:Mx4rvzYt3pwpEbGdrcN5Y29ycA
TAO:0000012
UMLS:C0927232
VHOG:0000293
XAO:0000215
ZFA:0000012
CNS
systema nervosum centrale
cerebrospinal axis
uberon
neuraxis
UBERON:0001017
central nervous system
FBbt
cjm
Bgee:AN
The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord.
GO:0021551
Part of the nervous system which includes the brain and spinal cord.[AAO]
2012-06-20
AAO:0000090
AAO
AAO:BJB
The brain and spinal cord. Kimmel et al, 1995.[TAO]
2012-08-14
TAO:0000012
TAO
ZFIN:curator
The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO).
BIRNLEX:1099
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG]
2012-09-17
VHOG:0000293
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 (reference 1), ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 (reference 2), DOI:10.1016/j.cell.2007.02.040 Denes AS, Jekely G, Steinmetz PRH, Raible F, Snyman H, Prud'homme B, Ferrier DEK, Balavoine G and Arendt D, Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in Bilateria. Cell (2007) (reference 3)
UMLS:C0927232
BIRNLEX:1099
UMLS:C0927232
ncithesaurus:Central_Nervous_System
CNS
systema nervosum centrale
FMA:55675
FMA:TA
cerebrospinal axis
FMA:55675
neuraxis
FMA:55675
Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information.
An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG]
note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs
AAO:0000555
BAMS:SEN
BILA:0000099
EFO:0000805
EHDAA2:0003094
EMAPA:16192
FBbt:00007692
FMA:75259
MA:0002442
MAT:0000031
MIAA:0000031
NLXANAT:090816
TAO:0000282
VHOG:0001674
XAO:0003194
ZFA:0000282
organa sensuum
sense organ subsystem
sense organs
sense organs set
sensory subsystem
sensory systems
uberon
organa sensuum
sensory organ system
set of sense organs
UBERON:0001032
sensory system
http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png
Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information.
An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG]
2012-09-17
VHOG:0001674
VHOG
DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)
organa sensuum
FMA:75259
FMA:TA
sense organs
FMA:75259
sense organs set
FMA:75259
sensory systems
TAO:0000282
organa sensuum
set of sense organs
FMA:75259
Anterior subdivision of a digestive tract.
Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. In vertebrates the term may refer to a developmental structure
The anterior portion of the primitive digestive tube of the embryo that lies cephalic to the junction of the yolk stalk, consists of endodermal tissue, and gives rise to the the pharynx, lower respiratory system, esophagus, stomach, duodenum proximal to the biliary tract, liver, pancreas, biliary tract, and gall bladder.
The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]
AAO:0011042
BILA:0000085
BTO:0000507
EHDAA2:0000557
EHDAA:520
EMAPA:16548
FBbt:00005379
FMA:45616
MA:0001526
NCIT:C34180
TGMA:0001014
UMLS:C0231051
VHOG:0000285
XAO:0000232
uberon
praeenteron
proenteron
UBERON:0001041
foregut
http://upload.wikimedia.org/wikipedia/commons/9/9a/Gray27.png
Anterior subdivision of a digestive tract.
The anterior portion of the primitive digestive tube of the embryo that lies cephalic to the junction of the yolk stalk, consists of endodermal tissue, and gives rise to the the pharynx, lower respiratory system, esophagus, stomach, duodenum proximal to the biliary tract, liver, pancreas, biliary tract, and gall bladder.
MP:0000474
The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]
2012-09-17
VHOG:0000285
VHOG
ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11
UMLS:C0231051
ncithesaurus:Foregut
praeenteron
proenteron
A portion of the respiratory and digestive tracts; its distal limit is the superior part of the esophagus and it connects the nasal and oral cavities with the esophagus and larynx; it contains the valleculae and the pyriform recesses; its upper limits are the nasal cavity and cranial base.[FEED].
A funnel-shaped fibromuscular tube that conducts food to the ESOPHAGUS, and air to the LARYNYX and LUNGS. It is located posterior to the NASAL CAVITY; ORAL CAVITY; and LARYNX, and extends from the SKULL BASE to the inferior border of the CRICOID CARTILAGE anteriorly and to the inferior border of the C6 vertebra posteriorly. It is divided into the NASOPHARYNX; OROPHARYNX; and HYPOPHARYNX (laryngopharynx)[MESH:A03.867].
Anatomical cavity bounded by the derivatives of the branchial arches.[AAO]
Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills. Kimmel et al, 1995.[TAO]
Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills[ZFA:0000056, ZFIN:ZDB-PUB-961014-576].
The portion of the alimentary canal between the mouth and the oesophagus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: develops_from respiratory system (UBERON:0001004)[AAO]
relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: part_of respiratory system (UBERON:0001004)[AAO]
(...) the earliest vertebrates possessed unjointed internal and external branchial arches, and musculature encircling the pharynx.[well established][VHOG]
MA/FMA pharynx not part of digestive/alimentary system, we are consistent with this scheme
pharynx
AAO:0000967
BTO:0001049
CALOHA:TS-0785
EFO:0000836
EHDAA2:0001458
EHDAA:2947
EMAPA:16706
EV:0100065
FMA:46688
GAID:155
MA:0000432
MESH:A03.867
NCIT:C12425
OpenCyc:Mx4rvViv7ZwpEbGdrcN5Y29ycA
TAO:0000056
UMLS:C0031354
VHOG:0000462
XAO:0003227
ZFA:0000056
galen:Pharynx
uberon
UBERON:0001042
Consider generalizing to deuterostome pharynx
chordate pharynx
EHDAA2
A portion of the respiratory and digestive tracts; its distal limit is the superior part of the esophagus and it connects the nasal and oral cavities with the esophagus and larynx; it contains the valleculae and the pyriform recesses; its upper limits are the nasal cavity and cranial base.[FEED].
A funnel-shaped fibromuscular tube that conducts food to the ESOPHAGUS, and air to the LARYNYX and LUNGS. It is located posterior to the NASAL CAVITY; ORAL CAVITY; and LARYNX, and extends from the SKULL BASE to the inferior border of the CRICOID CARTILAGE anteriorly and to the inferior border of the C6 vertebra posteriorly. It is divided into the NASOPHARYNX; OROPHARYNX; and HYPOPHARYNX (laryngopharynx)[MESH:A03.867].
MESH:A03.867
Anatomical cavity bounded by the derivatives of the branchial arches.[AAO]
2012-06-20
AAO:0000967
AAO
AAO:EJS
Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills. Kimmel et al, 1995.[TAO]
2012-08-14
TAO:0000056
TAO
ZFIN:curator
Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills[ZFA:0000056, ZFIN:ZDB-PUB-961014-576].
ZFIN:ZDB-PUB-961014-576
The portion of the alimentary canal between the mouth and the oesophagus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
2012-09-17
VHOG:0000462
VHOG
relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: develops_from respiratory system (UBERON:0001004)[AAO]
2012-06-20
AAO:0000967
AAO
relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: part_of respiratory system (UBERON:0001004)[AAO]
2012-06-20
AAO:0000967
AAO
(...) the earliest vertebrates possessed unjointed internal and external branchial arches, and musculature encircling the pharynx.[well established][VHOG]
2012-09-17
VHOG:0000462
VHOG
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) Box essay 13.1 and Box figure I, p.502-503
MA/FMA pharynx not part of digestive/alimentary system, we are consistent with this scheme
MA
pharynx
FMA:46688
UMLS:C0031354
ncithesaurus:Pharynx
Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt, Hartenstein, V. (2004)].
AEO:0000171
BTO:0001886
EFO:0001652
EHDAA2:0003171
FBbt:00005495
FMA:86589
MAT:0000482
NCIT:C34275
UMLS:C0678727
XAO:0003043
uberon
bud
future organ
placode
primordia
rudiment
UBERON:0001048
primordium
EHDAA2
Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt, Hartenstein, V. (2004)].
BTO:0001886
FB:DJS
FB:FBrf0089570
UMLS:C0678727
ncithesaurus:Primordium
placode
FBbt:00005495
primordia
XAO:0003043
In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted].
Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO]
The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG]
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]
The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium
AAO:0010617
BTO:0001057
CALOHA:TS-2371
DHBA:10154
EHDAA2:0001254
EHDAA:2869
EHDAA:908
EMAPA:16164
EMAPA:16757
FMA:293882
MAT:0000069
MIAA:0000069
NCIT:C34226
TAO:0001135
UMLS:C0231024
VHOG:0000307
XAO:0003204
ZFA:0001135
uberon
neural primordium
presumptive central nervous system
tubus neuralis
UBERON:0001049
neural tube
http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png
EHDAA2
In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted].
Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO]
2012-06-20
AAO:0010617
AAO
AAO:JOR
The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG]
2012-09-17
VHOG:0000307
VHOG
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]
2012-09-17
VHOG:0000307
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28
The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium
GO:0021915
UMLS:C0231024
ncithesaurus:Neural_Tube
tubus neuralis
Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
AAO:0010841
AEO:0000000
BILA:0000000
BIRNLEX:6
CARO:0000000
EHDAA2:0002229
FBbt:10000000
FBbt_root:00000000
FMA:62955
HAO:0000000
MA:0000001
NCIT:C12219
TAO:0100000
TGMA:0001822
UMLS:C1515976
WBbt:0000100
XAO:0000000
ZFA:0100000
uberon
UBERON:0001062
anatomical entity
Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
FMA:62955
UMLS:C1515976
ncithesaurus:Anatomic_Structure_System_or_Substance
A zone of skin that is part of a back [Automatically generated definition].
TODO - distinguish between entire skin of region and arbitrary zone of skin on region
EMAPA:36392
FMA:10462
FMA:22985
MA:0000498
back skin
back zone of skin
skin, dorsal region
zone of skin of back
uberon
UBERON:0001068
skin of back
MA
MA
A zone of skin that is part of a back [Automatically generated definition].
OBOL:automatic
back zone of skin
OBOL:automatic
skin, dorsal region
zone of skin of back
OBOL:automatic
It ascends beneath the anterior margin of the trapezius, distributing branches to it, and to the neighboring muscles and lymph glands in the neck, and anastomosing with the superficial branch of the descending branch of the occipital artery.
EMAPA:37117
FMA:10665
MA:0002052
NCIT:C53005
UMLS:C0226271
superficial branch of transverse cervical artery
uberon
UBERON:0001071
The transverse cervical artery splits into two branches, a superficial one and a deep one[WP]
superficial cervical artery
It ascends beneath the anterior margin of the trapezius, distributing branches to it, and to the neighboring muscles and lymph glands in the neck, and anastomosing with the superficial branch of the descending branch of the occipital artery.
EMAPA:37117
MA:th
UMLS:C0226271
ncithesaurus:Superficial_Cervical_Artery
superficial branch of transverse cervical artery
A potential space between the visceral and parietal layers of the pericardium.
Anatomical space in which the heart is located and is surrounded by the pericardium.[TAO]
In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart (of other tetrapods) is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG]
check ZFA, should actually be thoracic cavity. Note that Hyman defines the cavity as the space between the heart and the sac (but defines the sac as parietal)
BSA:0000091
EHDAA2:0001434
EMAPA:16131
EMAPA:16132
FMA:11350
MA:0000053
NCIT:C38662
TAO:0002220
UMLS:C0225972
VHOG:0000556
ZFA:0001655
galen:PericardialSpace
cavity of pericardial sac
pericardial space
uberon
cavitas pericardiaca
UBERON:0001074
pericardial cavity
MA
FMA
Wikipedia
A potential space between the visceral and parietal layers of the pericardium.
Anatomical space in which the heart is located and is surrounded by the pericardium.[TAO]
2012-08-14
TAO:0002220
TAO
ZFIN:curator
In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart (of other tetrapods) is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG]
2012-09-17
VHOG:0000556
VHOG
ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206
check ZFA, should actually be thoracic cavity. Note that Hyman defines the cavity as the space between the heart and the sac (but defines the sac as parietal)
ZFA
UMLS:C0225972
ncithesaurus:Pericardial_Cavity
pericardial space
cavitas pericardiaca
Endocardium that is part of the cardiac ventricle.
EMAPA:32747
FMA:12148
MA:0000079
TAO:0002247
VHOG:0000607
ZFA:0001615
cardiac ventricle endocardium
endocardium of cardiac ventricle
endocardium of heart ventricle
endocardium of lower chamber of heart
endocardium of ventricle of heart
heart ventricle endocardium
lower chamber of heart endocardium
ventricle endocardium
ventricle of heart endocardium
ventricular endocardium
uberon
ventricle endocardial tissue
UBERON:0001081
endocardium of ventricle
Endocardium that is part of the cardiac ventricle.
ZFIN:curator
cardiac ventricle endocardium
OBOL:automatic
endocardium of cardiac ventricle
OBOL:automatic
endocardium of heart ventricle
OBOL:automatic
endocardium of lower chamber of heart
OBOL:automatic
endocardium of ventricle of heart
OBOL:automatic
heart ventricle endocardium
OBOL:automatic
lower chamber of heart endocardium
OBOL:automatic
ventricle of heart endocardium
OBOL:automatic
ventricle endocardial tissue
VHOG:0000607
An epicardial layer that lines a cardiac ventricle
The external layer of the ventricle bounding the ventricular myocardium. It is formed by a single layer of mesothelial cells supported by a basal lamina, and imbricated with collagen, fibroblasts, and vascular structures in the subepicardial space. Hu et al. 2001.[TAO]
FMA:12150
TAO:0005058
ZFA:0005058
cardiac ventricle epicardium
ventricular epicardium
uberon
UBERON:0001082
epicardium of ventricle
An epicardial layer that lines a cardiac ventricle
The external layer of the ventricle bounding the ventricular myocardium. It is formed by a single layer of mesothelial cells supported by a basal lamina, and imbricated with collagen, fibroblasts, and vascular structures in the subepicardial space. Hu et al. 2001.[TAO]
2012-08-14
TAO:0005058
TAO
ZFIN:curator
cardiac ventricle epicardium
OBOL:automatic
Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer.
Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer Hu et al. 2001.[TAO]
As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[uncertain][VHOG]
EFO:0003088
EMAPA:32748
FMA:12151
MA:0000082
TAO:0005061
VHOG:0000604
ZFA:0005061
ventricle myocardium
ventricular myocardium
uberon
ventricle cardiac muscle
UBERON:0001083
myocardium of ventricle
Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer.
ZFIN:curator
Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer Hu et al. 2001.[TAO]
2012-08-14
TAO:0005061
TAO
ZFIN:curator
As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[uncertain][VHOG]
2012-09-17
VHOG:0000604
VHOG
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481
ventricle cardiac muscle
VHOG:0000604
A zone of skin that is part of a head [Automatically generated definition].
TODO - distinguish between entire skin of region and arbitrary zone of skin on region
FMA:12166
FMA:24756
MA:0000582
NCIT:C52757
UMLS:C0205029
adult head zone of skin
head skin
head zone of skin
zone of skin of adult head
zone of skin of head
uberon
UBERON:0001084
skin of head
A zone of skin that is part of a head [Automatically generated definition].
OBOL:automatic
UMLS:C0205029
ncithesaurus:Head_Skin
adult head zone of skin
OBOL:automatic
head zone of skin
OBOL:automatic
zone of skin of adult head
OBOL:automatic
zone of skin of head
OBOL:automatic
A zone of skin that is part of a trunk [Automatically generated definition].
TODO - distinguish between entire skin of region and arbitrary zone of skin on region
EMAPA:37278
FMA:12167
FMA:23093
MA:0000517
NCIT:C12295
UMLS:C0205031
torso zone of skin
trunk skin
trunk zone of skin
zone of skin of torso
zone of skin of trunk
uberon
UBERON:0001085
skin of trunk
A zone of skin that is part of a trunk [Automatically generated definition].
OBOL:automatic
EMAPA:37278
MA:th
UMLS:C0205031
ncithesaurus:Skin_of_the_Trunk
torso zone of skin
OBOL:automatic
trunk zone of skin
OBOL:automatic
zone of skin of torso
OBOL:automatic
zone of skin of trunk
OBOL:automatic
Joint fluid is a transudate of plasma that is actively secreted by synovial cells.
Portion of organism substance that is a clear fluid that occupies the space in synovial joints.[TAO]
It provides nutrients and lubrication for articular cartilage
The fluid contains hyaluronan secreted by fibroblast-like cells in the synovial membrane, lubricin (proteoglycan 4; PRG4) secreted by the surface chondrocytes of the articular cartilage and interstitial fluid filtered from the blood plasma
BTO:0001339
CALOHA:TS-0996
ENVO:02000039
FMA:12277
GAID:265
MA:0002544
MESH:D013582
NCIT:C33718
TAO:0005154
UMLS:C0039097
ZFA:0005154
galen:SynovialFluid
joint fluid
uberon
UBERON:0001090
synovial fluid
FMA
Joint fluid is a transudate of plasma that is actively secreted by synovial cells.
Portion of organism substance that is a clear fluid that occupies the space in synovial joints.[TAO]
2012-08-14
TAO:0005154
TAO
ZFIN:curator
UMLS:C0039097
ncithesaurus:Synovial_Fluid
joint fluid
Muscle tissue composed of cardiac muscle cells, forming the muscles of the heart[ZFA,modified].
check relationship with myocardium. part_of in MA - but we also have a more specific class 'cardiac muscle tissue of myocardium'. Check ncit
UBERON:0007096
AAO:0010245
AEO:0000142
BILA:0000134
BTO:0000199
CALOHA:TS-0440
EHDAA2:0003142
EMAPA:32688
FMA:14068
TAO:0005280
ZFA:0005280
galen:CardiacMuscle
galen:CardiacMuscleTissue
ncithesaurus:Heart_Muscle
cardiac muscle
cardiac muscle muscle tissue
cardiac muscle textus muscularis
heart muscle muscle tissue
heart muscle textus muscularis
heart myocardium muscle tissue
heart myocardium textus muscularis
muscle of heart muscle tissue
muscle of heart textus muscularis
muscle tissue of cardiac muscle
muscle tissue of heart muscle
muscle tissue of heart myocardium
muscle tissue of muscle of heart
muscle tissue of myocardium
myocardium muscle tissue
myocardium textus muscularis
textus muscularis of cardiac muscle
textus muscularis of heart muscle
textus muscularis of heart myocardium
textus muscularis of muscle of heart
textus muscularis of myocardium
uberon
cardiac musculature
UBERON:0001133
cardiac muscle tissue
ZFA
Muscle tissue composed of cardiac muscle cells, forming the muscles of the heart[ZFA,modified].
ZFA:0005280
cardiac muscle muscle tissue
OBOL:automatic
cardiac muscle textus muscularis
OBOL:automatic
heart muscle muscle tissue
OBOL:automatic
heart muscle textus muscularis
OBOL:automatic
heart myocardium muscle tissue
OBOL:automatic
heart myocardium textus muscularis
OBOL:automatic
muscle of heart muscle tissue
OBOL:automatic
muscle of heart textus muscularis
OBOL:automatic
muscle tissue of cardiac muscle
OBOL:automatic
muscle tissue of heart muscle
OBOL:automatic
muscle tissue of heart myocardium
OBOL:automatic
muscle tissue of muscle of heart
OBOL:automatic
muscle tissue of myocardium
OBOL:automatic
myocardium muscle tissue
OBOL:automatic
myocardium textus muscularis
OBOL:automatic
textus muscularis of cardiac muscle
OBOL:automatic
textus muscularis of heart muscle
OBOL:automatic
textus muscularis of heart myocardium
OBOL:automatic
textus muscularis of muscle of heart
OBOL:automatic
textus muscularis of myocardium
OBOL:automatic
cardiac musculature
BILA:0000134
Muscle tissue that consists primarily of skeletal muscle fibers.
TODO - add skeletal muscle organ? See GO:0060538 skeletal muscle organ development. Todo - group FBbt:00005073 - somatic muscle.
Muscle, composed of long cylindrical, multinucleated cells that attaches to the skeleton via tendons.[TAO]
Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm[FMA]
This result implies the following views in terms of evolutionary differentiation: (1) Arthropod striated muscle and vertebrate skeletal and cardiac muscles share a common ancestor. In other words, they did not evolve independently (...) (5) The divergence of vertebrate skeletal and cardiac muscles/vertebrate smooth muscle and nonmuscle is at least before that of vertebrates/arthropods. In other words, emergence of skeletal and cardiac musle type tissues preceded the vertebrate/arthropod divergence (ca. 700 MYA).[well established][VHOG]
skeletal muscle
EMAPA:32716
FMA:14069
MA:0002439
NCIT:C13050
UMLS:C0242692
uberon
skeletal muscle system
somatic muscle
UBERON:0001134
skeletal muscle tissue
Skeletal:muscle.jpg
Muscle tissue that consists primarily of skeletal muscle fibers.
Muscle, composed of long cylindrical, multinucleated cells that attaches to the skeleton via tendons.[TAO]
2012-08-14
TAO:0005277
TAO
ZFIN:curator
Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm[FMA]
FMA:14069
FMA
This result implies the following views in terms of evolutionary differentiation: (1) Arthropod striated muscle and vertebrate skeletal and cardiac muscles share a common ancestor. In other words, they did not evolve independently (...) (5) The divergence of vertebrate skeletal and cardiac muscles/vertebrate smooth muscle and nonmuscle is at least before that of vertebrates/arthropods. In other words, emergence of skeletal and cardiac musle type tissues preceded the vertebrate/arthropod divergence (ca. 700 MYA).[well established][VHOG]
2012-09-17
VHOG:0000319
VHOG
PMID:10368962 Oota S, Saitou N, Phylogenetic relationship of muscle tissues deduced from superimposition of gene trees. Mol Biol Evol (1999)
UMLS:C0242692
ncithesaurus:Skeletal_Muscle_Tissue
skeletal muscle system
BTO:0001103
somatic muscle
BTO:0001103
Muscle tissue which is unstriated, composed primarily of smooth muscle fibers surrounded by a reticulum of collagen and elastic fibers. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length[GO].
A non-striated muscle that is composed of spindle-shaped cells. Smooth muscle usually is organized into sheets that line cavitated organs.[TAO]
Involuntary muscle tissue consisting of uninucleate spindle-shaped fibers.[AAO]
(...) the first bilateral animals possessed only smooth muscles with the molecular repertoire necessary to build a striated muscle. (...) it is more parsimonious to regard striated muscle cells as a sister cell type to the smooth muscle cells. In this scenario, striated and smooth muscles would have arisen in the stem lineage that led to the Nephrozoa (i.e. all Bilateria exclusive the acoelomorphs) (Hejnol et al., 2009), from an 'acoel-like' smooth muscle, by segregation and divergence of functions and through differential recruitment of additional genes[well established][VHOG]
GO uses visceral and smooth interchangeably. However visceral can also be used in the sense of the viscera. Many fly annotations to smooth muscle terms. If we want to be inclusive of insects have to have a general definition of tissue that includes cells.
AAO:0010244
AEO:0000141
BTO:0001260
CALOHA:TS-0943
EFO:0000889
EHDAA2:0003141
EMAPA:32717
EV:0100378
FBbt:00003525
FMA:14070
GAID:167
MA:0000166
MAT:0000303
MESH:D009130
MIAA:0000303
NCIT:C12437
OpenCyc:Mx4rvvSS3pwpEbGdrcN5Y29ycA
TAO:0005274
UMLS:C1267092
VHOG:0001246
WBbt:0005781
XAO:0000175
ZFA:0005274
galen:SmoothMuscle
galen:SmoothMuscleTissue
involuntary muscle
non-striated muscle
smooth muscle
textus muscularis nonstriatus
visceral muscle
visceral muscle tissue
uberon
textus muscularis levis; textus muscularis nonstriatus
UBERON:0001135
smooth muscle tissue
Glatte:Muskelzellen.jpg
Muscle tissue which is unstriated, composed primarily of smooth muscle fibers surrounded by a reticulum of collagen and elastic fibers. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length[GO].
GO:0006939
A non-striated muscle that is composed of spindle-shaped cells. Smooth muscle usually is organized into sheets that line cavitated organs.[TAO]
2012-08-14
TAO:0005274
TAO
ZFIN:curator
Involuntary muscle tissue consisting of uninucleate spindle-shaped fibers.[AAO]
2012-06-20
AAO:0010244
AAO
AAO:CAM
(...) the first bilateral animals possessed only smooth muscles with the molecular repertoire necessary to build a striated muscle. (...) it is more parsimonious to regard striated muscle cells as a sister cell type to the smooth muscle cells. In this scenario, striated and smooth muscles would have arisen in the stem lineage that led to the Nephrozoa (i.e. all Bilateria exclusive the acoelomorphs) (Hejnol et al., 2009), from an 'acoel-like' smooth muscle, by segregation and divergence of functions and through differential recruitment of additional genes[well established][VHOG]
2012-09-17
VHOG:0001246
VHOG
DOI:10.1002/jez.b.21416 Chiodin M, Achatz JG, Wanninger A, Martinez P, Molecular architecture of muscles in an acoel and its evolutionary implications. Journal of Experimental Zoology (2011)
UMLS:C1267092
ncithesaurus:Smooth_Muscle_Tissue
textus muscularis nonstriatus
FMA:14070
FMA:TA
visceral muscle
visceral muscle tissue
textus muscularis levis; textus muscularis nonstriatus
Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. Wikipedia: The mesothelium is a membrane that forms the lining of several body cavities: the pleura (thoracal cavity), peritoneum (abdominal cavity including the mesentery) and pericardium (heart sac). Mesothelial tissue also surrounds the male internal reproductive organs (the tunica vaginalis testis) and covers the internal reproductive organs of women (the tunica serosa uteri).
AEO:0000111
BTO:0002422
CALOHA:TS-1183
EHDAA2_RETIRED:0003111
EHDAA:2331
EHDAA:2349
EHDAA:295
EHDAA:6073
EHDAA:640
EHDAA:646
EMAPA:32856
FMA:14074
MA:0000565
NCIT:C33105
UMLS:C0086610
uberon
UBERON:0001136
mesothelium
http://upload.wikimedia.org/wikipedia/commons/2/25/Mesothelium_peritoneal_wash_high_mag.jpg
Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. Wikipedia: The mesothelium is a membrane that forms the lining of several body cavities: the pleura (thoracal cavity), peritoneum (abdominal cavity including the mesentery) and pericardium (heart sac). Mesothelial tissue also surrounds the male internal reproductive organs (the tunica vaginalis testis) and covers the internal reproductive organs of women (the tunica serosa uteri).
FMA:14074
UMLS:C0086610
ncithesaurus:Mesothelium
A major subdivision of an organism that is the entire part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. In vertebrares this includes the vertebral column..
dorsal
In humans, called the back, a large posterior area of the human body, rising from the top of the buttocks to the back of the neck and the shoulders. It is the surface opposite to the chest, its height being defined by the vertebral column (commonly referred to as the spine or backbone) and its breadth being supported by the ribcage and shoulders. The spinal canal runs through the spine and provides nerves to the rest of the body
BTO:0001713
CALOHA:TS-2223
EFO:0001405
FMA:14181
GAID:30
MESH:A01.176
NCIT:C13062
OpenCyc:Mx4rvVkEU5wpEbGdrcN5Y29ycA
UMLS:C0004600
galen:Back
back
back of body proper
dorsal part of organism
uberon
UBERON:0001137
dorsum
http://upload.wikimedia.org/wikipedia/commons/e/ee/432px-Gray-back.PNG
A major subdivision of an organism that is the entire part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. In vertebrares this includes the vertebral column..
BSPO:0000063
UBERONREF:0000006
UMLS:C0004600
ncithesaurus:Back
back
FMA:14181
back of body proper
FMA:14181
A zone of skin that is part of a neck [Automatically generated definition].
EMAPA:37277
FMA:23021
FMA:23022
MA:0000590
NCIT:C52756
UMLS:C0205030
neck (volume) zone of skin
neck skin
neck zone of skin
zone of skin of neck
zone of skin of neck (volume)
uberon
UBERON:0001417
skin of neck
A zone of skin that is part of a neck [Automatically generated definition].
OBOL:automatic
EMAPA:37277
MA:th
UMLS:C0205030
ncithesaurus:Neck_Skin
neck (volume) zone of skin
OBOL:automatic
neck zone of skin
OBOL:automatic
zone of skin of neck
OBOL:automatic
zone of skin of neck (volume)
OBOL:automatic
A zone of skin that is part of a thorax [Automatically generated definition].
EMAPA:37765
FMA:23028
FMA:23029
MA:0000564
thoracic skin
thorax skin
thorax zone of skin
zone of skin of thorax
uberon
upper body skin
UBERON:0001418
skin of thorax
A zone of skin that is part of a thorax [Automatically generated definition].
OBOL:automatic
EMAPA:37765
MA:th
thorax zone of skin
OBOL:automatic
zone of skin of thorax
OBOL:automatic
Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.
Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO]
Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO]
System that provides physical support to the organism.[AAO]
By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG]
skeletal
GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates
AAO:0000566
BTO:0001486
CALOHA:TS-1320
EFO:0000806
EHDAA2:0003168
EMAPA:35773
FMA:23881
MA:0000018
NCIT:C12788
OpenCyc:Mx4rvVi1rpwpEbGdrcN5Y29ycA
TAO:0000434
UMLS:C0037253
VHOG:0001254
VSAO:0000027
XAO:0003060
ZFA:0000434
skeleton system
set of all bones and joints
uberon
Skelettsystem
UBERON:0001434
skeletal system
https://github.com/obophenotype/uberon/wiki/The-skeletal-system
Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.
GO_REF:0000034
VSAO:0000027
Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO]
2012-08-14
TAO:0000434
TAO
TAO:wd
Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO]
2012-08-14
VSAO:0000027
VSAO
GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070
PSPUB:0000170
System that provides physical support to the organism.[AAO]
2012-06-20
AAO:0000566
AAO
AAO:LAP
By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG]
2012-09-17
VHOG:0001254
VHOG
DOI:10.1159/000324245 Donoghue PCJ, Sansom IJ, Origin and early evolution of vertebrate skeletonization. Microscopy research and technique (2002)
GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates
GO
UMLS:C0037253
ncithesaurus:Skeletal_System
set of all bones and joints
Skelettsystem
BTO:0001486
FMA:24218
XAO:0000040
head subdivision
uberon
head region
region of head
UBERON:0001444
subdivision of head
A subdivision of the head that has as parts the layers deep to the surface of the anterior surface, including the mouth, eyes, and nose (when present). In vertebrates, this includes the facial skeleton and structures superficial to the facial skeleton (cheeks, mouth, eyeballs, skin of face, etc).
Subdivision of head which consists of the viscerocranium and all layers superficial to it. Examples: There is only one face.
The area that extends from the median ocellus to the oral foramen[HAO].
facial
The face develops from outward growth of tissue located rostral to the cranium & pharynx. The lower jaw and most of the upper jaw are formed by growth of the first pharyngeal (branchial) arch. The upper incisor region and the nose and forehead (frontal region) are formed from tissue located rostral to the neural tube (frontonasal prominence)
BTO:0003369
CALOHA:TS-2216
EMAPA:32763
FMA:24728
GAID:64
HAO:0000316
MA:0002473
MESH:D005145
NCIT:C13071
OpenCyc:Mx4rvVi5GZwpEbGdrcN5Y29ycA
UMLS:C0015450
galen:Face
uberon
facia/facies
visage
UBERON:0001456
face
http://upload.wikimedia.org/wikipedia/commons/5/55/Mona_Lisa_headcrop.jpg
A subdivision of the head that has as parts the layers deep to the surface of the anterior surface, including the mouth, eyes, and nose (when present). In vertebrates, this includes the facial skeleton and structures superficial to the facial skeleton (cheeks, mouth, eyeballs, skin of face, etc).
Subdivision of head which consists of the viscerocranium and all layers superficial to it. Examples: There is only one face.
FMA:24728
The area that extends from the median ocellus to the oral foramen[HAO].
HAO:0000316
NCBITaxon:7399
The face develops from outward growth of tissue located rostral to the cranium & pharynx. The lower jaw and most of the upper jaw are formed by growth of the first pharyngeal (branchial) arch. The upper incisor region and the nose and forehead (frontal region) are formed from tissue located rostral to the neural tube (frontonasal prominence)
vanat.cvm.umn.edu/TFFlectPDFs/LectFaceDevelop.pdf
UMLS:C0015450
ncithesaurus:Face
facia/facies
visage
BTO:0003369
A zone of skin that is part of a lip [Automatically generated definition].
EMAPA:37643
FMA:24764
MA:0001579
NCIT:C12291
UMLS:C0222101
lip skin
lip zone of skin
zone of skin of lip
uberon
skin of lips
UBERON:0001458
skin of lip
A zone of skin that is part of a lip [Automatically generated definition].
OBOL:automatic
EMAPA:37643
MA:th
UMLS:C0222101
ncithesaurus:Skin_of_the_Lip
lip zone of skin
OBOL:automatic
zone of skin of lip
OBOL:automatic
skin of lips
Skeletal element that is composed of bone tissue.
Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO]
Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO]
Skeletal element that is composed of bone tissue.[VSAO]
relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]
The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG]
AAO:0000047
AEO:0000082
BTO:0000140
CALOHA:TS-0088
EFO:0000298
EHDAA2:0003082
EMAPA:32782
ENVO:00002039
EV:0100140
FMA:30317
FMA:5018
GAID:92
MA:0001459
MAT:0000299
MIAA:0000299
NCIT:C12366
OpenCyc:Mx4rvViDlpwpEbGdrcN5Y29ycA
OpenCyc:Mx4rvVkCG5wpEbGdrcN5Y29ycA
TAO:0001514
UMLS:C0262950
VHOG:0001190
VSAO:0000057
XAO:0000169
ZFA:0001514
galen:Bone
bone organ
uberon
bone
bones
UBERON:0001474
bone element
VSAO-modified
Skeletal element that is composed of bone tissue.
GO_REF:0000034
PSPUB:0000170
VSAO:0000057
Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO]
2012-06-20
AAO:0000047
AAO
AAO:LAP
Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO]
2012-08-14
TAO:0001514
TAO
ZFIN:curator
Skeletal element that is composed of bone tissue.[VSAO]
2012-08-14
VSAO:0000057
VSAO
PSPUB:0000170
relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]
2012-06-20
AAO:0000047
AAO
The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG]
2012-09-17
VHOG:0001190
VHOG
DOI:10.1159/000324245 Murdock DJ, Donoghue PC, Evolutionary Origins of Animal Skeletal Biomineralization. Cells Tissues Organs (2011)
UMLS:C0262950
ncithesaurus:Bone
bone organ
FMA:5018
bone
AEO:0000082
BTO:0000140
MA:0001459
VHOG:0001190
bones
ZFA:0001514
An articular capsule (or joint capsule) is an envelope surrounding a synovial joint. [WP,unvetted].
check ncita
EMAPA:37621
FMA:34836
GAID:263
MA:0001519
MESH:D017746
NCIT:C32259
NCIT:C84388
UMLS:C0206207
galen:JointCapsule
capsula articularis
fibrous capsule of joint
joint capsule
joint fibrous capsule
uberon
capsulae articulares
UBERON:0001484
articular capsule
http://upload.wikimedia.org/wikipedia/commons/1/19/Joint.png
http://upload.wikimedia.org/wikipedia/commons/4/4a/Gray299.png
An articular capsule (or joint capsule) is an envelope surrounding a synovial joint. [WP,unvetted].
check ncita
ncit
EMAPA:37621
MA:th
UMLS:C0206207
ncithesaurus:Joint_Capsule
capsula articularis
FMA:34836
FMA:TA
capsulae articulares
A tube extending from the mouth to the anus.
The alimentary or digestive tract, and associated organs.[TAO]
The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]
FMA also has a term 'gastrointestinal tract', but this includes the liver.
we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509
we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this
gut
AAO:0010023
BILA:0000083
BTO:0000511
BTO:0000545
EHDAA2:0000726
EHDAA:518
EMAPA:16247
FBbt:00003125
FMA:45615
MA:0000917
NCIT:C34082
OpenCyc:Mx4rvVi0GpwpEbGdrcN5Y29ycA
TAO:0000112
TGMA:0001819
UMLS:C0017189
VHOG:0000309
WBbt:0005743
ZFA:0000112
galen:AlimentaryTract
digestive tube
enteric tract
alimentary canal
alimentary tract
uberon
digestive canal
gut tube
UBERON:0001555
digestive tract
NCBIBook:NBK10107
A tube extending from the mouth to the anus.
The alimentary or digestive tract, and associated organs.[TAO]
2012-08-14
TAO:0000112
TAO
ZFIN:curator
The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]
2012-09-17
VHOG:0000309
VHOG
ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11
FMA also has a term 'gastrointestinal tract', but this includes the liver.
FMA
we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509
MA
UMLS:C0017189
ncithesaurus:Gastrointestinal_Tract
enteric tract
ZFA:0000112
digestive canal
BTO:0000058
One of two jugular veins that collect the blood from the brain, the superficial parts of the face, and the neck. [WP,unvetted].
Vein which receives many veins draining the palate, brain, and the orbital, nasal, and auditory regions.[AAO]
AAO:0010236
EHDAA2:0000877
EHDAA:5407
EMAPA:17620
FMA:4724
MA:0002157
NCIT:C32849
OpenCyc:Mx4rvqdb95wpEbGdrcN5Y29ycA
RETIRED_EHDAA2:0000878
UMLS:C0226550
XAO:0000382
galen:InternalJugularVein
internal jugular
internal jugular venous tree
uberon
vena jugularis interna
UBERON:0001586
internal jugular vein
http://upload.wikimedia.org/wikipedia/commons/e/e9/Gray562.png
One of two jugular veins that collect the blood from the brain, the superficial parts of the face, and the neck. [WP,unvetted].
Vein which receives many veins draining the palate, brain, and the orbital, nasal, and auditory regions.[AAO]
2012-06-20
AAO:0010236
AAO
AAO:BJB
UMLS:C0226550
ncithesaurus:Internal_Jugular_Vein
internal jugular
EHDAA2:0000877
vena jugularis interna
The ciliary muscle is a ring of smooth muscle in the middle layer of the eye that controls the eye's accommodation for viewing objects at varying distances and regulates the flow of aqueous humour through Schlemm's canal. [WP,unvetted].
BTO:0000654
EMAPA:35240
FMA:49151
MA:0001269
NCIT:C32315
UMLS:C0559230
musculus ciliarus
uberon
Bowman`s muscles
ciliaris
musculus ciliaris
UBERON:0001605
ciliary muscle
http://upload.wikimedia.org/wikipedia/commons/2/28/Gray872.png
MA
FMA
FMA
The ciliary muscle is a ring of smooth muscle in the middle layer of the eye that controls the eye's accommodation for viewing objects at varying distances and regulates the flow of aqueous humour through Schlemm's canal. [WP,unvetted].
UMLS:C0559230
ncithesaurus:Ciliary_Muscle
musculus ciliarus
BTO:0000654
Bowman`s muscles
BTO:0000654
ciliaris
musculus ciliaris
.
revisit this, see issue #331
The muscle cells of the iris are smooth muscle in mammals and amphibians, but are striated muscle in birds and reptiles. Many fish have neither, and, as a result, their irides are unable to dilate and contract, so that the pupil always remains of a fixed size[Romer, via WP]
in aves, stromal mesenchymal cells may migrate to the iris and become skeletal
EMAPA:35448
FMA:49154
MA:0001287
iris muscle
iris muscle organ
muscle organ of iris
uberon
UBERON:0001606
muscle of iris
FMA
.
iris muscle organ
OBOL:automatic
muscle organ of iris
OBOL:automatic
Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO].
Portion of tissue composed of contractile fibers.[TAO]
It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG]
muscular
muscle
AAO:0011066
EMAPA:32715
EMAPA:37474
EV:0100146
FMA:5022
GAID:131
MA:0000015
OpenCyc:Mx4rv2kf-5wpEbGdrcN5Y29ycA
TAO:0005145
VHOG:0001245
XAO:0000172
ZFA:0005145
galen:Muscle
uberon
UBERON:0001630
muscle organ
Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO].
GO:0007517
Portion of tissue composed of contractile fibers.[TAO]
2012-08-14
TAO:0005145
TAO
ZFIN:curator
It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG]
2012-09-17
VHOG:0001245
VHOG
ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.75
muscle
ZFA:0005145
EMAPA:37474
MA:th
An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition].
Note that in FMA an artery is a tree, whereas AEO/JB defines it as a tube; FMA includes a separate class for what it calls the trunk. Classification in this ontology may currently (Jan 2012) represent a mix of both schemes, although we are gradually revising in the direction of the AEO scheme.
Part of the circulatory system composed of blood vessels which carry oxygenated blood away from the heart to the rest of the body.[AAO]
The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]
arterial
AAO:0010211
AEO:0000208
BTO:0000573
CALOHA:TS-0054
EFO:0000814
EHDAA2:0000143
EHDAA2:0003253
EMAPA:35147
EV:0100026
FMA:50720
GAID:468
MA:0000064
MAT:0000034
MESH:D001158
MIAA:0000034
NCIT:C12372
OpenCyc:Mx4rvVjknZwpEbGdrcN5Y29ycA
TAO:0000005
UMLS:C0003842
VHOG:0001251
XAO:0000114
ZFA:0000005
galen:Artery
arterial subtree
arterial tree organ part
arteries
uberon
arterial system
arterial vessel
UBERON:0001637
artery
An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition].
AEO:JB
Part of the circulatory system composed of blood vessels which carry oxygenated blood away from the heart to the rest of the body.[AAO]
2012-06-20
AAO:0010211
AAO
AAO:BJB
The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]
2012-09-17
VHOG:0001251
VHOG
DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)
UMLS:C0003842
ncithesaurus:Artery
arteries
TAO:0000005
Any of the tubular branching vessels that carry blood from the capillaries toward the heart.
TODO - check with MA - vein vs venous blood vessel
Part of the circulatory system composed of blood vessels which carry blood from other organs, tissues, and cells to the heart.[AAO]
The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]
venous
venous subtree
venous vessel
AAO:0010212
AEO:0000209
BTO:0000234
CALOHA:TS-1108
EFO:0000816
EHDAA2:0003254
EMAPA:35906
EV:0100031
FMA:50723
GAID:492
MA:0000067
MAT:0000037
MESH:D014680
MIAA:0000037
NCIT:C12814
OpenCyc:Mx4rvVjkWpwpEbGdrcN5Y29ycA
TAO:0000082
UMLS:C0042449
VHOG:0001743
XAO:0000115
ZFA:0000082
galen:Vein
venous tree organ part
uberon
vascular element
vena
venae
UBERON:0001638
vein
http://upload.wikimedia.org/wikipedia/commons/c/c2/Venous_system_en.svg
Any of the tubular branching vessels that carry blood from the capillaries toward the heart.
Part of the circulatory system composed of blood vessels which carry blood from other organs, tissues, and cells to the heart.[AAO]
2012-06-20
AAO:0010212
AAO
AAO:BJB
The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]
2012-09-17
VHOG:0001743
VHOG
DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)
UMLS:C0042449
ncithesaurus:Vein
vascular element
EMAPA:th
vena
venae
VHOG:0001743
The anterior facial vein (facial vein) commences at the side of the root of the nose, and is a direct continuation of the angular vein where it also receives a small nasal branch. It lies behind the facial artery and follows a less tortuous course. It receives blood from the external palatine vein before it either joins the anterior branch of the retromandibular vein to form the common facial vein, or drains directly into the internal jugular vein. [WP,unvetted].
Vein which collects blood from muscles of the head and drains into the external jugular vein.[AAO]
MA and NCITA also has 'anterior facial vein'
AAO:0010513
EMAPA:19220
FMA:50874
MA:0002115
NCIT:C32579
OpenCyc:Mx4rvziz3JwpEbGdrcN5Y29ycA
UMLS:C0226532
face vein
vein of face
uberon
anterior facial vein
vena facialis anterior
UBERON:0001653
facial vein
http://upload.wikimedia.org/wikipedia/commons/8/8c/Gray557.png
FMA
The anterior facial vein (facial vein) commences at the side of the root of the nose, and is a direct continuation of the angular vein where it also receives a small nasal branch. It lies behind the facial artery and follows a less tortuous course. It receives blood from the external palatine vein before it either joins the anterior branch of the retromandibular vein to form the common facial vein, or drains directly into the internal jugular vein. [WP,unvetted].
Vein which collects blood from muscles of the head and drains into the external jugular vein.[AAO]
2012-06-20
AAO:0010513
AAO
AAO:BJB
MA and NCITA also has 'anterior facial vein'
MA
UMLS:C0226532
ncithesaurus:Facial_Vein
face vein
OBOL:automatic
vein of face
OBOL:automatic
anterior facial vein
vena facialis anterior
the bone at the lower, posterior part of the skull
formed from the sclerotome of the occipital somites. It is not present in living or fossil agnathans or cartilaginous fishes, but appears to have arisen in parallel in many bony fishes. Incorporation of the occipital ver- tebrae into the skull was associated with the annexation of the upper part of the spinal cord into the brain, together with the first 2 spinal nerves as cranial nerves XI and XII
fusion of basi-, exo- and supra-occipitals (and maybe tabular)
EMAPA:25112
FMA:52735
GAID:227
MA:0001468
MESH:D009777
NCIT:C12757
OpenCyc:Mx4rwQtsiZwpEbGdrcN5Y29ycA
UMLS:C0028784
uberon
occipital complex
occipital squama
os occipitale
UBERON:0001676
occipital bone
http://upload.wikimedia.org/wikipedia/commons/2/27/Gray194.png
FMA
FMA
basi paired exo and supra occipital bones
MA-modified
interparietal (postparietal)
the bone at the lower, posterior part of the skull
ISBN:0-683-40008-8
MP:0005269
formed from the sclerotome of the occipital somites. It is not present in living or fossil agnathans or cartilaginous fishes, but appears to have arisen in parallel in many bony fishes. Incorporation of the occipital ver- tebrae into the skull was associated with the annexation of the upper part of the spinal cord into the brain, together with the first 2 spinal nerves as cranial nerves XI and XII
fusion of basi-, exo- and supra-occipitals (and maybe tabular)
Kardong
UMLS:C0028784
ncithesaurus:Occipital_Bone
occipital complex
os occipitale
Subdivision of skeletal system that surrounds and protects the brain. Includes the skull base, sensory capsules and the central part of the skull roof.
Anatomical cluster that consists of the cartilages and bones that surround the brain.[TAO]
neurocranial
It includes the following bones: Ethmoid bone, Frontal bone, Occipital bone, Parietal bone, Sphenoid bone, Temporal bone. The term cranium can be ambiguous, in that it can refer to the neurocranium, or the neurocranium and the Facial skeleton
The cartilaginous parts of the neurocranium undergo endochondral ossification in most species; ossification has been lost in cartilaginous fishes, but the cartilaginous condition of the skull of lampreys is considered to be primitive (Kardong, 1995)[PMID:11523816]. The neurocranium arises from paraxial mesoderm in the head (first five somites and the unsegmented somitomeres rostral to the first somite) and from ectoderm via the neural crest. In Chondrichthyes and other cartilaginous vertebrates this portion of the cranium does not ossify; it is not replaced via endochondral ossification[WP].
It seems MA uses 'neurocranium' as a synonym for chondrocranium. Note there are currently some structures part of both viscero and neurocranium - ethmoid, zyogomatic, ...
AAO:0010153
EHDAA2:0000243
EMAPA:17681
FMA:53672
MA:0000317
TAO:0001580
XAO:0003170
ZFA:0001580
brain box
uberon
brain case
brain pan
braincase
UBERON:0001703
neurocranium
FMA
Subdivision of skeletal system that surrounds and protects the brain. Includes the skull base, sensory capsules and the central part of the skull roof.
TAO:MAH
ZFA:0001580
Anatomical cluster that consists of the cartilages and bones that surround the brain.[TAO]
2012-08-14
TAO:0001580
TAO
TAO:MAH
The cartilaginous parts of the neurocranium undergo endochondral ossification in most species; ossification has been lost in cartilaginous fishes, but the cartilaginous condition of the skull of lampreys is considered to be primitive (Kardong, 1995)[PMID:11523816]. The neurocranium arises from paraxial mesoderm in the head (first five somites and the unsegmented somitomeres rostral to the first somite) and from ectoderm via the neural crest. In Chondrichthyes and other cartilaginous vertebrates this portion of the cranium does not ossify; it is not replaced via endochondral ossification[WP].
WP
It seems MA uses 'neurocranium' as a synonym for chondrocranium. Note there are currently some structures part of both viscero and neurocranium - ethmoid, zyogomatic, ...
MA
brain case
ZFA:0001580
brain pan
braincase
ZFA:0001580
Subdivision of skeleton which includes upper and lower jaw skeletons.
TODO - move ZFA:0001227 (it is the entire jaw skeleton).
Skeletal and cartilage elements of the first pharyngeal arch.[TAO]
There are cellular contributions from all three embryonic germ layers: pharyngeal mesoderm, endoderm and neural crest that migrates out of the ectoderm (Noden, 1983).
in FMA, the jaw is an organism subdivision cluster, and includes mucosal tissue such as the gingiva as parts. It appears to be skeletal in MA (and has teeth as parts). It is reasonable to assume that ZFA and XAO consider the upper and lower jaws to be skeletal elements or clusters. EHDAA2 also considers these clusters. TODO - follow EHDAA2 model. These arbitrary differences in terminology and classification have to be reconciled with the genuine well-known biological differences in the skeletal elements across vertebrates
AAO:0000988
BTO:0001749
EMAPA:35455
FMA:54396
GAID:214
MA:0001905
MESH:D007568
NCIT:C48821
OpenCyc:Mx4rvVjjEZwpEbGdrcN5Y29ycA
TAO:0001227
UMLS:C0022359
ZFA:0001227
galen:Jaw
jaw
jaw cartilage
mandibular arch skeleton
uberon
anterior splanchnocranium
jaws
mandibular arch
oral jaw skeleton
pharyngeal arch 1 skeleton
visceral arch 1
UBERON:0001708
jaw skeleton
cjm
Subdivision of skeleton which includes upper and lower jaw skeletons.
Skeletal and cartilage elements of the first pharyngeal arch.[TAO]
2012-08-14
TAO:0001227
TAO
ZFIN:curator
in FMA, the jaw is an organism subdivision cluster, and includes mucosal tissue such as the gingiva as parts. It appears to be skeletal in MA (and has teeth as parts). It is reasonable to assume that ZFA and XAO consider the upper and lower jaws to be skeletal elements or clusters. EHDAA2 also considers these clusters. TODO - follow EHDAA2 model. These arbitrary differences in terminology and classification have to be reconciled with the genuine well-known biological differences in the skeletal elements across vertebrates
FMA
UMLS:C0022359
ncithesaurus:Jaw
jaw
MA:0001905
jaw cartilage
ZFA:0001227
mandibular arch skeleton
ZFA:0001227
mandibular arch
TAO:0001227
Subdivision of head that consists of the lower jaw skeletal elements plus associated soft tissue (skin, lips, muscle)[cjm].
Inferior mandibular arch located on the anterior and lateral sides of the skull.[AAO]
Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG]
Note isa/partof difference MA/FMA
AAO:0000272
EFO:0003660
EHDAA2:0001018
EHDAA:7995
EMAPA:17906
FMA:59398
MESH:D008334
VHOG:0000453
ncithesaurus:Lower_Jaw
mandibular part of mouth
uberon
lower part of mouth
mandibular series
UBERON:0001710
See notes for jaw w.r.t skeletal element vs subdivision of head
lower jaw region
http://upload.wikimedia.org/wikipedia/commons/6/64/Gray176.png
Subdivision of head that consists of the lower jaw skeletal elements plus associated soft tissue (skin, lips, muscle)[cjm].
Inferior mandibular arch located on the anterior and lateral sides of the skull.[AAO]
2012-06-20
AAO:0000272
AAO
AAO:LAP
Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG]
2012-09-17
VHOG:0000453
VHOG
DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)
Note isa/partof difference MA/FMA
MA
mandibular part of mouth
FMA:59398
A anatomical space that is enclosed by a pharynx.
See notes for pharynx - as a grouping class this is probably too bad. We exclude WBbt:0005790 (pharyngeal lumen) because of the developmental relationship
TOODO check
AAO:0010435
BSA:0000113
BTO:0002097
EMAPA:18381
FMA:54935
XAO:0000105
lumen of pharynx
pharyngeal cavity
uberon
cavitas pharyngealis
cavitas pharyngis
UBERON:0001731
cavity of pharynx
XAO
A anatomical space that is enclosed by a pharynx.
OBOL:automatic
cavitas pharyngealis
cavitas pharyngis
BTO:0002097
the space in the eye, filled with aqueous humor, and bounded anteriorly by the cornea and a small portion of the sclera and posteriorly by a small portion of the ciliary body, the iris, and part of the crystalline lens
The part of the eyeball between the cornea and the iris, filled with aqueous humor. [TFD][VHOG]
space in EHDAA2 - consider adding Cavity of anterior chamber of eyeball
BTO:0002084
EHDAA2:0000129
EHDAA:9033
EMAPA:18231
FMA:58078
GAID:889
MA:0000262
MESH:D000867
NCIT:C12667
UMLS:C0003151
VHOG:0001431
anterior chamber
anterior chamber of eye
camera anterior
eye anterior chamber
uberon
camera anterior bulbi
camera anterior bulbi oculi
camera oculi anterior
UBERON:0001766
anterior chamber of eyeball
http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg
FMA
the space in the eye, filled with aqueous humor, and bounded anteriorly by the cornea and a small portion of the sclera and posteriorly by a small portion of the ciliary body, the iris, and part of the crystalline lens
MESH:A09.371.060.067
MP:0005205
The part of the eyeball between the cornea and the iris, filled with aqueous humor. [TFD][VHOG]
2012-09-17
VHOG:0001431
VHOG
space in EHDAA2 - consider adding Cavity of anterior chamber of eyeball
EHDAA2
UMLS:C0003151
ncithesaurus:Anterior_Chamber_of_the_Eye
anterior chamber
HP:0000593
MP:0010709
camera anterior bulbi
BTO:0002084
camera anterior bulbi oculi
camera oculi anterior
BTO:0002084
the pigmented middle of the three concentric layers that make up an eye, consisting of the iris, ciliary body and choroid[WP,edited].
TODO - check child terms, isa vs partof. See also MA:0001284 ! tunica vasculosa plexus
uveal
CALOHA:TS-2228
EMAPA:35901
FMA:58103
GAID:912
MA:0002480
MESH:D014602
NCIT:C12811
UMLS:C0042160
tunica vasculosa of eyeball
uvea
uveal tract
uberon
pars iridica retinae
tunica vasculatis oculi
tunica vasculosa bulbi
vascular layer of eyeball
UBERON:0001768
uvea
http://upload.wikimedia.org/wikipedia/commons/e/eb/Gray869.png
FMA
the pigmented middle of the three concentric layers that make up an eye, consisting of the iris, ciliary body and choroid[WP,edited].
MP:0005197
UMLS:C0042160
ncithesaurus:Uvea
tunica vasculosa of eyeball
FMA:58103
uvea
FMA:58103
uveal tract
FMA:58103
pars iridica retinae
tunica vasculatis oculi
tunica vasculosa bulbi
vascular layer of eyeball
FMA:58103
the adjustable membrane, composed of the stroma and pigmented epithelium, located just in front of the crystalline lens within the eye
The opaque muscular contractile diaphragm suspended in the aqueous humour in front of the lens of the eye. The organ is perforated by the pupil and continues peripherally with the ciliary body. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]
iridial
The avian iris and ciliary body undergoes a transition from smooth-to-striated muscle during embryonic development [DOI:dx.doi.org/10.1006/dbio.1998.9019]
AAO:0010347
BTO:0000653
CALOHA:TS-0491
EFO:0004245
EMAPA:19154
EV:0100345
FMA:58235
GAID:917
MA:0000273
MESH:D007498
NCIT:C12737
OpenCyc:Mx4rvVjbppwpEbGdrcN5Y29ycA
TAO:0001238
UMLS:C0022077
VHOG:0000101
XAO:0000185
ZFA:0001238
uberon
anterior uvea
irides
irises
UBERON:0001769
iris
XAO
the adjustable membrane, composed of the stroma and pigmented epithelium, located just in front of the crystalline lens within the eye
ISBN:0-683-40008-8
MP:0001322
The opaque muscular contractile diaphragm suspended in the aqueous humour in front of the lens of the eye. The organ is perforated by the pupil and continues peripherally with the ciliary body. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
2012-09-17
VHOG:0000101
VHOG
The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]
2012-09-17
VHOG:0000101
VHOG
DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)
UMLS:C0022077
ncithesaurus:Iris
irides
irises
VHOG:0000101
the smooth stratified squamous epithelium that covers the outer surface of the cornea
Portion of tissue comprised of four to six layers of nonkeratinized, stratified squamous cells and represents approximately 60% of the thickness of the cornea.[TAO]
In Humans: It consists of several layers of cells. The cells of the deepest layer are columnar; then follow two or three layers of polyhedral cells, the majority of which are prickle cells similar to those found in the stratum mucosum of the cuticle. Lastly, there are three or four layers of squamous cells, with flattened nuclei
In zebrafish: nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals
BTO:0000287
CALOHA:TS-0173
EFO:0001917
EHDAA2:0000319
EMAPA:17162
FMA:58263
GAID:895
MA:0001243
MESH:D019573
NCIT:C12928
TAO:0002187
UMLS:C0459875
ZFA:0001683
anterior corneal epithelium
cornea epithelial tissue
cornea epithelium
epithelial tissue of cornea
epithelium anterius (cornea)
epithelium anterius corneae
epithelium corneæ anterior layer
epithelium of cornea
external epithelium of cornea
uberon
anterior endothelium of cornea
e. anterius corneae
endothelium anterius corneae
endothelium camerae anterioris bulbi
endothelium corneale
epithelium posterius corneae
UBERON:0001772
corneal epithelium
http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png
ISBN:0781772214
the smooth stratified squamous epithelium that covers the outer surface of the cornea
MESH:A09.371.060.217.325
MGI:smb
MP:0006000
Portion of tissue comprised of four to six layers of nonkeratinized, stratified squamous cells and represents approximately 60% of the thickness of the cornea.[TAO]
2012-08-14
TAO:0002187
TAO
ZFIN:ZDB-PUB-061010-3
UMLS:C0459875
ncithesaurus:Corneal_Epithelium
cornea epithelial tissue
OBOL:automatic
cornea epithelium
OBOL:automatic
epithelial tissue of cornea
OBOL:automatic
epithelium anterius corneae
FMA:58263
FMA:TA
anterior endothelium of cornea
BTO:0000287
e. anterius corneae
endothelium anterius corneae
BTO:0000287
endothelium camerae anterioris bulbi
BTO:0000287
endothelium corneale
BTO:0000287
epithelium posterius corneae
BTO:0000287
Opaque fibrous outer layer of the eyeball[ZFA,Kardong,WP].
The sclera, also known as the white part of the eye, is the opaque (usually white, though certain animals, such as horses and lizards, can have black sclera), fibrous, protective, outer layer of the eye containing collagen and elastic fiber. It is derived from the neural crest. In children, it is thinner and shows some of the underlying pigment, appearing slightly blue. In the elderly, however, fatty deposits on the sclera can make it appear slightly yellow. The sclera forms the posterior five sixths of the connective tissue coat of the globe. It is continuous with the dura mater and the cornea, and maintains the shape of the globe, offering resistance to internal and external forces, and provides an attachment for the extraocular muscle insertions. The sclera is perforated by plenty of nerves and vessels passing through the posterior scleral foramen, the hole that is formed by the optic nerve. At the optic disk the outer two-thirds of the sclera continues with the dura mater (outer coat of the brain) via the dural sheath of the optic nerve. The inner third joins with some choroidal tissue to form a plate (lamina cribrosa) across the optic nerve with perforations through which the optic fibers (fasciculi). The thickness of the sclera varies from 1mm at the posterior pole to 0.3 mm just behind the rectus muscle insertions. The sclera's blood vessels are mainly on the surface, and together with the conjunctiva (which lies on top) This is a thin layer covering the sclera. Along with the vessels of the conjunctiva, those of the sclera renders the inflamed eye bright red. [WP,unvetted][Wikipedia:Sclera].
The tough, usually white, outer coat of the eyeball, covering all the posterior surface and continuous anteriorly with the cornea. [TFD][VHOG]
scleral
in fish, reptiles and monotremes the connective tissue of the sclera is skeletal
continuous with the dura mater and the cornea; The sclera forms the posterior five-sixths of the connective tissue coat of the globe.
Majority derives from NC that surrounds optic cup of neurectoderm; a small temporal portion develops from the mesoderm that contributes to striated extra-ocular muscles and vascular endothelia[Rada&Johnson].
Seko et al demonstrate chondrogenic potential and identify this as connective tissue[DOI:10.1371/journal.pone.0003709].
AAO:0010354
BTO:0001606
EMAPA:19027
EV:0100342
FMA:58269
GAID:911
MA:0000280
MESH:D012590
NCIT:C12784
OpenCyc:Mx4rv7yR55wpEbGdrcN5Y29ycA
UMLS:C0036410
VHOG:0001274
XAO:0000183
ZFA:0005563
uberon
scleral capsule
UBERON:0001773
Disease notes: implicated in rheumatoid arthritis.
sclera
http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg
FMA
ISBN:0781772214
Opaque fibrous outer layer of the eyeball[ZFA,Kardong,WP].
ZFIN:ZDB-PUB-050701-15
The sclera, also known as the white part of the eye, is the opaque (usually white, though certain animals, such as horses and lizards, can have black sclera), fibrous, protective, outer layer of the eye containing collagen and elastic fiber. It is derived from the neural crest. In children, it is thinner and shows some of the underlying pigment, appearing slightly blue. In the elderly, however, fatty deposits on the sclera can make it appear slightly yellow. The sclera forms the posterior five sixths of the connective tissue coat of the globe. It is continuous with the dura mater and the cornea, and maintains the shape of the globe, offering resistance to internal and external forces, and provides an attachment for the extraocular muscle insertions. The sclera is perforated by plenty of nerves and vessels passing through the posterior scleral foramen, the hole that is formed by the optic nerve. At the optic disk the outer two-thirds of the sclera continues with the dura mater (outer coat of the brain) via the dural sheath of the optic nerve. The inner third joins with some choroidal tissue to form a plate (lamina cribrosa) across the optic nerve with perforations through which the optic fibers (fasciculi). The thickness of the sclera varies from 1mm at the posterior pole to 0.3 mm just behind the rectus muscle insertions. The sclera's blood vessels are mainly on the surface, and together with the conjunctiva (which lies on top) This is a thin layer covering the sclera. Along with the vessels of the conjunctiva, those of the sclera renders the inflamed eye bright red. [WP,unvetted][Wikipedia:Sclera].
The tough, usually white, outer coat of the eyeball, covering all the posterior surface and continuous anteriorly with the cornea. [TFD][VHOG]
2012-09-17
VHOG:0001274
VHOG
UMLS:C0036410
ncithesaurus:Sclera
A skeletal muscle organ that is part of the trunk region.
Note that this class excludes smooth muscle elements in the trunk region, such as the internal anal sphincter. This appears to be consistent with other ontologies such as FMA and ZFA which appear to only include skeletal muscles here. In fact the MA class 'trunk muscle' is classified as a 'set of skeletal muscles'.
Many ontologies do not appear to have a coherent distinction between an individual muscle and the musculature (i.e. the set of muscles in a region), so we group all together here.
AAO:0000611
EMAPA:35888
FMA:58274
MA:0000514
TAO:0000473
XAO:0003230
ZFA:0000473
body musculature
muscle of trunk
muscle organ of torso
muscle organ of trunk
torso muscle organ
trunk muscle
trunk muscle organ
trunk musculature
uberon
UBERON:0001774
skeletal muscle of trunk
prolog
A skeletal muscle organ that is part of the trunk region.
body musculature
ZFA:0000473
muscle of trunk
FMA:58274
muscle organ of torso
OBOL:automatic
muscle organ of trunk
OBOL:automatic
torso muscle organ
OBOL:automatic
trunk muscle organ
OBOL:automatic
the thickened portion of the vascular tunic, which lies between the choroid and the iris, composed of ciliary muscle and ciliary processes
The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]
AAO:0010341
BTO:0000260
CALOHA:TS-0694
EMAPA:19065
EV:0100346
FMA:58295
GAID:916
MA:0000264
MESH:D002924
NCIT:C12345
UMLS:C0008779
VHOG:0000102
XAO:0000186
ocular ciliary body
uberon
anterior uvea
ciliary bodies
corpus ciliare
UBERON:0001775
ciliary body
http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg
ISBN:0781772214
the thickened portion of the vascular tunic, which lies between the choroid and the iris, composed of ciliary muscle and ciliary processes
ISBN:0-683-40008-8
MP:0005099
The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]
2012-09-17
VHOG:0000102
VHOG
DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)
UMLS:C0008779
ncithesaurus:Ciliary_Body
ciliary bodies
VHOG:0000102
corpus ciliare
corpus ciliare
vascular layer containing connective tissue, of the eye lying between the retina and the sclera. The choroid provides oxygen and nourishment to the outer layers of the retina. Along with the ciliary body and iris, the choroid forms the uveal tract[WP].
check choroid vs choroid layer; check ZFA/TAO placement - no homology assertion in VHOG. Note this is entirely in the posterior region of eyeball in ZFA
choroidal
MP treats posterior uvea and optic choroid as distinct
BTO:0001829
CALOHA:TS-2054
EMAPA:19077
EV:0100347
FMA:58298
GAID:913
MA:0000263
MESH:D002829
NCIT:C12344
TAO:0005229
UMLS:C0008520
VHOG:0001568
ZFA:0005229
choroid
choroid coat
choroidea
eye choroid
posterior uvea
uberon
chorioid
choroidea
optic choroid
UBERON:0001776
optic choroid
http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg
MA
Wikipedia
lexical
vascular layer containing connective tissue, of the eye lying between the retina and the sclera. The choroid provides oxygen and nourishment to the outer layers of the retina. Along with the ciliary body and iris, the choroid forms the uveal tract[WP].
MP treats posterior uvea and optic choroid as distinct
MP
UMLS:C0008520
ncithesaurus:Choroid
choroid
MA:0000263
choroid coat
choroidea
eye choroid
VHOG:0001568
posterior uvea
chorioid
BTO:0001829
choroidea
optic choroid
ZFA:0005229
A double layer covering the ciliary body that produces aqueous humor.
BTO:0001770
CALOHA:TS-0695
EMAPA:35239
FMA:58464
MA:0001238
NCIT:C32314
UMLS:C0459736
ciliary body epithelium
epithelium of ciliary body
ocular ciliary epithelium
uberon
UBERON:0001778
ciliary epithelium
FMA
MA
Wikipedia
A double layer covering the ciliary body that produces aqueous humor.
UMLS:C0459736
ncithesaurus:Ciliary_Epithelium
ciliary body epithelium
FMA:58464
epithelium of ciliary body
FMA:58464
Any of the layers that make up the retina[MP].
MA does not treat internal/external limiting memranes as layers - these are classified as laminae. Here we follow other ontologies in grouping with other layers. MA also treats retinal pigment epithelium and neural retina epithelium as distinct from the layers. We follow ontologies such as FMA and ZFA in first dividing into pigmented and neural layers - these are also classified as layers, giving us over the usual 10 layers
AAO:0010353
EMAPA:35742
FMA:58617
MA:0001319
NCIT:C49328
UMLS:C0459649
XAO:0000266
retina layer
retina neuronal layer
retinal layer
retinal neuronal layer
uberon
UBERON:0001781
layer of retina
Any of the layers that make up the retina[MP].
MP:0003727
MA does not treat internal/external limiting memranes as layers - these are classified as laminae. Here we follow other ontologies in grouping with other layers. MA also treats retinal pigment epithelium and neural retina epithelium as distinct from the layers. We follow ontologies such as FMA and ZFA in first dividing into pigmented and neural layers - these are also classified as layers, giving us over the usual 10 layers
MA
UMLS:C0459649
ncithesaurus:Retina_Layer
retina neuronal layer
MP:0006069
retinal neuronal layer
MP:0006069
A thick watery refractive medium that fills the space between the lens and the cornea[WP].
The fluid produced by the ciliary process in the eye and occupying the anterior and posterior chambers. It provides nourishment for the lens and cornea and maintains the ocular pressure, and hence the optical integrity of the eyeball. [TFD][VHOG]
(...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG]
FMA says A+P chambers, and MA states A chamber. ZFA states A chamber and tha it is produced primarily by dorsal ciliary epithelial cells.To be investigated across taxa.
EHDAA2:0000139
EHDAA:10196
EMAPA:18232
ENVO:02000024
FMA:58819
GAID:890
MA:0001236
MESH:D001082
NCIT:C13190
OpenCyc:Mx4rvdGd-5wpEbGdrcN5Y29ycA
UMLS:C0003662
VHOG:0000548
ZFA:0005564
aqueous humor
aqueous humour
humor aquosus
uberon
UBERON:0001796
aqueous humor of eyeball
http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg
FMA def states A and P
located_in in EHDAA2
VHOG
A thick watery refractive medium that fills the space between the lens and the cornea[WP].
The fluid produced by the ciliary process in the eye and occupying the anterior and posterior chambers. It provides nourishment for the lens and cornea and maintains the ocular pressure, and hence the optical integrity of the eyeball. [TFD][VHOG]
2012-09-17
VHOG:0000548
VHOG
(...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG]
2012-09-17
VHOG:0000548
VHOG
DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.424 and p.426 and p.429 and Figure 12-24
FMA says A+P chambers, and MA states A chamber. ZFA states A chamber and tha it is produced primarily by dorsal ciliary epithelial cells.To be investigated across taxa.
FMA
UMLS:C0003662
ncithesaurus:Aqueous_Humor
aqueous humour
EHDAA2:0000139
humor aquosus
FMA:58819
FMA:TA
any of the parts of the eye that lie in front of, or ventral to, the lens (inclusive)
EMAPA:36594
FMA:58865
MA:0002484
MESH:D000869
NCIT:C12668
UMLS:C0003153
ZFA:0005566
anterior eye segment
anterior segment eye
anterior segment of eye
anterior segment of the eye
eye anterior segment
segmentum anterius (bulbus oculi)
uberon
segmentum anterius bulbi oculi
UBERON:0001801
anterior segment of eyeball
http://upload.wikimedia.org/wikipedia/commons/b/ba/Cataract_in_human_eye.png
FMA
cjm
lexical
any of the parts of the eye that lie in front of, or ventral to, the lens (inclusive)
ISBN:0-683-40008-8
MESH:A09.371.060
MP:0005193
UMLS:C0003153
ncithesaurus:Anterior_Eye_Segment
anterior segment eye
ZFA:0005566
segmentum anterius bulbi oculi
any of the parts of the eye that lie in back of, or dorsal to, the lens (but not inclusive)
EMAPA:36595
FMA:58868
MA:0002485
NCIT:C12906
UMLS:C0278450
ZFA:0005567
eye posterior segment
posterior eye segment
posterior segment eye
posterior segment of eye
posterior segment of the eye
segmentum posterius (bulbus oculi)
uberon
segmentum posterius bulbi oculi
UBERON:0001802
posterior segment of eyeball
http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg
FMA
cjm
lexical
any of the parts of the eye that lie in back of, or dorsal to, the lens (but not inclusive)
ISBN:0-683-40008-8
MP:0005195
UMLS:C0278450
ncithesaurus:Posterior_Eye_Segment
posterior segment eye
ZFA:0005567
segmentum posterius bulbi oculi
A layer of epithelial cells that is part of the eye.
this class is the superclass of the anterior epithelium and equatorial epithlium, although the term 'lens epithelium' may refer specifically to the former
BTO:0001873
CALOHA:TS-0543
EMAPA:32871
FMA:58871
MA:0001301
TAO:0001326
XAO:0004094
ZFA:0001326
epithelial tissue of eye lens
epithelial tissue of lens
epithelium lentis
epithelium of eye lens
eye lens epithelial tissue
eye lens epithelium
lens epithelial tissue
lens epithelium
uberon
UBERON:0001803
epithelium of lens
A layer of epithelial cells that is part of the eye.
epithelial tissue of eye lens
OBOL:automatic
epithelial tissue of lens
OBOL:automatic
epithelium lentis
FMA:58871
FMA:TA
epithelium of eye lens
OBOL:automatic
eye lens epithelial tissue
OBOL:automatic
eye lens epithelium
OBOL:automatic
lens epithelial tissue
OBOL:automatic
the elastic, clear, membrane-like structure, that is outer most layer of the lens
The transparent membrane which surrounds the lens of the eye. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
(...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG]
synthesized by the lens epithelium and its main components are Type IV collagen and sulfated glycosaminoglycans (GAGs). [Wikipedia:Capsule_of_lens
FMA classifies this is a capsule and hence an organ part. In contrast we classify this as acellular
EHDAA2:0000977
EMAPA:18237
FMA:58881
MA:0001300
NCIT:C32975
UMLS:C0229232
VHOG:0000550
ZFA:0005574
capsula lentis
lens capsule
uberon
UBERON:0001804
capsule of lens
http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png
EHDAA2
the elastic, clear, membrane-like structure, that is outer most layer of the lens
MGI:smb
MP:0003236
The transparent membrane which surrounds the lens of the eye. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
2012-09-17
VHOG:0000550
VHOG
(...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG]
2012-09-17
VHOG:0000550
VHOG
DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.424 and p.426 and p.429 and Figure 12-24
FMA classifies this is a capsule and hence an organ part. In contrast we classify this as acellular
FMA
UMLS:C0229232
ncithesaurus:Lens_Capsule
capsula lentis
One of the two fleshy folds which surround the opening of the mouth.
Surface structure that is one of the two fleshy folds surrounding the opening of the mouth.[TAO]
labial
BTO:0001647
CALOHA:TS-0558
EMAPA:32839
FMA:59816
GAID:76
MA:0000343
MESH:D008046
NCIT:C12220
OpenCyc:Mx4rvVi4U5wpEbGdrcN5Y29ycA
TAO:0007006
UMLS:C0023759
VHOG:0000677
ZFA:0007006
galen:Lip
uberon
labia oris
lips
UBERON:0001833
lip
http://upload.wikimedia.org/wikipedia/commons/9/90/Lips.JPG
http://upload.wikimedia.org/wikipedia/commons/9/99/Mouth.jpg
ZFA
BTO
FMA-implicit
VHOG
ZFA
cjm
One of the two fleshy folds which surround the opening of the mouth.
Surface structure that is one of the two fleshy folds surrounding the opening of the mouth.[TAO]
2012-08-14
TAO:0007006
TAO
ZFIN:curator
UMLS:C0023759
ncithesaurus:Lip
labia oris
Lip that covers the lower portion of the mouth.[TAO].
Lip that covers the lower portion of the mouth.[TAO]
UBERON:0003392
EHDAA2:0001020
EMAPA:17909
FMA:59818
MA:0000921
NCIT:C94572
OpenCyc:Mx4rv842UpwpEbGdrcN5Y29ycA
TAO:0002060
UMLS:C0458583
ZFA:0005225
lower jaw lip
uberon
labium inferius oris
UBERON:0001835
lower lip
http://upload.wikimedia.org/wikipedia/commons/9/99/Mouth.jpg
Lip that covers the lower portion of the mouth.[TAO].
TAO:0002060
Lip that covers the lower portion of the mouth.[TAO]
2012-08-14
TAO:0002060
TAO
TAO:wd
UMLS:C0458583
ncithesaurus:Lower_Lip
lower jaw lip
labium inferius oris
The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO].
developmental relationships need revised
Middle part of the brain composed of the optic tectum and penducular region.[AAO]
The brain region between the forebrain anteriorly and the hindbrain posteriorly, including the tectum dorsally and the midbrain tegmentum ventrally. Kimmel et al, 1995.[TAO]
Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG]
mesencephalic
part of brainstem in ABA - we reject this in favor of ISBN:0471888893 which has an implicit overlaps relationships
MB
AAO:0010149
BAMS:MES
BIRNLEX:1667
BM:MB
BTO:0000138
CALOHA:TS-0630
DHBA:10648
DMBA:16649
EFO:0000919
EHDAA2:0001162
EHDAA:3694
EMAPA:16974
EV:0100242
FMA:61993
HBA:9001
MA:0000207
MAT:0000106
MBA:313
MESH:D008636
MIAA:0000106
NCIT:C12510
OpenCyc:Mx4rvsBUqpwpEbGdrcN5Y29ycA
RETIRED_EHDAA2:0001104
TAO:0000128
UMLS:C0025462
VHOG:0000069
XAO:0000014
ZFA:0000128
http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=462
uberon
mesencephalon
UBERON:0001891
midbrain
http://upload.wikimedia.org/wikipedia/commons/f/f9/Human_brain_inferior_view_description.JPG
definitional
Bgee:AN
The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO].
GO:0030901
Middle part of the brain composed of the optic tectum and penducular region.[AAO]
2012-06-20
AAO:0010149
AAO
AAO:BJB
The brain region between the forebrain anteriorly and the hindbrain posteriorly, including the tectum dorsally and the midbrain tegmentum ventrally. Kimmel et al, 1995.[TAO]
2012-08-14
TAO:0000128
TAO
ZFIN:curator
Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG]
2012-09-17
VHOG:0000069
VHOG
DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)
part of brainstem in ABA - we reject this in favor of ISBN:0471888893 which has an implicit overlaps relationships
ABA
MB
BIRNLEX:1667
NIFSTD:NeuroNames_abbrevSource
UMLS:C0025462
BIRNLEX:1667
UMLS:C0025462
ncithesaurus:Mesencephalon
http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=462
BIRNLEX:1667
mesencephalon
A segment of the developing hindbrain[ZFA]. In the vertebrate embryo, a rhombomere is a transiently divided segment of the developing neural tube, within the hindbrain region (a neuromere) in the area that will eventually become the rhombencephalon. The rhombomeres appear as a series of slightly constricted swellings in the neural tube, caudal to the cephalic flexure.[WP].
A segment of the developing hindbrain. Kimmel et al, 1995.[TAO]
Rhombomeric segmentation is found in all living vertebrates and is of fundamental importance to the development of the vertebrate head.[well established][VHOG]
In human embryonic development, the rhombomeres are present by day 29
DHBA divides this into A(1-3),B(4),C(5-7) and D(8)
hindbrain segment
segment of hindbrain
DHBA:12664
EFO:0003617
EMAPA:16148
FMA:295666
MAT:0000272
MIAA:0000272
RETIRED_EHDAA2:0000669
TAO:0001064
VHOG:0000672
XAO:0004079
ZFA:0001064
hindbrain neuromere
hindbrain neuromeres
rhombomere
uberon
future rhombencephalon
rhombomeres
UBERON:0001892
rhombomere
A segment of the developing hindbrain[ZFA]. In the vertebrate embryo, a rhombomere is a transiently divided segment of the developing neural tube, within the hindbrain region (a neuromere) in the area that will eventually become the rhombencephalon. The rhombomeres appear as a series of slightly constricted swellings in the neural tube, caudal to the cephalic flexure.[WP].
ZFIN:curator
A segment of the developing hindbrain. Kimmel et al, 1995.[TAO]
2012-08-14
TAO:0001064
TAO
ZFIN:curator
Rhombomeric segmentation is found in all living vertebrates and is of fundamental importance to the development of the vertebrate head.[well established][VHOG]
2012-09-17
VHOG:0000672
VHOG
DOI:10.1006/dbio.2002.0831 Mazet F, Shimeld SM, The Evolution of Chordate Neural Segmentation. Developmental Biology (2002)
hindbrain segment
ZFA:0001064
segment of hindbrain
ZFA:0001064
hindbrain neuromeres
DHBA:HNM
future rhombencephalon
MIAA:0000272
rhombomeres
VHOG:0000672
Organ component of neuraxis that has as its parts the medullary reticular formation, inferior olivary complex and cochlear nuclear complex, among other structures[FMA]. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate[GO].
Posterior portion of the hindbrain which controls respiration, heartbeat, digestion, and swallowing as well as some locomotor responses.[AAO]
The posterior region of the brain that is continuous with the spinal cord. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-17, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
Classical anatomical studies subdivided the vertebrate rhombencephalon into pons and medulla oblongata. (...) The medulla oblongata appears therefore as a tagma, that is, a group of segmental units (pseudorhombomeres, in this case) sharing some morphological and molecular characteristics, and in some aspects different from the segmental units present in adjoining brain regions, pons and spinal cord.[well established][VHOG]
bulb
medulla
AAO:0010486
BAMS:MY
BAMS:Md
BIRNLEX:957
BM:Me
BTO:0000041
CALOHA:TS-0607
DMBA:17352
EFO:0000924
EHDAA2:0001088
EHDAA:7588
EMAPA:17550
EV:0100275
FMA:62004
GAID:590
MA:0000206
MAT:0000111
MAT:0000367
MBA:354
MESH:D008526
MIAA:0000111
NCIT:C12442
OpenCyc:Mx4rvVjxSJwpEbGdrcN5Y29ycA
OpenCyc:Mx4rwCqnXJwpEbGdrcN5Y29ycA
TAO:0000545
UMLS:C0025148
UMLS:C1269575
VHOG:0000181
XAO:0003100
ZFA:0000545
http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=698
bulbus
uberon
medulla oblonzata
metepencephalon
UBERON:0001896
medulla oblongata
http://upload.wikimedia.org/wikipedia/commons/6/6b/Illu_pituitary_pineal_glands.jpg
Organ component of neuraxis that has as its parts the medullary reticular formation, inferior olivary complex and cochlear nuclear complex, among other structures[FMA]. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate[GO].
FMA:62004
GO:0021550
Posterior portion of the hindbrain which controls respiration, heartbeat, digestion, and swallowing as well as some locomotor responses.[AAO]
2012-06-20
AAO:0010486
AAO
AAO:BJB
The posterior region of the brain that is continuous with the spinal cord. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-17, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
2012-09-17
VHOG:0000181
VHOG
Classical anatomical studies subdivided the vertebrate rhombencephalon into pons and medulla oblongata. (...) The medulla oblongata appears therefore as a tagma, that is, a group of segmental units (pseudorhombomeres, in this case) sharing some morphological and molecular characteristics, and in some aspects different from the segmental units present in adjoining brain regions, pons and spinal cord.[well established][VHOG]
2012-09-17
VHOG:0000181
VHOG
DOI:10.1016/j.ydbio.2008.08.017 Marin F, Aroca P, Puelles L, Hox gene colinear expression in the avian medulla oblongata is correlated with pseudorhombomeric domains. Developmental Biology (2008)
medulla
ABA:MY
UMLS:C0025148
BIRNLEX:957
UMLS:C0025148
ncithesaurus:Medulla_Oblongata
UMLS:C1269575
BIRNLEX:957
http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=698
BIRNLEX:957
bulbus
FMA:62004
FMA:TA
medulla oblonzata
metepencephalon
FMA:62004
An endothelium that is part of a capillary [Automatically generated definition].
BTO:0004954
CALOHA:TS-0112
EMAPA:36292
FMA:62114
MA:0000711
NCIT:C49215
UMLS:C0006904
blood capillary endothelium
capillary endothelium
capillary vessel endothelium
endothelium of blood capillary
endothelium of capillary vessel
uberon
UBERON:0001915
endothelium of capillary
An endothelium that is part of a capillary [Automatically generated definition].
OBOL:automatic
UMLS:C0006904
ncithesaurus:Capillary_Endothelium
blood capillary endothelium
OBOL:automatic
capillary vessel endothelium
OBOL:automatic
endothelium of blood capillary
OBOL:automatic
endothelium of capillary vessel
OBOL:automatic
An endothelium that is part of an arteriole [Automatically generated definition].
EMAPA:36286
FMA:62115
MA:0000705
NCIT:C49192
UMLS:C1179024
arteriole endothelium
uberon
UBERON:0001916
endothelium of arteriole
An endothelium that is part of an arteriole [Automatically generated definition].
OBOL:automatic
UMLS:C1179024
ncithesaurus:Arteriole_Endothelium
An endothelium that is part of an artery [Automatically generated definition].
The endothelium is the thin layer of cells that lines the interior surface of blood vessels, forming an interface between circulating blood in the lumen and the rest of the vessel wall.[AAO]
Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]
AAO:0011013
BTO:0004757
EMAPA:35148
FMA:62116
MA:0000707
NCIT:C49194
UMLS:C1179025
VHOG:0001215
XAO:0000357
arterial endothelium
artery endothelium
uberon
UBERON:0001917
endothelium of artery
An endothelium that is part of an artery [Automatically generated definition].
OBOL:automatic
The endothelium is the thin layer of cells that lines the interior surface of blood vessels, forming an interface between circulating blood in the lumen and the rest of the vessel wall.[AAO]
2012-06-20
AAO:0011013
AAO
XAO:curator
Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]
2012-09-17
VHOG:0001215
VHOG
ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207
UMLS:C1179025
ncithesaurus:Artery_Endothelium
An endothelium that is part of a venule [Automatically generated definition].
EMAPA:36290
FMA:62117
MA:0000716
NCIT:C49319
UMLS:C1179026
venule endothelium
uberon
UBERON:0001918
endothelium of venule
An endothelium that is part of a venule [Automatically generated definition].
OBOL:automatic
UMLS:C1179026
ncithesaurus:Venule_Endothelium
An endothelium that is part of a vein [Automatically generated definition].
Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]
AAO:0011110
BTO:0004756
EMAPA:36288
FMA:62118
MA:0000712
NCIT:C49317
UMLS:C1179027
VHOG:0001216
XAO:0000358
vein endothelium
venous endothelium
uberon
veinous endothelium
UBERON:0001919
endothelium of vein
An endothelium that is part of a vein [Automatically generated definition].
OBOL:automatic
Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]
2012-09-17
VHOG:0001216
VHOG
ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207
UMLS:C1179027
ncithesaurus:Vein_Endothelium
veinous endothelium
VHOG:0001216
Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP].
Together, our results reveal a shared basic organization in the tegmental domains of the diencephalon and midbrain of developing lamprey, indicating early appearance of the domain in vertebrate phylogeny.[well established][VHOG]
MTg
tegmentum
BAMS:MTg
BIRNLEX:1200
BTO:0003388
DHBA:12195
EFO:0000921
EHDAA2:0004475
EMAPA:18215
FMA:62393
HBA:9002
MA:0000212
MAT:0000452
TAO:0000160
UMLS:C0039441
VHOG:0001367
XAO:0004271
ZFA:0000160
http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=491
tegmentum mesencephali
tegmentum of midbrain
uberon
mesencephalic tegmentum
tegmentum mesencephalicum
UBERON:0001943
'tegmentum' is used generically for the ventral part of the brainstem (ISBN:0471888893). We use the label 'midbrain tegmentum' to denote the midbrain structure. In NIFSTD tegmentum is a composite structure and there is a separate class for midbrain tegmentum and pontine tegmentum
midbrain tegmentum
http://upload.wikimedia.org/wikipedia/commons/b/b6/Gray712.png
ZFA
Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP].
FMA:FMA
ISBN:0471888893
Together, our results reveal a shared basic organization in the tegmental domains of the diencephalon and midbrain of developing lamprey, indicating early appearance of the domain in vertebrate phylogeny.[well established][VHOG]
2012-09-17
VHOG:0001367
VHOG
DOI:10.1016/j.brainresbull.2005.05.001 Villar-Cheda B, Abalo XM, Anadon R, Rodicio MC, The tegmental proliferation region in the sea lamprey. Brain Research Bulletin (2005)
MTg
BIRNLEX:1200
NIFSTD:NeuroNames_abbrevSource
tegmentum
ISBN:0471888893
UMLS:C0039441
BIRNLEX:1200
http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=491
BIRNLEX:1200
tegmentum mesencephali
mesencephalic tegmentum
VHOG:0001367
tegmentum mesencephalicum
NeuroNames:491
A multi-tissue structure that is part of a spinal cord.
BIRNLEX:1496
NCIT:C33969
UMLS:C1268166
uberon
spinal cord part
UBERON:0001948
regional part of spinal cord
A multi-tissue structure that is part of a spinal cord.
OBOL:automatic
UMLS:C1268166
ncithesaurus:Spinal_Cord_Part
The liquid component of blood, in which erythrocytes are suspended.
plasma
portion of plasma
BTO:0000131
CALOHA:TS-0800
EFO:0001905
EMAPA:35690
FMA:62970
GAID:1178
MA:0002501
MAT:0000052
MESH:D010949
MIAA:0000052
NCIT:C13356
OpenCyc:Mx4rEg4ZYrIbEduAAAAOpmP6tw
UMLS:C0032105
blood plasm
portion of blood plasma
uberon
UBERON:0001969
blood plasma
The liquid component of blood, in which erythrocytes are suspended.
plasma
MA:0002501
portion of plasma
FMA:62970
UMLS:C0032105
ncithesaurus:Plasma
One of the minute vessels that collect deoxygenated blood from the capillary plexuses returns it to the veins
Multi-tissue structure part of the blood vasculature formed by the anastomosis of capillaries. Venules carry blood toward the heart.[TAO]
BTO:0002626
EMAPA:35917
FMA:63130
MA:0000071
MESH:A07.231.432.952
NCIT:C12818
TAO:0005315
UMLS:C0042520
VHOG:0001765
ZFA:0005315
uberon
venula
UBERON:0001979
venule
Illu:capillary.jpg
One of the minute vessels that collect deoxygenated blood from the capillary plexuses returns it to the veins
MESH:A07.231.432.952
MP:0004125
Multi-tissue structure part of the blood vasculature formed by the anastomosis of capillaries. Venules carry blood toward the heart.[TAO]
2012-08-14
TAO:0005315
TAO
ZFIN:curator
UMLS:C0042520
ncithesaurus:Venule
venula
The smallest division of the artery located between the muscular arteries and the capillaries[GO].
Multi-tissue structure part of the blood vasculature, feeds into capillaries. Arterioles carry blood away from the heart.[TAO]
Small, terminal branch of an artery which generally connects to capillaries.[AAO]
AAO:0010253
BTO:0001997
EMAPA:35146
FMA:63182
MA:0000063
MESH:D001160
NCIT:C12672
TAO:0002138
UMLS:C0003847
VHOG:0001763
ZFA:0005255
uberon
arteriola
UBERON:0001980
arteriole
Illu:capillary.jpg
MA
The smallest division of the artery located between the muscular arteries and the capillaries[GO].
GO:0014830
Multi-tissue structure part of the blood vasculature, feeds into capillaries. Arterioles carry blood away from the heart.[TAO]
2012-08-14
TAO:0002138
TAO
ZFIN:curator
Small, terminal branch of an artery which generally connects to capillaries.[AAO]
2012-06-20
AAO:0010253
AAO
AAO:BJB
UMLS:C0003847
ncithesaurus:Arteriole
arteriola
A vessel through which blood circulates in the body.
consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus
Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG]
Any of the vessels through which blood circulates in the body.[AAO]
The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]
annelids have blood vessels, but this class is not applicable to annelids.
FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX
vascular element
AAO:0011004
AEO:0000207
BTO:0001102
CALOHA:TS-0080
EFO:0000817
EHDAA2:0003252
EHDAA:240
EMAPA:32743
EMAPA:35993
FMA:50722
FMA:63183
GAID:169
MA:0000060
MAT:0000393
MESH:D001808
NCIT:C12679
NLXANAT:090901
OpenCyc:Mx4rvVjxlpwpEbGdrcN5Y29ycA
TAO:0002137
UMLS:C0005847
VHOG:0001250
XAO:0001011
ZFA:0005314
region of vascular tree organ
vascular tree organ region
uberon
vas sanguineum
UBERON:0001981
blood vessel
http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg
EHDAA2
GO:0072360
A vessel through which blood circulates in the body.
BTO:0001102
Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG]
2012-09-17
VHOG:0001250
VHOG
Any of the vessels through which blood circulates in the body.[AAO]
2012-06-20
AAO:0011004
AAO
AAO:EJS
The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]
2012-09-17
VHOG:0001250
VHOG
DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)
FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX
FMA
vascular element
EMAPA:35993
UMLS:C0005847
ncithesaurus:Blood_Vessel
region of vascular tree organ
FMA:50722
vascular tree organ region
FMA:50722
vas sanguineum
Any of the smallest blood vessels connecting arterioles with venules.
not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element
Any of the tiny blood vessels connecting the arterioles to the venules.[AAO]
The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]
capillaries lack tunica media and tunica adventitia; only the endothelial wall of the tunica intima belongs
AAO:0010252
BTO:0002045
CALOHA:TS-2006
EFO:0001906
EMAPA:35198
EV:0100035
FMA:63194
MA:0000065
MESH:A07.231.432.410
NCIT:C12685
NLXANAT:090902
OpenCyc:Mx4rvWEU-5wpEbGdrcN5Y29ycA
TAO:0005250
UMLS:C0935624
VHOG:0001253
XAO:0000116
ZFA:0005250
blood capillary
capillary vessel
uberon
UBERON:0001982
capillary
http://upload.wikimedia.org/wikipedia/commons/2/2f/A_red_blood_cell_in_a_capillary,_pancreatic_tissue_-_TEM.jpg
FMA
MA
XAO
ZFA
Any of the smallest blood vessels connecting arterioles with venules.
ISBN:0073040584
Any of the tiny blood vessels connecting the arterioles to the venules.[AAO]
2012-06-20
AAO:0010252
AAO
AAO:BJB
The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]
2012-09-17
VHOG:0001253
VHOG
DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)
UMLS:C0935624
ncithesaurus:Capillary
A monolayer of specialized, flattened, mitochondria-rich cells that lines the posterior surface of the cornea and faces the anterior chamber of the eye[WP].
CALOHA:TS-0172
EMAPA:35935
FMA:63882
GAID:891
MA:0001242
MESH:D004728
NCIT:C12707
TAO:0002186
UMLS:C0014259
ZFA:0001687
cornea endothelium
endothelium of cornea
uberon
epithelium posterius corneae
UBERON:0001985
corneal endothelium
http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png
A monolayer of specialized, flattened, mitochondria-rich cells that lines the posterior surface of the cornea and faces the anterior chamber of the eye[WP].
UMLS:C0014259
ncithesaurus:Corneal_Endothelium
cornea endothelium
OBOL:automatic
endothelium of cornea
OBOL:automatic
epithelium posterius corneae
A layer of epithelium that lines the heart, blood vessels (endothelium, vascular), lymph vessels (endothelium, lymphatic), and the serous cavities of the body[MESH]. Simple squamous epithelium which lines blood and lymphatic vessels and the heart[FMA]
endothelial
BTO:0000393
CALOHA:TS-0278
EFO:0002548
FMA:63916
GAID:520
MESH:D004727
NCIT:C12481
UMLS:C0014257
galen:Endothelium
uberon
UBERON:0001986
The term 'endothelium' has been either restricted to the continuous cell layer of the vertebrates, as we are assuming here, or applied to all the cells able to adhere to the luminal surface of the vascular basement membrane (Casley-Smith 1980)
endothelium
FMA-text-def
A layer of epithelium that lines the heart, blood vessels (endothelium, vascular), lymph vessels (endothelium, lymphatic), and the serous cavities of the body[MESH]. Simple squamous epithelium which lines blood and lymphatic vessels and the heart[FMA]
FMA:63916
MESH:A10.272.491
UMLS:C0014257
ncithesaurus:Endothelium
A nervous system structure composed primarily of nerve cell bodies (somas). May also include dendrites and the initial unmyelinated portion of axons.
Multi-tissue comprised of neurons, dendrites, axon terminals, glial cells, and capillaries.[TAO]
AEO:0001012
EHDAA2:0003136
EHDAA2_RETIRED:0004658
EMAPA:37596
FMA:67242
HBA:4006
MA:0001112
NCIT:C32695
OpenCyc:Mx4rwDdKMpwpEbGdrcN5Y29ycA
TAO:0002197
UMLS:C0018220
VHOG:0001768
ZFA:0001681
gray matter
gray matter of neuraxis
grey matter
grey matter of neuraxis
grey substance
neuronal grey matter
substantia grisea
uberon
gray mater
grisea
UBERON:0002020
gray matter
Spinal:nerve.svg
A nervous system structure composed primarily of nerve cell bodies (somas). May also include dendrites and the initial unmyelinated portion of axons.
Multi-tissue comprised of neurons, dendrites, axon terminals, glial cells, and capillaries.[TAO]
2012-08-14
TAO:0002197
TAO
ZFIN:curator
EMAPA:37596
MA:th
UMLS:C0018220
ncithesaurus:Gray_Matter
gray matter of neuraxis
FMA:67242
neuronal grey matter
AEO:0001012
substantia grisea
FMA:67242
FMA:TA
gray mater
ZFA:0001681
grisea
The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA].
Posterior part of the brain consisting of the cerebellum and medulla oblongata.[AAO]
The most posterior of the three principal regions of the brain, forming the rhombencephalon and all or most of the metencephalon. Kimmel et al, 1995.[TAO]
relationship loss: develops_from hindbrain neural tube (TAO:0007043)[TAO]
Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG]
rhombencephalic
in MA, brainstem and hindbrain and part-of siblings under brain, consistent with FMA and NIF. See also notes for cerebellum. We weaken the relation in ABA to overlaps
AAO:0010150
BAMS:HB
BIRNLEX:942
BTO:0000672
CALOHA:TS-0457
DHBA:10653
DMBA:16808
EFO:0000923
EHDAA2:0000746
EHDAA:3514
EHDAA:6487
EMAPA:16916
FMA:67687
MA:0000195
MAT:0000107
MBA:1065
MESH:D012249
MIAA:0000107
NCIT:C40336
TAO:0000029
UMLS:C0035507
UMLS:C1522180
VHOG:0000070
XAO:0000015
ZFA:0000029
http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=540
uberon
rhombencephalon
UBERON:0002028
hindbrain
http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg
modified-source-relation
ABA
Bgee:AN
The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA].
ZFA:0000029
ZFIN:curator
Posterior part of the brain consisting of the cerebellum and medulla oblongata.[AAO]
2012-06-20
AAO:0010150
AAO
AAO:BJB
The most posterior of the three principal regions of the brain, forming the rhombencephalon and all or most of the metencephalon. Kimmel et al, 1995.[TAO]
2012-08-14
TAO:0000029
TAO
ZFIN:curator
relationship loss: develops_from hindbrain neural tube (TAO:0007043)[TAO]
2012-08-14
TAO:0000029
TAO
Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG]
2012-09-17
VHOG:0000070
VHOG
DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)
in MA, brainstem and hindbrain and part-of siblings under brain, consistent with FMA and NIF. See also notes for cerebellum. We weaken the relation in ABA to overlaps
MA
UMLS:C0035507
BIRNLEX:942
UMLS:C0035507
ncithesaurus:Hind-Brain
UMLS:C1522180
BIRNLEX:942
http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=540
BIRNLEX:942
Muscle tissue that contains fibers that are divided by transverse bands into striations.
Voluntary muscle tissue arranged in bundles of fibers.[AAO]
AAO:0010762
AEO:0000140
CALOHA:TS-2047
EHDAA2:0003140
EMAPA:36390
FMA:67905
MA:0002438
NCIT:C12436
OpenCyc:Mx4rwAoze5wpEbGdrcN5Y29ycA
UMLS:C1331262
WBbt:0005779
galen:StriatedMuscle
striated muscle
uberon
UBERON:0002036
striated muscle tissue
Muscle tissue that contains fibers that are divided by transverse bands into striations.
CL:0000737
GOC:dph
GOC:mtg_muscle
Voluntary muscle tissue arranged in bundles of fibers.[AAO]
2012-06-20
AAO:0010762
AAO
AAO:CAM
UMLS:C1331262
ncithesaurus:Striated_Muscle_Tissue
An interconnected tubular multi-tissue structure contains fluid that is actively transported around the organism[ZFA]. Examples: vasculature of lung, vasculature of face.
see also: vascular system. Consider merging?
vascular
BTO:0003718
FMA:69050
TAO:0005249
ZFA:0005249
vascular network
uberon
UBERON:0002049
vasculature
http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg
FMA
An interconnected tubular multi-tissue structure contains fluid that is actively transported around the organism[ZFA]. Examples: vasculature of lung, vasculature of face.
ZFA:0005249
vascular network
FMA:69050
Anatomical structure that is part of an embryo.
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO]
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO]
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO]
in FMA embryo is_a embryonic structure
AAO:0000138
BILA:0000034
BTO:0000174
CALOHA:TS-2110
EFO:0000461
FBbt:00004208
FMA:69067
GAID:407
MESH:D004628
NCIT:C13229
RETIRED_EHDAA2:0003169
TAO:0001105
UMLS:C0013948
VSAO:0000178
XAO:0003042
ZFA:0001105
developing embryonic structure
embryonic anatomical structure
uberon
developing structure
embryonale Struktur
embryonic structures
UBERON:0002050
embryonic structure
Anatomical structure that is part of an embryo.
BTO:0000174
ZFIN:curator
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO]
2012-06-20
AAO:0000138
AAO
AAO:BJB
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO]
2012-08-14
TAO:0001105
TAO
ZFIN:curator
Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO]
2012-08-14
VSAO:0000178
VSAO
ZFIN:curator
in FMA embryo is_a embryonic structure
FMA
UMLS:C0013948
ncithesaurus:Embryonic_Structure
developing embryonic structure
FBbt:00004208
embryonic anatomical structure
RETIRED_EHDAA2:0003169
embryonale Struktur
BTO:0000174
embryonic structures
ZFA:0001105
The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP].
Consider adding a layer-of-skin grouping class for all skin layers
A collagenous layer of the skin subjacent to the epidermis and covering the hypodermis. It contains various types of cells (e.g. fibroblasts, pigment cells, nerve, blood vessels and scales. Le Guellec et al, 2004.[TAO]
When approaching controversies surrounding skin evolution, we need to remember that the skin consists of two layers, an epidermis and a dermis, not a single evolving structure. (...) It is little wonder that controversies about homology exist. If we think of the epidermis, the dermis, and their interactions as an evolving unit, then their specialized products (hair, feathers, and reptilian scales) are broadly homologous.[well established][VHOG]
dermal
AAO:0000128
BTO:0000294
CALOHA:TS-2076
EFO:0000953
EMAPA:17527
EV:0100154
FMA:70323
GAID:1321
MA:0000152
MAT:0000153
MESH:D020405
MIAA:0000153
NCIT:C12701
TAO:0001119
UMLS:C0011646
VHOG:0000108
XAO:0000217
ZFA:0001119
vertebrate dermis
uberon
corium
cutis
UBERON:0002067
dermis
http://upload.wikimedia.org/wikipedia/commons/2/23/EpidermisPainted.svg
FMA
definitional
The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP].
ZFIN:curator
A collagenous layer of the skin subjacent to the epidermis and covering the hypodermis. It contains various types of cells (e.g. fibroblasts, pigment cells, nerve, blood vessels and scales. Le Guellec et al, 2004.[TAO]
2012-08-14
TAO:0001119
TAO
ZFIN:curator
When approaching controversies surrounding skin evolution, we need to remember that the skin consists of two layers, an epidermis and a dermis, not a single evolving structure. (...) It is little wonder that controversies about homology exist. If we think of the epidermis, the dermis, and their interactions as an evolving unit, then their specialized products (hair, feathers, and reptilian scales) are broadly homologous.[well established][VHOG]
2012-09-17
VHOG:0000108
VHOG
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.231-232 see also p.209 and p.228 and Figure 6-1
UMLS:C0011646
ncithesaurus:Dermis
corium
corium
BTO:0000294
cutis
BTO:0000294
Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP].
A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells. Le Guellec et al, 2004.[TAO]
A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells[FMA:70544].
hypodermal
subcutaneous
subcutaneus
BTO has 'subcutis', as part of dermis. We follow FMA in having distinct classes for hypodermis and superficial fascia, and including these as part of the non-skin intgeument.
BTO:0001314
CALOHA:TS-2366
EMAPA:37505
FMA:70544
NCIT:C33645
TAO:0001136
UMLS:C0278403
ZFA:0001136
hypoderm
vertebrate hypodermis
uberon
sub-tegumental tissue
subcutaneous tissue
subcutis
subtegumental tissue
superficial fascia
tela subcutanea
UBERON:0002072
hypodermis
http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg
ZFA
FMA-modified
Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP].
A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells. Le Guellec et al, 2004.[TAO]
2012-08-14
TAO:0001136
TAO
ZFIN:curator
A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells[FMA:70544].
FMA:70544
BTO has 'subcutis', as part of dermis. We follow FMA in having distinct classes for hypodermis and superficial fascia, and including these as part of the non-skin intgeument.
BTO
EMAPA:37505
MA:th
UMLS:C0278403
ncithesaurus:Subcutis
sub-tegumental tissue
BTO:0004525
subcutaneous tissue
subtegumental tissue
BTO:0004525
superficial fascia
tela subcutanea
An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen.
An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO]
general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs.
AAO:0010386
BTO:0001491
EHDAA:512
EMAPA:16245
FMA:7085
MA:0000019
MESH:D014781
NCIT:C28287
RETIRED_EHDAA2:0002201
UMLS:C0042779
XAO:0003034
visceral organ
visceral organ system
uberon
Organsystem@de
splanchnic tissue
viscera
visceral tissue
UBERON:0002075
viscus
An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen.
BTO:0001491
An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO]
2012-06-20
AAO:0010386
AAO
BTO:0001491
general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs.
FMA
UMLS:C0042779
ncithesaurus:Viscera
visceral organ
RETIRED_EHDAA2:0002201
visceral organ system
MA:0000019
Organsystem@de
BTO:0001491
splanchnic tissue
BTO:0001491
visceral tissue
BTO:0001491
Cardiac chamber in which blood enters the heart.
One of four heart chambers.[TAO]
One of two chambers of the heart which receive blood from the veins and forces it by muscular contration to the ventricle.[AAO]
In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...).[well established][VHOG]
AAO:0010246
BTO:0000903
CALOHA:TS-0437
EFO:0000277
EHDAA2:0000154
EHDAA:1265
EMAPA:16688
EV:0100019
FMA:7099
GAID:555
MA:0000073
MAT:0000496
MESH:D006325
NCIT:C12728
TAO:0000471
UMLS:C0018792
VHOG:0000175
ZFA:0000471
galen:Atrium
atria
atrium
atrium of heart
cardiac atria
heart atrium
uberon
atrial tissue
UBERON:0002081
cardiac atrium
Cardiac chamber in which blood enters the heart.
One of four heart chambers.[TAO]
2012-08-14
TAO:0000471
TAO
ZFIN:curator
One of two chambers of the heart which receive blood from the veins and forces it by muscular contration to the ventricle.[AAO]
2012-06-20
AAO:0010246
AAO
AAO:BJB
In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...).[well established][VHOG]
2012-09-17
VHOG:0000175
VHOG
ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.428
UMLS:C0018792
ncithesaurus:Cardiac_Atrium
atria
atrium
ZFA:0000471
cardiac atria
atrial tissue
BTO:0000903
Cardiac chamber through which blood leaves the heart.
A chamber of the heart that receives blood from one or more atria and pumps it by muscular contraction into the arteries.[AAO]
One of four heart chambers.[TAO]
In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...)[well established][VHOG]
ventricle
AAO:0010249
BTO:0000862
CALOHA:TS-0444
EFO:0000317
EHDAA2:0004164
EHDAA:1912
EMAPA:17331
EV:0100020
FMA:7100
GAID:568
MA:0000091
MAT:0000497
MESH:D006352
NCIT:C12730
OpenCyc:Mx4rvVjj1pwpEbGdrcN5Y29ycA
TAO:0000009
UMLS:C0018827
VHOG:0000435
XAO:0003193
ZFA:0000009
galen:Ventricle
heart ventricle
lower chamber of heart
ventricle of heart
uberon
UBERON:0002082
cardiac ventricle
Bgee:AN
Cardiac chamber through which blood leaves the heart.
A chamber of the heart that receives blood from one or more atria and pumps it by muscular contraction into the arteries.[AAO]
2012-06-20
AAO:0010249
AAO
AAO:BJB
One of four heart chambers.[TAO]
2012-08-14
TAO:0000009
TAO
ZFIN:curator
In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...)[well established][VHOG]
2012-09-17
VHOG:0000435
VHOG
ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.428
UMLS:C0018827
ncithesaurus:Cardiac_Ventricle
The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA].
Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO]
The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO]
The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO]
The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG]
axial skeleton
AAO:0000034
EFO:0000942
EHDAA2:0000161
EHDAA:5049
EMAPA:17214
EMAPA:37721
FMA:71221
MA:0002986
MAT:0000148
MIAA:0000148
TAO:0000317
VHOG:0000317
VSAO:0000093
XAO:0003073
ZFA:0000317
post-cranial axial skeleton
uberon
UBERON:0002090
previous some AOs had used the term 'axial skeleton' to include the skull. This is being resolved (see tracker items above). Status: MA - fixed.
postcranial axial skeleton
http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton
The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA].
ZFA:0000317
Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO]
2012-08-14
VSAO:0000093
VSAO
PSPUB:0000170
The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO]
2012-06-20
AAO:0000034
AAO
AAO:LAP
The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO]
2012-08-14
TAO:0000317
TAO
ZFIN:curator
The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG]
2012-09-17
VHOG:0000317
VHOG
DOI:10.1186/1742-9994-8-4 Schilling N, Evolution of the axial system in craniates: morphology and function of the perivertebral musculature. Frontiers in Zoology (2011)
axial skeleton
FMA:71221
EMAPA:37721
MA:th
The organ covering the body that consists of the dermis and epidermis.
consider 'integumentary system' for invertebrates
MA uses the term skin to refer to what is called here: zone of skin
BTO:0001253
CALOHA:TS-0934
EFO:0000962
EHDAA2:0001844
EMAPA:17525
FMA:7163
MESH:D012867
MFMO:0000099
NCIT:C12470
OpenCyc:Mx4rvVjX3ZwpEbGdrcN5Y29ycA
UMLS:C1123023
XAO:0000023
galen:Skin
entire skin
skin organ
uberon
entire integument
integument
integumental organ
pelt
skin
UBERON:0002097
skin of body
http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg
Wikipathways:WP2062
The organ covering the body that consists of the dermis and epidermis.
UBERON:cjm
MA uses the term skin to refer to what is called here: zone of skin
FMA
UMLS:C1123023
ncithesaurus:Skin
The thin membranous structure between the two heart atria or the thick muscular structure between the two heart ventricles.
'Terrestrial vertebrates have divided hearts in which septae separate the oxygenated and deoxygenated blood within the pulmonary and systemic circulations'
in GO, septum morphogenesis is part of cardiac chamber morphogenesis; need to add axioms to infer this
EMAPA:35400
FMA:7180
GAID:562
MA:0000083
MESH:D006346
NCIT:C49485
UMLS:C0018819
XAO:0004141
cardiac septa
heart septa
heart septum
septum of heart
uberon
spiral septa
UBERON:0002099
cardiac septum
The thin membranous structure between the two heart atria or the thick muscular structure between the two heart ventricles.
MESH:A07.541.459
in GO, septum morphogenesis is part of cardiac chamber morphogenesis; need to add axioms to infer this
GO
UMLS:C0018819
ncithesaurus:Heart_Septum
cardiac septa
heart septa
spiral septa
XAO:0004141
Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present.
Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO]
Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO]
AAO:0010339
BILA:0000116
BTO:0001493
CALOHA:TS-1071
EFO:0000966
EMAPA:31857
FMA:7181
MA:0000004
MAT:0000296
MIAA:0000296
NCIT:C33816
OpenCyc:Mx4rvVkJjpwpEbGdrcN5Y29ycA
TAO:0001115
UMLS:C0460005
XAO:0000054
XAO:0003025
ZFA:0001115
galen:Trunk
thoracolumbar region
torso
trunk region
uberon
Rumpf
UBERON:0002100
trunk
Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present.
TAO:0001115
UBERONREF:0000006
Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO]
2012-06-20
AAO:0010339
AAO
AAO:BJB
Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO]
2012-08-14
TAO:0001115
TAO
ZFIN:curator
UMLS:C0460005
ncithesaurus:Trunk
trunk region
XAO:0000054
Rumpf
BTO:0001493
The sensory system subserving the sense of vision.
The sensory system used for sight.[AAO]
UBERON:0007036
AAO:0000632
BILA:0000140
EMAPA:36003
FMA:7191
MA:0002444
NCIT:C12888
OpenCyc:Mx4rvViCtpwpEbGdrcN5Y29ycA
TAO:0001127
UMLS:C0587900
XAO:0003198
ZFA:0001127
photosensory system
visual organ system
uberon
UBERON:0002104
visual system
The sensory system subserving the sense of vision.
NIFSTD:FMAID_7191
The sensory system used for sight.[AAO]
2012-06-20
AAO:0000632
AAO
AAO:EJS
UMLS:C0587900
ncithesaurus:Visual_System
photosensory system
BILA:0000140
A portion of smooth muscle tissue that is part of an artery [Automatically generated definition].
BTO:0000087
CALOHA:TS-1198
EMAPA:36285
FMA:72024
MA:0000708
NCIT:C49195
UMLS:C1706851
arterial smooth muscle
artery smooth muscle
artery smooth muscle tissue
smooth muscle of artery
uberon
arterial smooth muscle cell
UBERON:0002111
artery smooth muscle tissue
A portion of smooth muscle tissue that is part of an artery [Automatically generated definition].
OBOL:automatic
UMLS:C1706851
ncithesaurus:Artery_Smooth_Muscle_Tissue
arterial smooth muscle
BTO:0000087
smooth muscle of artery
FMA:72024
arterial smooth muscle cell
BTO:0000087
The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers[GO].
Layer that lines the lumen of the heart.[TAO]
Part of the heart comprised of thin serous membrane, composed of endothelial tissue, that lines the interior of the heart.[AAO]
Tunica intima which has as its parts the endothelium of endocardium and the fibroelastic connective tissue that surrounds the cavity of a cardiac chamber.
UBERON:0006225
AAO:0010408
BTO:0000387
CALOHA:TS-2075
EFO:0000821
EHDAA2:0004153
EMAPA:17868
EMAPA:32686
EV:0100021
FMA:7280
GAID:550
MA:0000076
MAT:0000455
MESH:D004699
NCIT:C13004
OpenCyc:Mx4rsWA75K1cEduAAADggVaqvw
TAO:0001320
UMLS:C0014124
VHOG:0000084
XAO:0000066
ZFA:0001320
galen:Endocardium
endocardial lining
endocardial tissue
heart endocardium
uberon
heart endocardial tissue
UBERON:0002165
fixed in GO to reflect FMA. See email to David/Varsha June 18 2010
endocardium
http://upload.wikimedia.org/wikipedia/commons/6/6c/Gray493.png
Bgee:AN
The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers[GO].
GO:0003157
Layer that lines the lumen of the heart.[TAO]
2012-08-14
TAO:0001320
TAO
ZFIN:curator
Part of the heart comprised of thin serous membrane, composed of endothelial tissue, that lines the interior of the heart.[AAO]
2012-06-20
AAO:0010408
AAO
AAO:BJB
Tunica intima which has as its parts the endothelium of endocardium and the fibroelastic connective tissue that surrounds the cavity of a cardiac chamber.
FMA:7280
UMLS:C0014124
ncithesaurus:Endocardium
endocardial lining
EMAPA:32686
endocardial tissue
EMAPA:17868
heart endocardial tissue
VHOG:0000084
Endocardium that is part of the atrium.
EMAPA:32745
FMA:7284
MA:0000077
TAO:0002169
VHOG:0000606
ZFA:0001614
Cardiac atria endocardium
atrial endocardium
atrium endocardium
atrium of heart endocardium
cardiac atrium endocardium
endocardium of Cardiac atria
endocardium of atrium of heart
endocardium of cardiac atrium
endocardium of heart atrium
heart atrium endocardium
uberon
atrium endocardial tissue
UBERON:0002166
endocardium of atrium
Endocardium that is part of the atrium.
ZFIN:curator
Cardiac atria endocardium
OBOL:automatic
atrium of heart endocardium
OBOL:automatic
cardiac atrium endocardium
OBOL:automatic
endocardium of Cardiac atria
OBOL:automatic
endocardium of atrium of heart
OBOL:automatic
endocardium of cardiac atrium
OBOL:automatic
endocardium of heart atrium
OBOL:automatic
heart atrium endocardium
OBOL:automatic
atrium endocardial tissue
VHOG:0000606
A portion of adipose tissue that is part of the hypodermis, beneath the dermis.
the superficial portion of the subcutaneous tissue which is specialized for fat storage[MP:0011156]
UBERON:0008875
panniculus adiposus
BTO:0004042
EMAPA:35829
FMA:74315
MA:0000473
fatty layer of subcutaneous tissue
hypodermis fat layer
panniculus adiposus (tela subcutanea)
panniculus adiposus telae subcutaneae
subcutaneous fat layer
uberon
fatty layer of superficial fascia
subcutaneous fat
UBERON:0002190
subcutaneous adipose tissue
A portion of adipose tissue that is part of the hypodermis, beneath the dermis.
the superficial portion of the subcutaneous tissue which is specialized for fat storage[MP:0011156]
MP:0011156
panniculus adiposus
MP:0011156
fatty layer of subcutaneous tissue
FMA:74315
hypodermis fat layer
MP:0011156
panniculus adiposus (tela subcutanea)
FMA:74315
FMA:TA
panniculus adiposus telae subcutaneae
FMA:74315
FMA:TA
subcutaneous fat layer
MP:0011156
fatty layer of superficial fascia
FMA:74315
subcutaneous fat
BTO:0004042
Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs.
CALOHA:TS-2018
EHDAA2:0004615
EMAPA:18765
FMA:74562
MA:0000013
hematolymphoid system
lymphomyeloid complex
uberon
haemolymphoid system
UBERON:0002193
hemolymphoid system
MA
Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs.
The dermis, epidermis and hypodermis.
in FMA intergument = skin+superficial fascia(hypodermis), skin=dermis+epidermis+hair_nail. Note that the definition provided here excludes the more general sense of the term 'integument' used in invertebrates; consider 'integumental system'. Note that the VSAO class appears to include adnexa by its definition.
Anatomical system that protects the body from damage, comprising the skin and its appendages.[AAO]
Surface structure that is the outer protective covering of the body.[VSAO]
The outer protective barrier that separates the animal from its aquatic environment. Le Guellec et al, 2004.[TAO]
integumental
integumentary
AAO:0000239
BTO:0000634
EMAPA:37504
FMA:74657
TAO:0000368
VSAO:0000029
ZFA:0000368
galen:Integument
dermis plus epidermis plus hypodermis
integumentum commune
skin and subcutaneous tissue
skin plus hypodermis
the integument
uberon
Hautsystem@de
dermal system
dermoid system
skin
tegument
vertebrate integument
UBERON:0002199
integument
FMA
FMA
The dermis, epidermis and hypodermis.
Anatomical system that protects the body from damage, comprising the skin and its appendages.[AAO]
2012-06-20
AAO:0000239
AAO
AAO:EJS
Surface structure that is the outer protective covering of the body.[VSAO]
2012-08-14
VSAO:0000029
VSAO
PSPUB:0000170
The outer protective barrier that separates the animal from its aquatic environment. Le Guellec et al, 2004.[TAO]
2012-08-14
TAO:0000368
TAO
ZFIN:curator
EMAPA:37504
MA:th
integumentum commune
FMA:74657
FMA:TA
the integument
FMA:74657
Hautsystem@de
BTO:0000634
dermal system
BTO:0000634
dermoid system
BTO:0000634
tegument
BTO:0000634
Vasculature that is part of a head [Automatically generated definition].
EFO:0003656
FMA:74710
TAO:0001267
XAO:0004152
ZFA:0001267
adult head vascular network
adult head vasculature
cranial vasculature
head vascular network
vascular network of adult head
vascular network of head
vasculature of adult head
uberon
head vasculature
UBERON:0002200
vasculature of head
Vasculature that is part of a head [Automatically generated definition].
OBOL:automatic
adult head vascular network
OBOL:automatic
adult head vasculature
OBOL:automatic
head vascular network
OBOL:automatic
vascular network of adult head
OBOL:automatic
vascular network of head
OBOL:automatic
vasculature of adult head
OBOL:automatic
A vasculature that is part of a trunk [Automatically generated definition].
FMA:74712
TAO:0005024
ZFA:0005024
torso vascular network
torso vasculature
trunk vascular network
trunk vasculature
vascular network of torso
vascular network of trunk
vasculature of torso
uberon
UBERON:0002201
vasculature of trunk
A vasculature that is part of a trunk [Automatically generated definition].
OBOL:automatic
torso vascular network
OBOL:automatic
torso vasculature
OBOL:automatic
trunk vascular network
OBOL:automatic
vascular network of torso
OBOL:automatic
vascular network of trunk
OBOL:automatic
vasculature of torso
OBOL:automatic
Vasculature that is part of the eye region.
not part of the eye in ZFA. Note this changed to a blood vessel in ZFA
FMA:74743
TAO:0007057
ZFA:0007057
eye vascular network
ocular blood vessel
ocular vasculature
vascular network of eye
uberon
eye vasculature
optic vasculature
UBERON:0002203
vasculature of eye
ISBN:0781772214
Vasculature that is part of the eye region.
OBOL:automatic
not part of the eye in ZFA. Note this changed to a blood vessel in ZFA
ZFA
eye vascular network
OBOL:automatic
ocular blood vessel
ZFA:0007057
vascular network of eye
OBOL:automatic
Anatomical system that consists of the muscular and skeletal systems.
Anatomical system that provides locomotion and physical support to the organism.[AAO]
There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG]
musculoskeletal
AAO:0010546
CALOHA:TS-1311
EMAPA:32714
EV:0100139
FMA:7482
GAID:98
MA:0002418
MESH:D009141
NCIT:C12754
OpenCyc:Mx4rQRpVNgAKEdyHxgDggVfs8g
UMLS:C0026860
VHOG:0001275
VSAO:0000031
XAO:0000168
musculo-skeletal system
uberon
UBERON:0002204
musculoskeletal system
check ctenophore
Anatomical system that consists of the muscular and skeletal systems.
VSAO:0000031
VSAO:curator
Anatomical system that provides locomotion and physical support to the organism.[AAO]
2012-06-20
AAO:0010546
AAO
AAO:EJS
There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG]
2012-09-17
VHOG:0001275
VHOG
DOI:10.1002/jez.b.21246 Shearman RM, Burke AC, The lateral somitic frontier in ontogeny and phylogeny. Journal of Experimental Zoology (2009)
UMLS:C0026860
ncithesaurus:Musculoskeletal_System
Nonsynovial joint in which the articulating bones or cartilages are connected by cartilage. Examples: Spheno-occipital synchondrosis, first sternocostal joint, pubic symphysis.[FMA]
EMAPA:36581
FMA:7496
MA:0000320
TAO:0005155
ZFA:0005155
articulatio cartilaginea
uberon
junctura cartilaginea
UBERON:0002213
cartilaginous joint
FMA
Nonsynovial joint in which the articulating bones or cartilages are connected by cartilage. Examples: Spheno-occipital synchondrosis, first sternocostal joint, pubic symphysis.[FMA]
FMA:FMA
junctura cartilaginea
Joint in which the articulating bones or cartilages are connected by an articular capsule which encloses a synovial membrane and a synovial cavity. Examples: Temporomandibular joint, knee joint.[FMA]
Is a joint that is located at the point of contact of articulating bones allowing movement. The joint has a capsule containing synovial fluid surrounding the articulating bone surfaces.[TAO]
AEO:0000183
CALOHA:TS-2138
EHDAA2:0003183
FMA:7501
MA:0000322
NCIT:C32461
OpenCyc:Mx4rv2bBV5wpEbGdrcN5Y29ycA
TAO:0005153
ZFA:0005153
galen:SynovialJoint
articulatio synoviale
diarthroses
diarthrosis
diarthrosis joint
uberon
diarthrodial joints
UBERON:0002217
synovial joint
Joint in which the articulating bones or cartilages are connected by an articular capsule which encloses a synovial membrane and a synovial cavity. Examples: Temporomandibular joint, knee joint.[FMA]
FMA:7501
Is a joint that is located at the point of contact of articulating bones allowing movement. The joint has a capsule containing synovial fluid surrounding the articulating bone surfaces.[TAO]
2012-08-14
TAO:0005153
TAO
ZFIN:Curator
diarthroses
ZFA:0005153
diarthrodial joints
ZFA:0005153
The part of the coelemic cavity lumen that is enclosed by the walls of the thorax.
In many species, the diaphragm separates thoracic and abdominal cavities
EMAPA:36497
FMA:7565
GAID:93
MA:0000032
MESH:A01.911.800
NCIT:C12905
OpenCyc:Mx4rmvyleLfEEduAAAACs6hRXg
OpenCyc:Mx4rvhU_TpwpEbGdrcN5Y29ycA
UMLS:C0230139
cavitas thoracis
cavity of chest
cavity of thorax
chest cavity
pectoral cavity
space of thoracic compartment
thoracic lumen
uberon
UBERON:0002224
thoracic cavity
http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray846.png
http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg
The part of the coelemic cavity lumen that is enclosed by the walls of the thorax.
UBERON:cjm
UMLS:C0230139
ncithesaurus:Thoracic_Cavity
cavitas thoracis
space of thoracic compartment
FMA:7565
Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal. (CUMBO)
TODO - add superclass to unify with VNC?
Part of the central nervous system which descends from the hindbrain within the vertebral column.[AAO]
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG]
AAO:0010151
BAMS:SP
BAMS:Spinal
BIRNLEX:1709
BM:SpC
BTO:0001279
CALOHA:TS-0953
DHBA:12890
DMBA:17651
EFO:0000110
EHDAA2:0001255
EHDAA:2863
EMAPA:17577
EV:0100316
FMA:7647
GAID:695
MA:0000216
MAT:0000183
MESH:D013116
MIAA:0000183
NCIT:C12464
OpenCyc:Mx4rvVjjk5wpEbGdrcN5Y29ycA
TAO:0000075
UMLS:C0037925
VHOG:0000601
XAO:0000020
ZFA:0000075
http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=22
uberon
SpC
cerebro-cerebellar fissure
cerebrocerebellar fissure
fissura cerebro-cerebellaris
fissura cerebrocerebellaris
medulla spinalis
spinal cord structure
spinal medulla
UBERON:0002240
spinal cord
http://upload.wikimedia.org/wikipedia/commons/5/58/Spinal_cord_direv.svg
definitional
definitional
Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal. (CUMBO)
BIRNLEX:1709
Part of the central nervous system which descends from the hindbrain within the vertebral column.[AAO]
2012-06-20
AAO:0010151
AAO
AAO:BJB
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG]
2012-09-17
VHOG:0000601
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165
UMLS:C0037925
BIRNLEX:1709
UMLS:C0037925
ncithesaurus:Spinal_Cord
http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=22
BIRNLEX:1709
SpC
cerebro-cerebellar fissure
NeuroNames:22
cerebrocerebellar fissure
NeuroNames:22
fissura cerebro-cerebellaris
NeuroNames:22
fissura cerebrocerebellaris
NeuroNames:22
medulla spinalis
medulla spinalis
BTO:0001279
spinal cord structure
ZFA:0000075
spinal medulla
BTO:0001279
Endoskeletal elements that encase the brain, nose, inner ear[cjm]. that part of the neurocranium formed by endochondral ossification and comprising the bones of the base of the skull[TFD].
we follow the standard evolutionary classification and treat this as endoskeletal. This means what MA calls 'chondrocranium' must in fact be neurocranium, as it includes parts of the dermatocranium (e.g. frontal, parietal)
Anatomical cluster that is part of the cranium and composed of cartilage and cartilage replacement bones.[AAO]
Anatomical cluster that is part of the cranium and composed of cartilage and cartilage replacement bones.[TAO]
chondrocranial
covers the brain dorsally in chondrichthyans
AAO:0010169
EHDAA2:0000243
EMAPA:17681
TAO:0001424
VHOG:0000288
ZFA:0001424
uberon
calvarium
neurocranium
UBERON:0002241
chondrocranium
Endoskeletal elements that encase the brain, nose, inner ear[cjm]. that part of the neurocranium formed by endochondral ossification and comprising the bones of the base of the skull[TFD].
Anatomical cluster that is part of the cranium and composed of cartilage and cartilage replacement bones.[AAO]
2012-06-20
AAO:0010169
AAO
AAO:BJB
Anatomical cluster that is part of the cranium and composed of cartilage and cartilage replacement bones.[TAO]
2012-08-14
TAO:0001424
TAO
ZFIN:curator
calvarium
MA:0000317
neurocranium
MA:0000317
Stalk-like part of the brain that includes amongst its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,MP,generalized].
Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain.[TAO]
Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,adopted][ZFA:0001707].
the stalk-like part of the brain that comprises the midbrain (aka mesencephalon), the pons (aka pons Varolii), and the medulla oblongata, and connects the cerebral hemispheres with the cervical spinal cord[MP]
BAMS:BS
BIRNLEX:1565
BTO:0000146
CALOHA:TS-0093
EFO:0001962
EMAPA:32678
EV:0100241
FMA:79876
MA:0000169
MBA:343
MESH:D001933
NCIT:C12441
TAO:0002156
UMLS:C0006121
VHOG:0001457
ZFA:0001707
http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=236
brain stem
truncus encephali
uberon
accessory medullary lamina of pallidum
lamella pallidi incompleta
lamina medullaris accessoria
lamina medullaris incompleta pallidi
lamina pallidi incompleta
truncus encephalicus
UBERON:0002298
'brainstem' is a loose term that sometimes refers to the ventral parts o the brain except for any part of the telencephalon - sometimes it includes the diencephalon or subpallial telencephalon structures (ISBN:0471888893). Here we use it in a more restriced sense, to include only the medulla oblongata, pons (when present) and the midbrain tegmentum (following the ZFA definitions).
brainstem
http://upload.wikimedia.org/wikipedia/commons/b/b7/Gray719.png
Stalk-like part of the brain that includes amongst its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,MP,generalized].
ISBN:0471888893
MP:0005277
ZFA:0001707
Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain.[TAO]
2012-08-14
TAO:0002156
TAO
ISBN:3764351209
Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,adopted][ZFA:0001707].
ZFA:0001707
the stalk-like part of the brain that comprises the midbrain (aka mesencephalon), the pons (aka pons Varolii), and the medulla oblongata, and connects the cerebral hemispheres with the cervical spinal cord[MP]
MP:0005277
UMLS:C0006121
BIRNLEX:1565
UMLS:C0006121
ncithesaurus:Brain_Stem
http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=236
BIRNLEX:1565
brain stem
ABA:BS
truncus encephali
accessory medullary lamina of pallidum
NeuroNames:236
lamella pallidi incompleta
NeuroNames:236
lamina medullaris accessoria
NeuroNames:236
lamina medullaris incompleta pallidi
NeuroNames:236
lamina pallidi incompleta
NeuroNames:236
truncus encephalicus
BTO:0000146
the atrial part of middle layer of the heart, comprised of involuntary muscle
As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[uncertain][VHOG]
EFO:0003087
EMAPA:32746
FMA:83509
MA:0000081
TAO:0001374
VHOG:0000602
ZFA:0001374
atrial myocardium
atrium myocardium
uberon
atrium cardiac muscle
UBERON:0002302
myocardium of atrium
the atrial part of middle layer of the heart, comprised of involuntary muscle
ISBN:0-683-40008-8
MP:0010493
As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[uncertain][VHOG]
2012-09-17
VHOG:0000602
VHOG
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481
atrial myocardium
ZFA:0001374
atrium cardiac muscle
VHOG:0000602
The ridge-shaped grey matter of the spinal cord that extends longitudunally through the center of each half of the spinal cord, and are largely or entirely composed of nerve cell bodies and their dendrites and some supportive tissue.
BAMS:Scgrey
DHBA:146035048
EMAPA:35792
FMA:256580
MA:0000002
NCIT:C32696
NLXANAT:100204
UMLS:C0475853
gray matter of spinal cord
gray substance of spinal cord
grey matter of spinal cord
grey substance of spinal cord
spinal cord gray matter
spinal cord grey matter
spinal cord grey substance
substantia grisea medullae spinalis
uberon
UBERON:0002315
gray matter of spinal cord
The ridge-shaped grey matter of the spinal cord that extends longitudunally through the center of each half of the spinal cord, and are largely or entirely composed of nerve cell bodies and their dendrites and some supportive tissue.
MP:0008503
UMLS:C0475853
ncithesaurus:Gray_Matter_of_the_Spinal_Cord
gray matter of spinal cord
OBOL:automatic
gray substance of spinal cord
FMA:256580
spinal cord gray matter
OBOL:automatic
spinal cord grey substance
OBOL:automatic
substantia grisea medullae spinalis
FMA:256580
FMA:TA
The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities.
check the FMA placement here; ncit placement of body cavity here probably not correct
Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA].
The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO].
In mammals it forms the peritoneal, pleural, and pericardial cavities
UBERON:0000169
body cavity
AEO:0000186
BTO:0001707
EHDAA2:0000267
FBbt:00005060
FMA:85006
NCIT:C25444
RETIRED_EHDAA2:0003186
TAO:0001438
UMLS:C0333343
ZFA:0001438
galen:BodyCavity
coelomic cavity
coelomic cavity lumen
main body cavity
space of body compartment
ventral body cavity
uberon
celom
coelom
coelome
hemocoel
UBERON:0002323
coelemic cavity lumen
definitional
The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities.
BTO:0001707
Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA].
2012-09-12
ZFA:0001438
ZFA
ZFIN:curator
The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO].
2012-09-12
BTO:0001707
BTO
BTO
body cavity
BTO:0001707
UMLS:C0333343
ncithesaurus:Cavity
coelomic cavity
EHDAA2:0000267
coelomic cavity lumen
EHDAA2:0000267
space of body compartment
FMA:85006
ventral body cavity
NCBITaxon:7742
celom
BTO:0001707
coelome
BTO:0001707
hemocoel
FBbt:00005060
Any muscle organ that is part of a back [Automatically generated definition].
EMAPA:35161
FMA:85216
MA:0000496
back muscle
back muscle organ
muscle organ of back
uberon
UBERON:0002324
muscle of back
prolog
Any muscle organ that is part of a back [Automatically generated definition].
OBOL:automatic
back muscle organ
OBOL:automatic
muscle organ of back
OBOL:automatic
A flexible rod-shaped body found in embryos of all chordates. It is composed of cells derived from the mesoderm and defines the primitive axis of the embryo. In some chordates, it persists throughout life as the main axial support of the body, while in most vertebrates it becomes the nucleus pulposus of the intervertebral disc. The notochord is found ventral to the neural tube.
Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO]
Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO]
Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO]
relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO]
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG]
notochordal
In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord.
AAO:0000327
BTO:0001768
CALOHA:TS-0690
EHDAA2:0001277
EHDAA:1241
EHDAA:6021
EMAPA:16191
EV:0100002
FMA:85521
GAID:1311
MAT:0000281
MESH:A16.254.610
NCIT:C12463
TAO:0000135
UMLS:C0028439
VHOG:0000199
VSAO:0000032
XAO:0000055
ZFA:0000135
embryonic notocord
notocord
uberon
notochorda
UBERON:0002328
The notochord appears early in embryogeny and plays an important role in promoting or organizing the embryonic development of nearby structures. In most adult chordates the notochord disappears or becomes highly modified. In some non-vertebrate chordates and fishes the notochord persists as a laterally flexible but incompressible skeletal rod that prevents telescopic collapse of the body during swimming[TOLWEB]
notochord
http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png
VSAO
ZFA
EHDAA2
A flexible rod-shaped body found in embryos of all chordates. It is composed of cells derived from the mesoderm and defines the primitive axis of the embryo. In some chordates, it persists throughout life as the main axial support of the body, while in most vertebrates it becomes the nucleus pulposus of the intervertebral disc. The notochord is found ventral to the neural tube.
ISBN:0815318960
Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO]
2012-08-14
VSAO:0000032
VSAO
PSPUB:0000170
Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO]
2012-08-14
TAO:0000135
TAO
ZFIN:curator
Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO]
2012-06-20
AAO:0000327
AAO
AAO:LAP
relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO]
2012-06-20
AAO:0000327
AAO
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG]
2012-09-17
VHOG:0000199
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28
UMLS:C0028439
ncithesaurus:Notochord
notocord
ZFA:0000135
notochorda
Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm.
currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk
Post-cranial axial segments which form sclerotome and dermomyotome.[AAO]
Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO]
relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO]
relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO]
relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO]
(...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG]
somitic
mesodermal cluster
AAO:0010569
AEO:0001015
BTO:0001558
EHDAA2:0003436
EHDAA:366
EHDAA:699
EMAPA:31169
FMA:85522
GAID:1306
MAT:0000068
MESH:A16.254.425.660.750
MIAA:0000068
NCIT:C34302
TAO:0000155
UMLS:C0376449
VHOG:0000191
XAO:0000058
ZFA:0000155
uberon
epimere
epimere mesoderm
epithelial somite
somites
somitic mesoderm
somitus
UBERON:0002329
When the somite becomes segmented from the segmental plate, it is composed of an epithelial sac enclosing mesenchymal somitocoel cells. Thereafter the somite differentiates into two parts, the ventro-medial mesenchymal sclerotome and the dorso-lateral epithelial dermomyotome. This change in the epithelial somite depends on surrounding tissue [PMID:15906248]
somite
http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png
EHDAA2
ZFA
Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm.
Post-cranial axial segments which form sclerotome and dermomyotome.[AAO]
2012-06-20
AAO:0010569
AAO
AAO:EJS
Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO]
2012-08-14
TAO:0000155
TAO
ZFIN:curator
relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO]
2012-08-14
TAO:0000155
TAO
relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO]
2012-08-14
TAO:0000155
TAO
relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO]
2012-06-20
AAO:0010569
AAO
(...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG]
2012-09-17
VHOG:0000191
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.40, DOI:10.1093/icb/43.1.137 Balavoine G, Adoutte A, The segmented urbilateria: a testable scenario. Integrative and Comparative Biology (2003)
mesodermal cluster
GO:0001756
UMLS:C0376449
ncithesaurus:Somite
epimere
ISBN:0073040584
epithelial somite
somites
somitus
Anatomical system that consists of the glands and parts of glands that produce exocrine secretions and help to integrate and control bodily metabolic activity. Exocrine glands are glands that secrete their products (hormones) into ducts (duct glands). They are the counterparts to endocrine glands, which secrete their products (hormones) directly into the bloodstream (ductless glands) or release hormones (paracrines) that affect only target cells nearby the release site. [Wikipedia].
CALOHA:TS-2057
EHDAA2:0002225
EMAPA:35329
FMA:85539
MA:0002411
NCIT:C12957
UMLS:C1516995
WikipediaCategory:Exocrine_system
exocrine glandular system
uberon
UBERON:0002330
exocrine system
Anatomical system that consists of the glands and parts of glands that produce exocrine secretions and help to integrate and control bodily metabolic activity. Exocrine glands are glands that secrete their products (hormones) into ducts (duct glands). They are the counterparts to endocrine glands, which secrete their products (hormones) directly into the bloodstream (ductless glands) or release hormones (paracrines) that affect only target cells nearby the release site. [Wikipedia].
UMLS:C1516995
ncithesaurus:Exocrine_System
exocrine glandular system
EHDAA2:0002225
A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP].
consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams).
A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO]
Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO]
A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831]
We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG]
AAO:0010578
BTO:0001764
CALOHA:TS-0676
EHDAA2:0004419
EMAPA:32737
FMA:86666
GAID:1310
MAT:0000066
MESH:A16.254.600
MIAA:0000066
NCIT:C34222
TAO:0000045
UMLS:C0027789
VHOG:0000057
XAO:0000048
ZFA:0000045
NC
uberon
crista neuralis
neural crest material
UBERON:0002342
Gene notes: Many factors and genes, such as Pax3 (Tremblay et al., 1995), slug (Nieto et al., 1994), AP-2 (Zhang et al., 1996; Schorle et al., 1996), and Wnt-1/3a (Ikeya et al., 1997) are expressed in the dorsal most region of the neural tube, and have been shown to be involved in the generation of neural crest cells.
neural crest
Neural:Crest.png
http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png
XAO
BTO
A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP].
MP:0009846
ISBN:0073040584
A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO]
2012-08-14
TAO:0000045
TAO
ZFIN:curator
Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO]
2012-06-20
AAO:0010578
AAO
AAO:EJS
A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831]
We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG]
2012-09-17
VHOG:0000057
VHOG
DOI:10.1111/j.1469-7580.2012.01495.x Hall BK, Gillis JA, Incremental evolution of the neural crest, neural crest cells and neural crest-derived skeletal tissues. J Anat (2012)
UMLS:C0027789
ncithesaurus:Neural_Crest
NC
XAO:0000048
crista neuralis
neural crest material
VHOG:0000057
Embryonic ectoderm that gives rise to nervous tissue.
(...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG]
neurectodermal
we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here
AAO:0011074
BILA:0000039
CALOHA:TS-1212
EHDAA2:0001248
EHDAA:1498
EHDAA:255
EMAPA:16073
EV:0100004
FBbt:00001061
FMA:87657
MAT:0000176
MIAA:0000176
NCIT:C34228
TAO:0001120
UMLS:C1518271
VHOG:0000150
XAO:0000042
ZFA:0001120
neural ectoderm
neuroectoderm
uberon
epithelium tubi neuralis; neuroectoderma
neuaral ectoderm
presumptive central nervous system
ventral neurogenic region
UBERON:0002346
neurectoderm
Embryonic ectoderm that gives rise to nervous tissue.
(...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG]
2012-09-17
VHOG:0000150
VHOG
DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)
UMLS:C1518271
ncithesaurus:Neuroectoderm
epithelium tubi neuralis; neuroectoderma
ventral neurogenic region
VHOG:0000150
a region of the serous membrane that forms the innermost layer of the pericardium and the outer surface of the heart.
TODO - check links with UBERON:0002425 visceral serous pericardium. develops from proepicardium. WP:Epicardium -- When considered as a part of the pericardium, it is the inner layer, or visceral pericardium, continuous with the serous layer.
External layer of the heart.[TAO]
The inner layer of the pericardium that is in contact with the surface of the heart.[AAO]
The visceral pericardium apparently produces the pericardial fluid, which lubricates motion between the inner and outer layers of the pericardium. During ventricular contraction, the wave of depolarization moves from endocardial to epicardial surface. [Wikipedia:Epicardium]
AAO:0010409
EHDAA2:0002202
FMA:9461
NCIT:C13164
TAO:0005057
UMLS:C0225968
VHOG:0000119
XAO:0000316
ZFA:0005057
galen:Epicardium
heart epicardium
visceral serous pericardium of heart
visceral serous pericardium proper
uberon
pericardium visceral mesothelium
UBERON:0002348
epicardium
multiple
FMA-inferred
FMA
a region of the serous membrane that forms the innermost layer of the pericardium and the outer surface of the heart.
External layer of the heart.[TAO]
2012-08-14
TAO:0005057
TAO
ZFIN:curator
The inner layer of the pericardium that is in contact with the surface of the heart.[AAO]
2012-06-20
AAO:0010409
AAO
AAO:BJB
UMLS:C0225968
ncithesaurus:Epicardium
visceral serous pericardium of heart
FMA:9461
visceral serous pericardium proper
FMA:9461
pericardium visceral mesothelium
EMAPA:16589
the middle layer of the heart, comprised mainly of striated cardiac muscle fibers
TODO - check 'Myocardum proper' in FMA. We superclass the more generic class for now. FMA has is_a muscle layer - should we add this? ZFA and BTO both have is_a 'cardiac muscle' (tissue?). But in U we also follow FMA and have cardiac muscle tissue of myocardium (there is also Fibrocollagenous connective tissue of myocardium), which would be identical (see issue-10). Note that GO also treats left/right ventricular cardiac muscle tissue synonymous with ventricular myocardium
Robust muscular tunic of the heart which forms the basic part of its walls. Its external surface is covered by the pericardium and its internal one by the endocardium. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
The middle layer of the heart, consisting of cardiac muscle.[AAO]
myocardial
AAO:0010410
BSA:0000089
BTO:0000901
CALOHA:TS-0440
EFO:0000819
EHDAA2:0004150
EMAPA:32688
EV:0100022
FMA:9462
GAID:173
MA:0000164
MAT:0000453
MESH:D009206
NCIT:C12371
OpenCyc:Mx4ro36AFrCvEduAAAAOpmP6tw
RETIRED_EHDAA2:0001220
TAO:0001319
UMLS:C0027061
VHOG:0000083
XAO:0000065
ZFA:0001319
galen:Myocardium
heart myocardium
muscle of heart
uberon
cardiac muscle
heart muscle
UBERON:0002349
myocardium
http://upload.wikimedia.org/wikipedia/commons/6/6e/Glanzstreifen.jpg
the middle layer of the heart, comprised mainly of striated cardiac muscle fibers
ISBN:0-683-40008-8
MP:0005329
Robust muscular tunic of the heart which forms the basic part of its walls. Its external surface is covered by the pericardium and its internal one by the endocardium. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
2012-09-17
VHOG:0000083
VHOG
The middle layer of the heart, consisting of cardiac muscle.[AAO]
2012-06-20
AAO:0010410
AAO
AAO:BJB
UMLS:C0027061
ncithesaurus:Myocardium
muscle of heart
FMA:9462
cardiac muscle
ZFA:0001319
heart muscle
FMA:9462
heart muscle
ZFA:0001319
The cardiac conduction system consists of specialized cardiomyocytes that regulate the frequency of heart beat[GO]
EHDAA2 divides the system from the tissue
The fish heart displays clear polarity of contraction in a posterior-to-anterior direction. The contraction waves originate in the sinus venosus and terminate in the conus arteriosus. The nodal phenotype persists in the inflow region of the heart, varying from the venosinus to the sinoatrial junctional areas in different species . Similar to the mammalian situation, pacemaker tissue with a lower intrinsic rhythmicity is also found at the atrioventricular junction.[uncertain][VHOG]
EFO:0003909
EHDAA2:0004185
EMAPA:35428
EV:0100025
FMA:9476
MA:0000094
MESH:D006329
TAO:0005063
VHOG:0001271
ZFA:0005063
cardiac conducting system
cardiac conduction system
cardiac impulse conducting system
cardionector
complexus stimulans cordis
heart conduction system
impulse conducting system
systema conducente cordis
uberon
central conduction system
UBERON:0002350
conducting system of heart
FMA
The cardiac conduction system consists of specialized cardiomyocytes that regulate the frequency of heart beat[GO]
GO:0003161
The fish heart displays clear polarity of contraction in a posterior-to-anterior direction. The contraction waves originate in the sinus venosus and terminate in the conus arteriosus. The nodal phenotype persists in the inflow region of the heart, varying from the venosinus to the sinoatrial junctional areas in different species . Similar to the mammalian situation, pacemaker tissue with a lower intrinsic rhythmicity is also found at the atrioventricular junction.[uncertain][VHOG]
2012-09-17
VHOG:0001271
VHOG
DOI:10.1152/physrev.00006.2003 Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003)
cardiac conducting system
VHOG:0001271
cardiac impulse conducting system
GO:0003161
complexus stimulans cordis
FMA:9476
FMA:TA
heart conduction system
GO:0003161
impulse conducting system
MA:0000094
systema conducente cordis
FMA:9476
FMA:TA
Serous membrane which is divided into parietal and visceral serous pericardium.
EMAPA:19030
FMA:9582
MA:0002739
serous portion of pericardium
uberon
pericardium serosum
UBERON:0002357
serous pericardium
FMA
FMA
Serous membrane which is divided into parietal and visceral serous pericardium.
serous portion of pericardium
FMA:9582
pericardium serosum
Membrane organ which is attached to the pericardial sac proper and the central tendon of diaphragm and is continuous with the pretracheal fascia.[FMA]
most superficial part of pericardium; continuous with the outer adventitial layer of the neighboring great blood vessels. [Wikipedia:Pericardium]
EMAPA:19029
FMA:9586
MA:0002738
fibrous portion of pericardium
uberon
pericardium fibrosum
UBERON:0002359
fibrous pericardium
FMA
FMA
WP
Membrane organ which is attached to the pericardial sac proper and the central tendon of diaphragm and is continuous with the pretracheal fascia.[FMA]
FMA:9586
pericardium fibrosum
A gland that secretes products (excluding hormones and other chemical messengers) into ducts (duct glands) which lead directly into the external environment[WP]. Typical exocrine glands include sweat glands, salivary glands, mammary glands, stomach, liver, pancreas
Currently this is logically defined by the system it belongs to, but a better system may be base this on presence/absence of ducts. However, the dual nature of the liver should be taken into consideration here. Consider adding subclasses
AEO:0000097
BTO:0000765
CALOHA:TS-2012
EHDAA2:0003097
EMAPA:35327
FMA:9596
GAID:34
MA:0002564
MESH:D005088
NCIT:C12712
UMLS:C0015282
ducted gland
glandula exocrina
uberon
UBERON:0002365
exocrine gland
A gland that secretes products (excluding hormones and other chemical messengers) into ducts (duct glands) which lead directly into the external environment[WP]. Typical exocrine glands include sweat glands, salivary glands, mammary glands, stomach, liver, pancreas
UMLS:C0015282
ncithesaurus:Exocrine_Gland
ducted gland
AEO:0000097
glandula exocrina
Any skeletal muscle that is part of the head region.
UBERON:0003899
AAO:0000107
BTO:0000021
EFO:0003524
EHDAA2:0000322
EMAPA:18172
FMA:9616
MA:0000578
ZFA:0001652
cephalic muscle
cephalic musculature
head muscle
head muscle organ
muscle of head
muscle organ of adult head
muscle organ of head
musculus caput
adult head muscle organ
uberon
cranial muscle
head muscles
UBERON:0002376
defined generically so could in theory encompass FBbt:00003260 'skeletal muscle of head', or the muscle of a starfish Aristotle's lantern, but we restrict this to craniates. Skeletal muscles of the head originate from the non-segmented head mesoderm (Noden, 1983; Wachtler et al., 1984)
cranial muscle
EHDAA2-abduced
Any skeletal muscle that is part of the head region.
cephalic muscle
ZFA:0001652
head muscle
MA:0000578
head muscle organ
OBOL:automatic
muscle of head
FMA:9616
muscle organ of adult head
OBOL:automatic
muscle organ of head
OBOL:automatic
adult head muscle organ
OBOL:automatic
cranial muscle
ZFA:0001652
Any muscle that is part of the cervical (neck) region.
EMAPA:36050
FMA:9617
GAID:149
MA:0000587
MESH:D009334
NCIT:C33163
UMLS:C0027532
muscle organ of neck
muscle organ of neck (volume)
neck (volume) muscle organ
neck muscle
neck muscle organ
uberon
UBERON:0002377
muscle of neck
prolog
Any muscle that is part of the cervical (neck) region.
UMLS:C0027532
ncithesaurus:Neck_Muscle
muscle organ of neck
OBOL:automatic
muscle organ of neck (volume)
OBOL:automatic
neck (volume) muscle organ
OBOL:automatic
neck muscle organ
OBOL:automatic
Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.
One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO]
Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO]
Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO]
MA also has set of connective tissues
AAO:0000098
BTO:0000421
CALOHA:TS-2009
EFO:0000952
EMAPA:35251
FMA:9640
GAID:100
MA:0000011
MAT:0000301
MESH:D003238
MIAA:0000301
NCIT:C12374
OpenCyc:Mx4rv-aBgZwpEbGdrcN5Y29ycA
TAO:0001641
UMLS:C0009780
VSAO:0000017
XAO:0001017
ZFA:0001632
galen:ConnectiveTissue
portion of connective tissue
textus connectivus
uberon
Bindegewebe
UBERON:0002384
connective tissue
Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.
GO_REF:0000034
PSPUB:0000170
VSAO:0000017
One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO]
2012-06-20
AAO:0000098
AAO
AAO:LAP
Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO]
2012-08-14
TAO:0001641
TAO
TAO:wd
Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO]
2012-08-14
VSAO:0000017
VSAO
GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070
PSPUB:0000170
MA also has set of connective tissues
MA
UMLS:C0009780
ncithesaurus:Connective_Tissue
portion of connective tissue
FMA:9640
Bindegewebe
BTO:0000421
Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO].
One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO]
AAO:0000306
AEO:0000122
CALOHA:TS-0642
EHDAA2:0003122
EMAPA:32715
FMA:9641
MA:0002437
MESH:D009132
NCIT:C12435
UMLS:C2328219
galen:MuscleTissue
muscular tissue
portion of muscle tissue
textus muscularis
uberon
UBERON:0002385
Vertebrate muscle is categorized into three major muscle types defined by their structural and functional properties: skeletal, cardiac and smooth. In Dmel the counterparts are somatic, heart/cardiac and visceral. Here we take a cell type based approach.
muscle tissue
Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO].
GO:0060537
One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO]
2012-06-20
AAO:0000306
AAO
AAO:LAP
UMLS:C2328219
ncithesaurus:Muscle_Tissue
muscular tissue
portion of muscle tissue
FMA:9641
Anatomical system that is involved in the production of hematopoietic cells.
Anatomical system that consists of the blood and blood forming tissues.[AAO]
Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG]
hematopoietic
In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes
AAO:0011002
BTO:0000570
CALOHA:TS-0449
EFO:0000798
EMAPA:35402
EV:0100045
FMA:9667
GAID:1008
MA:0002434
MAT:0000022
MESH:D006413
MIAA:0000022
NCIT:C12909
TAO:0005023
UMLS:C0018957
VHOG:0001624
XAO:0000122
ZFA:0005023
haematological system
haemopoietic system
organa haemopoietica
uberon
Blutbildungssystem
haematopoietic system
hematological system
hematolymphoid system
hemopoietic system
UBERON:0002390
hematopoietic system
FMA
definitional
Anatomical system that is involved in the production of hematopoietic cells.
Anatomical system that consists of the blood and blood forming tissues.[AAO]
2012-06-20
AAO:0011002
AAO
AAO:EJS
Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG]
2012-09-17
VHOG:0001624
VHOG
DOI:10.1016/j.coph.2010.05.004 Ellett F, Lieschke GJ, Zebrafish as a model for vertebrate hematopoiesis. Current Opinion in Pharmacology (2010)
In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes
WP
UMLS:C0018957
ncithesaurus:Hematopoietic_System
Blutbildungssystem
BTO:0000570
a double-walled sac containing the heart and the roots of the great vessels.
FMA:9868
RETIRED_EHDAA2:0001443
TAO:0000054
uberon
pericardium
UBERON:0002406
pericardial sac
http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png
FMA
a double-walled sac containing the heart and the roots of the great vessels.
The combination of pericardial sac (a double-walled sac containing the heart and the roots of the great vessels) plus fibrous pericardium.
Peritoneum that surrounds the heart.[AAO]
pericardial
In GO the concept of pericardium is developmental implicitly epithelial, but here it represents a multi-tissue structure encompassing the sac (epithelium plus connective) and cavity
this class denotes a combination of fibrous PC + PC sac (itself a combination of cavity, epithelium and connective tissue). Many sources use the term 'pericardium' to denote either just the serous membrane (ZFA) or the epithelium (GO)
we follow FMA in dividing pericardium into pericardial sac and fibrous pericardium
AAO:0010817
BSA:0000090
BTO:0000717
CALOHA:TS-0761
EFO:0000820
EHDAA:5376
EMAPA:16133
EV:0100023
FMA:9869
GAID:569
MA:0000099
MAT:0000454
MESH:D010496
NCIT:C13005
OpenCyc:Mx4rvoCLgJwpEbGdrcN5Y29ycA
RETIRED_EHDAA2:0001443
TAO:0000054
UMLS:C0031050
VHOG:0001280
XAO:0004182
ZFA:0000054
galen:Pericardium
uberon
UBERON:0002407
pericardium
http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png
MA
The combination of pericardial sac (a double-walled sac containing the heart and the roots of the great vessels) plus fibrous pericardium.
Peritoneum that surrounds the heart.[AAO]
2012-06-20
AAO:0010817
AAO
AAO:JMG
In GO the concept of pericardium is developmental implicitly epithelial, but here it represents a multi-tissue structure encompassing the sac (epithelium plus connective) and cavity
FMA
this class denotes a combination of fibrous PC + PC sac (itself a combination of cavity, epithelium and connective tissue). Many sources use the term 'pericardium' to denote either just the serous membrane (ZFA) or the epithelium (GO)
ZFA
we follow FMA in dividing pericardium into pericardial sac and fibrous pericardium
FMA
UMLS:C0031050
ncithesaurus:Pericardium
Parietal serous membrane which is part of the pericardium and forms the outer layer of the pericardial sac.
EHDAA:3422
EHDAA:5378
EMAPA:19031
FMA:9870
MA:0000483
NCIT:C94500
UMLS:C0225969
VHOG:0000537
lamina parietalis (pericardii serosum)
lamina parietalis pericardii
parietal layer of serous pericardium
parietal pericardium
uberon
pericardial sac
UBERON:0002408
parietal serous pericardium
http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png
Parietal serous membrane which is part of the pericardium and forms the outer layer of the pericardial sac.
UMLS:C0225969
ncithesaurus:Parietal_Pericardium
lamina parietalis pericardii
FMA:9870
FMA:TA
parietal pericardium
VHOG:0000537
pericardial sac
Transudate contained in the pericardial cavity.[FMA]
BTO:0001016
FMA:9887
MA:0002530
uberon
UBERON:0002409
pericardial fluid
FMA
Transudate contained in the pericardial cavity.[FMA]
FMA:9887
Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle.
(...) the integument of many tetrapods is reinforced by a morphologically and structurally diverse assemblage of skeletal elements. These elements are widely understood to be derivatives of the once all-encompassing dermal skeleton of stem-gnathostomes (...).[well established][VHOG]
UBERON:0007029
AEO:0000154
BILA:0000118
CALOHA:TS-1299
CARO:0002001
EFO:0000807
EHDAA2:0000836
EHDAA2_RETIRED:0003154
EHDAA:6520
EMAPA:17524
EV:0100151
FBbt:00004969
FMA:72979
HAO:0000421
MA:0000014
MAT:0000033
MESH:D034582
MIAA:0000033
NCIT:C12907
TADS:0000108
UMLS:C0037267
VHOG:0000403
XAO:0000176
galen:Surface
integumentary system
uberon
body surface
dermal system
external covering of organism
integumentum commune
organism surface
surface
UBERON:0002416
integumental system
Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle.
CARO:0002001
(...) the integument of many tetrapods is reinforced by a morphologically and structurally diverse assemblage of skeletal elements. These elements are widely understood to be derivatives of the once all-encompassing dermal skeleton of stem-gnathostomes (...).[well established][VHOG]
2012-09-17
VHOG:0000403
VHOG
DOI:10.1111/j.1469-7580.2008.01043.x Vickaryous MK, Sire JY, The integumentary skeleton of tetrapods: origin, evolution, and development. J Anat (2009)
UMLS:C0037267
ncithesaurus:Integumentary_System
integumentary system
FMA:72979
dermal system
MIAA:0000033
integumentum commune
organism surface
EHDAA2:0003154
surface
BILA:0000118
Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts.
A type of dense connective tissue. It is composed of cells called chondrocytes which are dispersed in a firm gel-like ground substance, called the matrix. Cartilage is avascular (contains no blood vessels) and nutrients are diffused through the matrix. Cartilage is found in the joints, the rib cage, the ear, the nose, in the throat and between intervertebral disks. It makes up virtually the entire skeleton in chondrichthyes.[AAO]
Portion of tissue which is connective tissue composed of collagen and/or elastin fibers and chondrocytes. Cartilage is avascular and provides both skeletal functions and a framework upon which bone is deposited.[TAO]
Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts.[VSAO]
relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]
Phylogenetic analysis suggests that cartilage arose independently in cnidarians, hemichordates, vertebrates, arthropods, annelids, brachiopods, and molluscs - or a common ancestor of brachiopods and molluscs (...). Analyses of cartilage as a tissue and of the development of invertebrate cartilages are consistent with homology between invertebrate and vertebrate cartilage. From the discussion above, it will be clear that understanding genetic changes underlying cartilage evolution is key to determining whether the multiple origins of cartilage represent parallel evolution.[well established][VHOG]
AAO:0000060
AEO:0000087
BTO:0000206
EFO:0000949
EHDAA2:0003087
EMAPA:32730
EV:0100141
FMA:37377
GAID:99
MA:0000104
MAT:0000189
MESH:D002356
MIAA:0000189
NCIT:C12373
NCIT:C32268
OpenCyc:Mx4rvVjeOZwpEbGdrcN5Y29ycA
TAO:0001501
UMLS:C0007301
VHOG:0001207
VSAO:0000040
XAO:0000170
ZFA:0005622
galen:Cartilage
cartilage tissue
cartilaginous tissue
chondrogenic tissue
uberon
cartilage
cartilages
portion of cartilage tissue
UBERON:0002418
Previous: "A portion of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate[GO]. Regular connective tissue, which consists of chondrocytes and related cells, the intercellular matrix of which is chondrified. Examples: hyaline cartilage, fibrocartilage, elastic cartilage[FMA]. an avascular supporting and articular skeletal tissue. It also functions as the primary endoskeletal support in vertebrate embryos. Cartilage is deposited by and is composed of chondroblasts and chondrocytes separated by an extracellular matrix, which may or may not mineralize depending on cartilage type, age, or taxon[Hall and Witten]." See also FMA:71500 Set of cartilages, FMA:55107 Cartilage organ, FMA:12264 Articular cartilage. // elements made from cartilage, cartilage-like, or chondroid tissues evolved in invertebrates[H&W]
cartilage tissue
http://upload.wikimedia.org/wikipedia/commons/e/ee/Hypertrophic_Zone_of_Epiphyseal_Plate.jpg
Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts.
GO_REF:0000034
PSPUB:0000170
VSAO:0000040
A type of dense connective tissue. It is composed of cells called chondrocytes which are dispersed in a firm gel-like ground substance, called the matrix. Cartilage is avascular (contains no blood vessels) and nutrients are diffused through the matrix. Cartilage is found in the joints, the rib cage, the ear, the nose, in the throat and between intervertebral disks. It makes up virtually the entire skeleton in chondrichthyes.[AAO]
2012-06-20
AAO:0000060
AAO
AAO:LAP
Portion of tissue which is connective tissue composed of collagen and/or elastin fibers and chondrocytes. Cartilage is avascular and provides both skeletal functions and a framework upon which bone is deposited.[TAO]
2012-08-14
TAO:0001501
TAO
ZFIN:curator
Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts.[VSAO]
2012-08-14
VSAO:0000040
VSAO
GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070
PSPUB:0000170
relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]
2012-06-20
AAO:0000060
AAO
Phylogenetic analysis suggests that cartilage arose independently in cnidarians, hemichordates, vertebrates, arthropods, annelids, brachiopods, and molluscs - or a common ancestor of brachiopods and molluscs (...). Analyses of cartilage as a tissue and of the development of invertebrate cartilages are consistent with homology between invertebrate and vertebrate cartilage. From the discussion above, it will be clear that understanding genetic changes underlying cartilage evolution is key to determining whether the multiple origins of cartilage represent parallel evolution.[well established][VHOG]
2012-09-17
VHOG:0001207
VHOG
DOI:10.1111/j.1525-142X.2011.00520.x Hall BK, Parallelism, deep homology, and evo-devo. Evolution and Development (2012)
UMLS:C0007301
ncithesaurus:Cartilage
cartilage tissue
FMA:37377
chondrogenic tissue
VSAO:0000040
cartilages
VHOG:0001207
portion of cartilage tissue
FMA:37377
A gland that is part of a skin of body [Automatically generated definition].
check FMA, use plural for now as general class not there
EMAPA:35774
FMA:71878
MA:0000146
glandulae cutis
uberon
set of skin glands
skin glands
skin glands set
UBERON:0002419
skin gland
A gland that is part of a skin of body [Automatically generated definition].
OBOL:automatic
glandulae cutis
FMA:71878
FMA:TA
set of skin glands
FMA:71878
skin glands
skin glands set
An epithelium that is part of the mouth and lines the oral cavity, typically stratified squamous, and may be para-, ortho- or non- keratinized. Primary barrier between oral environment and deeper tissues
consider including separate class for developmental structure (adult human is stratified; in EHDAA2 is unilaminar)
The epithelium that lines the oral cavity. The oral epithelium epithelial cells with many short microvilli as well as mucous cells, rodlet cells and taste buds[ZFIN:ZDB-PUB-060921-12, ZFIN:ZDB-PUB-091204-24].
the avian oral epithelium has the developmental capacity to initiate tooth developmental programs with underlying grafts of non-avian oral ectomesenchyme
AAO:0010357
BTO:0001775
CALOHA:TS-0715
EHDAA2:0001325
EHDAA:2187
EMAPA:16839
EMAPA:26942
FMA:265152
MA:0000344
NCIT:C49595
TAO:0000816
UMLS:C1709332
VHOG:0000187
XAO:0003201
ZFA:0000816
epithelium of mucosa of mouth
epithelium of oral mucosa
uberon
UBERON:0002424
oral epithelium
AAO-modified
An epithelium that is part of the mouth and lines the oral cavity, typically stratified squamous, and may be para-, ortho- or non- keratinized. Primary barrier between oral environment and deeper tissues
The epithelium that lines the oral cavity. The oral epithelium epithelial cells with many short microvilli as well as mucous cells, rodlet cells and taste buds[ZFIN:ZDB-PUB-060921-12, ZFIN:ZDB-PUB-091204-24].
ZFA:0000816
the avian oral epithelium has the developmental capacity to initiate tooth developmental programs with underlying grafts of non-avian oral ectomesenchyme
UMLS:C1709332
ncithesaurus:Oral_Cavity_Epithelium
epithelium of mucosa of mouth
FMA:265152
epithelium of oral mucosa
FMA:265152
Visceral serous membrane which is continuous with the parietal serous pericardium and is attached to the myocardium[FMA].
EMAPA:16589
EMAPA:19032
FMA:84882
MA:0000484
VHOG:0000538
lamina visceralis pericardii serosi
serous visceral pericardium
visceral lamina of serous pericardium
visceral layer of serous pericardium
visceral pericardium
uberon
epicardium
pericardium visceral mesothelium
UBERON:0002425
visceral serous pericardium
cjm
FMA
Visceral serous membrane which is continuous with the parietal serous pericardium and is attached to the myocardium[FMA].
lamina visceralis pericardii serosi
visceral pericardium
VHOG:0000538
epicardium
MA:0000484
pericardium visceral mesothelium
EMAPA:16589
A blood vessel that is part of a choroid [Automatically generated definition].
EMAPA:17828
FMA:76550
MA:0001237
blood vessel of choroid
blood vessel of choroid coat
blood vessel of choroidea
blood vessel of posterior uvea
choroid blood vessel
choroid blood vessels
choroid blood vessels set
choroid coat blood vessel
choroidea blood vessel
posterior uvea blood vessel
vasa sanguinea choroideae
uberon
set of choroid blood vessels
UBERON:0002443
cannot find singular in FMA, using Set class
choroidal blood vessel
A blood vessel that is part of a choroid [Automatically generated definition].
OBOL:automatic
blood vessel of choroid
OBOL:automatic
blood vessel of choroid coat
OBOL:automatic
blood vessel of choroidea
OBOL:automatic
blood vessel of posterior uvea
OBOL:automatic
choroid blood vessel
OBOL:automatic
choroid coat blood vessel
OBOL:automatic
choroidea blood vessel
OBOL:automatic
posterior uvea blood vessel
OBOL:automatic
vasa sanguinea choroideae
FMA:76550
FMA:TA
set of choroid blood vessels
FMA:76550
Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.
see https://github.com/obophenotype/uberon/issues/27
Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.[VSAO]
CALOHA:TS-2011
EMAPA:35179
FMA:224804
MA:0002780
MESH:D001842
NCIT:C13076
UMLS:C0391978
VSAO:0000047
XAO:0004040
ZFA:0005621
galen:BoneTissue
calcium tissue
osseous tissue
osteogenic tissue
mineralized bone tissue
uberon
bone
portion of bone tissue
UBERON:0002481
bone tissue
VSAO
Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.
GO_REF:0000034
PSPUB:0000170
VSAO:0000047
Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.[VSAO]
2012-08-14
VSAO:0000047
VSAO
GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070
PSPUB:0000170
UMLS:C0391978
ncithesaurus:Bone_Tissue
osteogenic tissue
VSAO:curator
mineralized bone tissue
XAO:0004040
bone
MESH:A02.835.232
portion of bone tissue
FMA:224804
An epithelium that is part of a iris [Automatically generated definition].
EMAPA:35447
FMA:58517
MA:0002826
epithelial tissue of iris
epithelium of iris
epithelium pigmentosum (iris)
epithelium pigmentosum iridis
iris epithelial tissue
iris epithelium
pigmented epithelium of iris
uberon
iris pigmented epithelium
UBERON:0002506
iris epithelium
FMA
MA
An epithelium that is part of a iris [Automatically generated definition].
OBOL:automatic
epithelial tissue of iris
OBOL:automatic
epithelium of iris
OBOL:automatic
epithelium pigmentosum (iris)
FMA:58517
epithelium pigmentosum iridis
FMA:58517
FMA:TA
iris epithelial tissue
OBOL:automatic
iris epithelium
FMA:58517
pigmented epithelium of iris
FMA:58517
iris pigmented epithelium
MA:0002826
Replacement bone that forms within cartilage.
placement in this class to be inferred
Replacement bone that forms within cartilage.[VSAO]
some structures, e.g. in ZFA are both intramembrane and endochondral
AAO:0010776
AEO:0000083
BTO:0002157
EHDAA2:0003083
FMA:24321
TAO:0001591
VSAO:0000145
XAO:0004018
ZFA:0001591
ossified chondrogenic bone
uberon
cartilaginous bone
endochondral bones
UBERON:0002513
endochondral bone
https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern
http://upload.wikimedia.org/wikipedia/commons/e/ee/Hypertrophic_Zone_of_Epiphyseal_Plate.jpg
VSAO
VSAO
Replacement bone that forms within cartilage.
GO:0001958
GO_REF:0000034
VSAO:0000145
Replacement bone that forms within cartilage.[VSAO]
2012-08-14
VSAO:0000145
VSAO
GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070
PSPUB:0000170
some structures, e.g. in ZFA are both intramembrane and endochondral
ZFA
ossified chondrogenic bone
VSAO:0000145
cartilaginous bone
BTO:0002157
endochondral bones
ZFA:0001591
Connective tissue composed of elastic fibers.
FMA:20113
GAID:926
MA:0002853
MESH:D004547
NCIT:C32495
elastic connective tissue
textus connectivus elasticus
elastic fiber
uberon
UBERON:0002521
elastic tissue
http://upload.wikimedia.org/wikipedia/commons/c/cb/Gray377.png
Connective tissue composed of elastic fibers.
textus connectivus elasticus
The middle layer of an artery or vein. [WP,unvetted].
BTO:0002011
EMAPA:36298
FMA:55590
GAID:170
MA:0002855
MESH:D017540
NCIT:C33821
UMLS:C0162867
uberon
tunica media vasorum
UBERON:0002522
May be composed of smooth muscle and elastic tissue
tunica media
Illu:artery.jpg
MA
cjm
cjm
The middle layer of an artery or vein. [WP,unvetted].
UMLS:C0162867
ncithesaurus:Tunica_Media
tunica media vasorum
tunica media vasorum
BTO:0002011
The innermost layer of a blood vessel which is a lining of endothelial cells facing the lumen[Kardong].
the FMA class represents a more generic layer which is the superclass of the layer found in both blood vessels and lymph vessels (and also endocardium) - we should probably follow this structure
the FMA class represents a structure which may have both epithelium and fibroelastic connective tissue as parts
The tunica intima (or just intima) is the innermost layer of an artery or vein. It is made up of one layer of endothelial cells and is supported by an internal elastic lamina. The endothelial cells are in direct contact with the blood flow. The inner coat (tunica intima) can be separated from the middle by a little maceration, or it may be stripped off in small pieces; but, on account of its friability, it cannot be separated as a complete membrane. It is a fine, transparent, colorless structure which is highly elastic, and, after death, is commonly corrugated into longitudinal wrinkles. The inner coat consists of: A layer of pavement endothelium, the cells of which are polygonal, oval, or fusiform, and have very distinct round or oval nuclei. This endothelium is brought into view most distinctly by staining with silver nitrate. A subendothelial layer, consisting of delicate connective tissue with branched cells lying in the interspaces of the tissue; in arteries of less than 2 mm. in diameter the subendothelial layer consists of a single stratum of stellate cells, and the connective tissue is only largely developed in vessels of a considerable size. An elastic or fenestrated layer, which consists of a membrane containing a net-work of elastic fibers, having principally a longitudinal direction, and in which, under the microscope, small elongated apertures or perforations may be seen, giving it a fenestrated appearance. It was therefore called by Henle the fenestrated membrane. This membrane forms the chief thickness of the inner coat, and can be separated into several layers, some of which present the appearance of a network of longitudinal elastic fibers, and others a more membranous character, marked by pale lines having a longitudinal direction. In minute arteries the fenestrated membrane is a very thin layer; but in the larger arteries, and especially in the aorta, it has a very considerable thickness. [WP,unvetted].[Wikipedia]
BTO:0002012
EMAPA:36297
FMA:55589
GAID:523
MA:0002861
MESH:D017539
NCIT:C33820
UMLS:C0162864
uberon
Bichat's tunic
intima
tunica intima vasorum
UBERON:0002523
tunica intima
Illu:artery.jpg
FMA
check for exceptions, e.g. capillaries
ISBN:0073040584
The innermost layer of a blood vessel which is a lining of endothelial cells facing the lumen[Kardong].
ISBN:0073040584
NCIT:C33820
The tunica intima (or just intima) is the innermost layer of an artery or vein. It is made up of one layer of endothelial cells and is supported by an internal elastic lamina. The endothelial cells are in direct contact with the blood flow. The inner coat (tunica intima) can be separated from the middle by a little maceration, or it may be stripped off in small pieces; but, on account of its friability, it cannot be separated as a complete membrane. It is a fine, transparent, colorless structure which is highly elastic, and, after death, is commonly corrugated into longitudinal wrinkles. The inner coat consists of: A layer of pavement endothelium, the cells of which are polygonal, oval, or fusiform, and have very distinct round or oval nuclei. This endothelium is brought into view most distinctly by staining with silver nitrate. A subendothelial layer, consisting of delicate connective tissue with branched cells lying in the interspaces of the tissue; in arteries of less than 2 mm. in diameter the subendothelial layer consists of a single stratum of stellate cells, and the connective tissue is only largely developed in vessels of a considerable size. An elastic or fenestrated layer, which consists of a membrane containing a net-work of elastic fibers, having principally a longitudinal direction, and in which, under the microscope, small elongated apertures or perforations may be seen, giving it a fenestrated appearance. It was therefore called by Henle the fenestrated membrane. This membrane forms the chief thickness of the inner coat, and can be separated into several layers, some of which present the appearance of a network of longitudinal elastic fibers, and others a more membranous character, marked by pale lines having a longitudinal direction. In minute arteries the fenestrated membrane is a very thin layer; but in the larger arteries, and especially in the aorta, it has a very considerable thickness. [WP,unvetted].[Wikipedia]
Wikipedia
UMLS:C0162864
ncithesaurus:Tunica_Intima
Bichat's tunic
BTO:0002012
intima
BTO:0002012
tunica intima vasorum
BTO:0002012
an organ that functions as a secretory or excretory organ
glandular
UBERON:MIAA_0000021
AAO:0000212
AEO:0000096
BTO:0000522
EFO:0000797
EHDAA2:0003096
EHDAA:2161
EHDAA:4475
EHDAA:6522
EMAPA:18425
FBbt:00100317
FMA:7146
FMA:86294
HAO:0000375
MA:0003038
MAT:0000021
MIAA:0000021
NCIT:C13319
OpenCyc:Mx4rwP3vyJwpEbGdrcN5Y29ycA
UMLS:C1285092
WikipediaCategory:Glands
galen:Gland
glandular organ
uberon
Druese
glandula
UBERON:0002530
gland
http://upload.wikimedia.org/wikipedia/commons/a/a1/Gray1026.png
an organ that functions as a secretory or excretory organ
MGI:csmith
MP:0002163
UMLS:C1285092
ncithesaurus:Gland
glandular organ
Druese
BTO:0000522
glandula
glandula
BTO:0000522
In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA]
MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class
In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG]
BTO:0004593
FMA:296704
MAT:0000067
MIAA:0000067
VHOG:0000243
epiblast
uberon
blastocyst
ectoblast
epiblastus
primitive ectoderm
UBERON:0002532
epiblast (generic)
http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png
In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA]
ZFIN:curator
In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG]
2012-09-17
VHOG:0000243
VHOG
DOI:10.1146/annurev.cellbio.042308.113344 Zorn AM, Wells JM, Vertebrate endoderm development and organ formation. Annual Review of Cell Developmental Biology (2009)
epiblast
VHOG:0000243
ectoblast
MP:0003886
epiblastus
primitive ectoderm
VHOG:0000243
One of a series of paired bulges that develop along the lateral walls of the foregut. The pharyngeal arches have developmental contributions from endoderm, mesoderm, and neural crest cells and are separated by anterior lateral endoderm out-pockets known as pharyngeal pouches.
One of a series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO]
A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down.[well established][VHOG]
Numbered cranial to caudal. different in mammals. branchial arch = ZFA:0001613 pharyngeal arch 3-7. generally gill arch 1 = pharyngeal arch 3. terminology varies as to whether branchial arch follows gill or pharyngeal numbering
AAO:0010359
BTO:0001785
EFO:0000959
EHDAA:571
EMAPA:16117
FMA:293015
GAID:1292
MAT:0000242
MESH:A16.254.160
MIAA:0000242
NCIT:C34249
TAO:0001306
UMLS:C0080322
VHOG:0000155
XAO:0000096
ZFA:0001306
pharyngeal arches
branchial arch
uberon
arcus pharyngei
visceral arch
UBERON:0002539
pharyngeal arch
http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray41.png
EHDAA2
One of a series of paired bulges that develop along the lateral walls of the foregut. The pharyngeal arches have developmental contributions from endoderm, mesoderm, and neural crest cells and are separated by anterior lateral endoderm out-pockets known as pharyngeal pouches.
ZFA:yb
One of a series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO]
2012-06-20
AAO:0010359
AAO
NLM:branchial+arch
A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down.[well established][VHOG]
2012-09-17
VHOG:0000155
VHOG
DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)
UMLS:C0080322
ncithesaurus:Pharyngeal_Arch
pharyngeal arches
branchial arch
BTO:0001785
MP:0002884
arcus pharyngei
Ectodermal placode that develops in the head into a part of the sensory nervous system. With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic.
Do not merge with neurogenic placode
Comparisons of developmental gene expression suggest that the anterior ectoderm in amphioxus may be homologous to the vertebrate olfactory placode, the only vertebrate placode with primary, not secondary, neurons
The term placode or placodes also applies to developing organs such as teeth, mammary glands, hair follicles, feathers and scales. We include a separate parent class for this. to avoid confusion, we include neurogenic placode as a subclass
ectodermal placode
placode
AAO:0010466
EFO:0001650
FMA:293966
MAT:0000369
MIAA:0000369
XAO:0000305
ectodermal cranial placode
uberon
cranial placodes
UBERON:0002546
cranial placode
cjm
Ectodermal placode that develops in the head into a part of the sensory nervous system. With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic.
Comparisons of developmental gene expression suggest that the anterior ectoderm in amphioxus may be homologous to the vertebrate olfactory placode, the only vertebrate placode with primary, not secondary, neurons
ectodermal placode
FMA:293966
placode
ectodermal cranial placode
UBERON:cjm
cranial placodes
XAO:0000305
Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina.
cavity
BIRNLEX:1011
EMAPA:37442
FMA:67552
MA:0002447
NCIT:C34007
galen:Cavity
uberon
UBERON:0002553
anatomical cavity
Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina.
FMA:67552
EMAPA:37442
MA:th
Anatomical divisons of the brain according to one or more criteria, e.g. cytoarchitectural, gross anatomy. Parts may be contiguous in 3D or not, e.g., basal ganglia.
BIRNLEX:1167
FMA:55676
NCIT:C13031
UMLS:C0445620
anatomical structure of brain
biological structure of brain
brain anatomical structure
brain biological structure
brain part
neuraxis segment
neuroanatomical region
segment of brain
uberon
UBERON:0002616
regional part of brain
Anatomical divisons of the brain according to one or more criteria, e.g. cytoarchitectural, gross anatomy. Parts may be contiguous in 3D or not, e.g., basal ganglia.
BIRNLEX:1167
UMLS:C0445620
ncithesaurus:Brain_Part
anatomical structure of brain
OBOL:automatic
biological structure of brain
OBOL:automatic
brain anatomical structure
OBOL:automatic
brain biological structure
OBOL:automatic
neuraxis segment
FMA:55676
segment of brain
BIRNLEX:1167
A wall, dividing a cavity or structure into smaller ones[WP].
septal
AAO:0011127
FMA:86461
OpenCyc:Mx4rrqot_on_EdaAAAACs0uFOQ
septa
uberon
UBERON:0003037
general anatomical term in FMA
septum
A wall, dividing a cavity or structure into smaller ones[WP].
septa
The part of the brain that is the morphological boundary between the midbrain and hindbrain and that is the location of an organizing center which patterns the midbrain and hindbrain primordia of the neural plate.
consider adding class for organizer. Consider adding separate class for isthmus as a structure
Lampreys also have an MHB [midbrain hindbrain boundary], expressing a similar repertoire of regulatory gene cognates as in gnathostomes.[well established][VHOG]
AAO:0011064
DMBA:16810
EHDAA2:0004395
EHDAA:5789
EMAPA:32857
NCIT:C93172
TAO:0000042
VHOG:0000649
XAO:0000016
ZFA:0000042
MHB
mid-hindbrain boundary
mid-hindbrain junction
midbrain hindbrain boundary
uberon
isthmic organizer territory
isthmo-cerebellar region
isthmus
isthmus/MHB
UBERON:0003052
midbrain-hindbrain boundary
ZFA
ZFA
ZFA
The part of the brain that is the morphological boundary between the midbrain and hindbrain and that is the location of an organizing center which patterns the midbrain and hindbrain primordia of the neural plate.
GO:0021555
Lampreys also have an MHB [midbrain hindbrain boundary], expressing a similar repertoire of regulatory gene cognates as in gnathostomes.[well established][VHOG]
2012-09-17
VHOG:0000649
VHOG
DOI:10.1016/j.ydbio.2005.02.008 Murakami Y, Uchida K, Rijli FM and Kuratani S, Evolution of the brain developmental plan: Insights from agnathans. Developmental Biology (2005)
isthmic organizer territory
XAO:0000016
isthmo-cerebellar region
VHOG:0000649
isthmus/MHB
Geisha:syn
NCBITaxon:8782
A temporary epithelium that derives from the outer layer of the ectdoerm and is shed once the inner layer differentiates to form a true epidermis.
The outermost epidermal layer covering the fish at embryonic stages; derived from the EVL and thought to eventually be replaced by the superficial stratum of the epidermis. Sometimes used synonymously with EVL. Le Guellec et al, 2004.[TAO]
relationship type change: OBO_REL:part_of ectoderm (TAO:0000016) CHANGED TO: develops_from ectoderm (UBERON:0000924)[TAO]
In mice, the first non-basal layer formed at ~E9.5; it is a temporary structure composed of simple squamous epithelium that serves as the first barrier to the embryo's physical environment, exists throughout the entire keratinocyte stratification process, and sheds off at ~E17, when it is replaced by corneocytes[MP]
In some mammals, Eyelid Fusion is thought to be driven by a population of cells which are derived from the periderm, the outermost layer of the developing epidermis
Originally the epidermis is one layer thick, in most vertebrates it soon becomes a two-layered structure. The outer layer gives rise to the periderm. The periderm goes through distinct developmental phases and is ultimately sloughed into the amniotic fluid when differentiation of the underlying epidermal layers is complete. The function of the periderm is not known, but is thought to be related to transport/exchange between the fetus and the amniotic fluid (http://courses.washington.edu/hubio567/devbio/periderm.html)
EHDAA2:0001846
EHDAA:6538
FMA:295662
NCIT:C34247
TAO:0001185
UMLS:C1518973
VHOG:0001680
XAO:0000029
ZFA:0001185
skin periderm
uberon
EVL
epidermis epithelial layer
epidermis outer layer
epitrichium
periderm
UBERON:0003055
periderm
EHDAA2
EHDAA2
ZFA
A temporary epithelium that derives from the outer layer of the ectdoerm and is shed once the inner layer differentiates to form a true epidermis.
ISBN:9780878932504
The outermost epidermal layer covering the fish at embryonic stages; derived from the EVL and thought to eventually be replaced by the superficial stratum of the epidermis. Sometimes used synonymously with EVL. Le Guellec et al, 2004.[TAO]
2012-08-14
TAO:0001185
TAO
ZFIN:curator
relationship type change: OBO_REL:part_of ectoderm (TAO:0000016) CHANGED TO: develops_from ectoderm (UBERON:0000924)[TAO]
2012-08-14
TAO:0001185
TAO
UMLS:C1518973
ncithesaurus:Periderm
skin periderm
EHDAA2:0001846
EVL
ZFA:0001185
epitrichium
MP:0013530
The portion of neural plate anterior to the mid-hindbrain junction.
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]
AAO:0011084
TAO:0007016
VHOG:0001200
XAO:0000045
ZFA:0007016
uberon
anterior neural plate
UBERON:0003056
pre-chordal neural plate
The portion of neural plate anterior to the mid-hindbrain junction.
XB:curator
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]
2012-09-17
VHOG:0001200
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28
The portion of neural plate posterior to the mid-hindbrain junction.
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]
TAO:0007017
VHOG:0001201
XAO:0000046
ZFA:0007017
uberon
posterior neural plate
UBERON:0003057
chordal neural plate
The portion of neural plate posterior to the mid-hindbrain junction.
XB:curator
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]
2012-09-17
VHOG:0001201
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28
Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form.
Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO]
It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG]
AAO:0011086
EFO:0001982
EMAPA:16189
EMAPA:16752
TAO:0000279
VHOG:0000559
XAO:0000057
ZFA:0000279
segmental plate
unsegmented paraxial mesoderm
uberon
PSM
presumptive somite mesoderm
somitogenic mesoderm
somitomeric mesoderm
unsegmented mesenchyme
UBERON:0003059
presomitic mesoderm
Bgee:AN
Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form.
ZFIN:curator
Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO]
2012-08-14
TAO:0000279
TAO
ZFIN:curator
It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG]
2012-09-17
VHOG:0000559
VHOG
DOI:10.1006/dbio.2001.0460 Schubert M, Holland LZ, Dale Stokes M and Holland ND, Three Amphoxius Wnt Genes (AmphiWnt3, AmphiWnt5, and AmphiWnt6) Associated with the Tail Bud: the Evolution of Somitogenesis in Chordates. Developmental Biology (2001)
unsegmented paraxial mesoderm
somitomeric mesoderm
GO:0002075
unsegmented mesenchyme
VHOG:0000559
Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted].
Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO]
Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO]
relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO]
Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG]
EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac
ventral lateral plate mesoderm
AAO:0011006
EFO:0003489
EHDAA:207
NCIT:C34113
TAO:0000094
TE:E5.11.2.0.0.0.4
UMLS:C1511224
VHOG:0000085
XAO:0000067
ZFA:0000094
blood islands
uberon
VBI
caudal hematopoietic tissue
posterior ICM
posterior blood island
ventral blood island
UBERON:0003061
blood island
Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted].
Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO]
2012-08-14
TAO:0000094
TAO
ZFIN:curator
Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO]
2012-06-20
AAO:0011006
AAO
AAO:EJS
relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO]
2012-08-14
TAO:0000094
TAO
Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG]
2012-09-17
VHOG:0000085
VHOG
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.450, DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual Review of Cell and Developmental Biology (2006)
EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac
EHDAA2
UMLS:C1511224
ncithesaurus:Blood_Island
blood islands
A horseshoe-shaped thickening of the endoderm at the cranial (rostral) end of the primitive streak formed by the involution of Spemann's organizer cells which, together with the notochord, induces the formation of the neural plate from the overlying ectodermal cells and contributes mesodermal type cells to the surrounding tissue
TODO - check; developmental relationship to anterior hypoblast in ZFA?
Axial hypoblast located anterior to the chorda mesoderm; the polster is its most anterior region. Kimmel et al, 1995.[TAO]
Axial mesoderm that lies anterior to the notochord and that underlies the forebrain. [Amphioxus_goosecoid_and_the_evolution_of_the_head_organizer_and_prechordal_plate._Evolution_and_Development_(2008)_2(6):303-310, Neidert_AH, Panopoulou_G_and_Langeland_JA][VHOG]
There are two opposing models that can potentially explain the differences in gsc (goosecoid) expression between amphioxus and vertebrates. In one model, the vertebrate gsc expression pattern more closely resembles the common ancestral state and the amphioxus gsc expression pattern is a derivation associated with its unique morphology. (...) In an alternate model, the amphioxus gsc expression pattern most closely represents the common ancestral state and the vertebrate pattern is derived. This model suggests that the evolution of vertebrates was accompanied by the segregation of gsc expression, from a more general domain underlying the entire brain anlage to a distinct forebrain organizer domain and subsequent prechordal plate. We feel this second model is more parsimonious than the first model in that what would be novel anterior gsc expression in vertebrates directly correlates with a novel vertebrate anterior structure, the prechordal plate.[well established][VHOG]
UBERON:0004881
head mesenchyme
head mesoderm
AAO:0011085
EHDAA2:0001493
EHDAA:181
FMA:295532
TAO:0000060
VHOG:0000086
XAO:0000079
ZFA:0000060
uberon
UBERON:0003063
prechordal plate
ZFA
PMID:16313393
A horseshoe-shaped thickening of the endoderm at the cranial (rostral) end of the primitive streak formed by the involution of Spemann's organizer cells which, together with the notochord, induces the formation of the neural plate from the overlying ectodermal cells and contributes mesodermal type cells to the surrounding tissue
ISBN:0838580343
MP:0004387
Axial hypoblast located anterior to the chorda mesoderm; the polster is its most anterior region. Kimmel et al, 1995.[TAO]
2012-08-14
TAO:0000060
TAO
ZFIN:curator
Axial mesoderm that lies anterior to the notochord and that underlies the forebrain. [Amphioxus_goosecoid_and_the_evolution_of_the_head_organizer_and_prechordal_plate._Evolution_and_Development_(2008)_2(6):303-310, Neidert_AH, Panopoulou_G_and_Langeland_JA][VHOG]
2012-09-17
VHOG:0000086
VHOG
There are two opposing models that can potentially explain the differences in gsc (goosecoid) expression between amphioxus and vertebrates. In one model, the vertebrate gsc expression pattern more closely resembles the common ancestral state and the amphioxus gsc expression pattern is a derivation associated with its unique morphology. (...) In an alternate model, the amphioxus gsc expression pattern most closely represents the common ancestral state and the vertebrate pattern is derived. This model suggests that the evolution of vertebrates was accompanied by the segregation of gsc expression, from a more general domain underlying the entire brain anlage to a distinct forebrain organizer domain and subsequent prechordal plate. We feel this second model is more parsimonious than the first model in that what would be novel anterior gsc expression in vertebrates directly correlates with a novel vertebrate anterior structure, the prechordal plate.[well established][VHOG]
2012-09-17
VHOG:0000086
VHOG
DOI:10.1046/j.1525-142x.2000.00073.x Neidert AH, Panopoulou G and Langeland JA, Amphioxus goosecoid and the evolution of the head organizer and prechordal plate. Evolution and Development (2008)
head mesenchyme
XAO:0000079
head mesoderm
XAO:0000079
The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord.
The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]
AAO:0011017
EFO:0003647
TAO:0001204
VHOG:0000107
XAO:0000205
ZFA:0001204
uberon
chordamesoderm
UBERON:0003068
axial mesoderm
http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png
The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord.
GO:0048318
The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]
2012-09-17
VHOG:0000107
VHOG
chordamesoderm
Portion of tissue that is part of the anterior neural keel and will form the optic vesicle[ZFA]. A paired ectodermal placode that becomes invaginated to form the embryonic lens vesicles.
TODO - check that GO's optic placode is the same as ZFA's eye primordium; we may want to have separate term for ocular primordium precursor. XAO has both optic field and eye primordium.
UBERON:0005060
AAO:0011038
EFO:0003541
EHDAA2:0004431
TAO:0000570
XAO:0000227
XAO:0004090
ZFA:0000570
eye placode
occular primordium
ocular primordium
optic placode
optic placode of camera-type eye
optic primordium
uberon
eye anlage
eye field
optic field
optic placodes
UBERON:0003071
eye primordium
EHDAA2
XAO
Portion of tissue that is part of the anterior neural keel and will form the optic vesicle[ZFA]. A paired ectodermal placode that becomes invaginated to form the embryonic lens vesicles.
GO:0046619
ZFA:0000570
TODO - check that GO's optic placode is the same as ZFA's eye primordium; we may want to have separate term for ocular primordium precursor. XAO has both optic field and eye primordium.
GO
eye placode
OBOL:automatic
optic placode
GO:0046619
optic placode of camera-type eye
GO:0046619
eye anlage
XAO:0000227
optic placodes
Multi-tissue structure that is comprised of neural and non-neural epithelial layers which will form the retina and retinal pigmented epithelium of the mature eye[ZFA]. double walled structured formed by expansion and invagination of the distal end of the optic vesicle that develops into the pigmented and sensory layers of the retina while the mouth of the optic cup eventually forms the pupil of the eye[MP].
(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup.[well established][VHOG]
BTO:0005351
EHDAA2:0001303
EHDAA:2912
EMAPA:16674
NCIT:C34233
TAO:0001202
UMLS:C0231109
VHOG:0000167
ZFA:0001202
uberon
eye cup
eyecup
ocular cup
ophtalmic cup
UBERON:0003072
optic cup
ZFA
ZFA
Multi-tissue structure that is comprised of neural and non-neural epithelial layers which will form the retina and retinal pigmented epithelium of the mature eye[ZFA]. double walled structured formed by expansion and invagination of the distal end of the optic vesicle that develops into the pigmented and sensory layers of the retina while the mouth of the optic cup eventually forms the pupil of the eye[MP].
MP:0004269
ZFA:0001202
(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup.[well established][VHOG]
2012-09-17
VHOG:0000167
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429
UMLS:C0231109
ncithesaurus:Optic_Cup
eyecup
BTO:0005351
ocular cup
VHOG:0000167
ophtalmic cup
BTO:0005351
A thickened portion of ectoderm which serves as the precursor to the lens. SOX2 and Pou2f1 are involved in its development[WP].
Ectodermal primordium of the lens of the eye. Kimmel et al, 1995.[TAO]
(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG]
Classical transplantation experiments using amphibian embryos suggested that the optic vesicle is the source of lens-inducing signals sufficient to generate lens tissues in competent ectoderm (reviewed in Grainger et al., 1996). More recent findings suggest a multistep model for lens induction. There is now good evidence that lens specification occurs at the neurula stage, before the optic vesicle contact the surface ectoderm, and that neural crest cell migration in the frontonasal region is required to restrict the position of the lens placode (Bailey et al., 2006)
AAO:0011055
EFO:0003494
EHDAA2:0000982
EHDAA:2908
EMAPA:16672
FMA:296767
NCIT:C34202
TAO:0000122
UMLS:C1517770
VHOG:0000166
XAO:0000240
ZFA:0000122
uberon
lens placodes
placoda lentis
UBERON:0003073
lens placode
http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png
NCBIBook:NBK53175
A thickened portion of ectoderm which serves as the precursor to the lens. SOX2 and Pou2f1 are involved in its development[WP].
ZFIN:curator
Ectodermal primordium of the lens of the eye. Kimmel et al, 1995.[TAO]
2012-08-14
TAO:0000122
TAO
ZFIN:curator
(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG]
2012-09-17
VHOG:0000166
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429
Classical transplantation experiments using amphibian embryos suggested that the optic vesicle is the source of lens-inducing signals sufficient to generate lens tissues in competent ectoderm (reviewed in Grainger et al., 1996). More recent findings suggest a multistep model for lens induction. There is now good evidence that lens specification occurs at the neurula stage, before the optic vesicle contact the surface ectoderm, and that neural crest cell migration in the frontonasal region is required to restrict the position of the lens placode (Bailey et al., 2006)
NCBIBook:NBK53175
UMLS:C1517770
ncithesaurus:Lens_Placodes
lens placodes
ZFA:0000122
placoda lentis
A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]
The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO]
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]
AAO:0011072
BTO:0001765
DHBA:10153
DMBA:15565
EHDAA:346
EHDAA:902
EMAPA:35593
FMA:293879
NCIT:C34225
RETIRED_EHDAA2:0001252
TAO:0000132
UMLS:C0920623
VHOG:0000068
XAO:0000249
ZFA:0000132
uberon
lamina neuralis
presumptive central nervous system
UBERON:0003075
neural plate
Neural:Crest.png
Wikipedia
Bgee:AN
A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]
ISBN:0815318960
OMD:neural+plate
ZFIN:curator
The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO]
2012-08-14
TAO:0000132
TAO
ZFIN:curator
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]
2012-09-17
VHOG:0000068
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28
UMLS:C0920623
ncithesaurus:Neural_Plate
lamina neuralis
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]
AAO:0011082
TAO:0007037
VHOG:0001383
XAO:0000250
ZFA:0007037
uberon
UBERON:0003076
posterior neural tube
lexical
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]
2012-09-17
VHOG:0001383
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28
The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]
Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO]
Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG]
note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here)
AAO:0010568
EFO:0003515
EMAPA:16183
EMAPA:16751
FMA:293145
NCIT:C34244
TAO:0000255
UMLS:C1284009
VHOG:0000114
XAO:0000259
ZFA:0000255
paraxial mesenchyme
somitic mesoderm
uberon
mesoderma paraxiale
UBERON:0003077
paraxial mesoderm
http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png
EHDAA2
Bgee:AN
The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]
GO:0048339
Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO]
2012-06-20
AAO:0010568
AAO
AAO:EJS
Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG]
2012-09-17
VHOG:0000114
VHOG
DOI:10.1002/dvdy.21177 Kusakabe R and Kuratani S. Evolutionary perspectives from development of mesodermal components in the lamprey. Developmental dynamics (2007)
note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here)
ZFA
UMLS:C1284009
ncithesaurus:Paraxial_Mesoderm
paraxial mesenchyme
ZFA:0000255
somitic mesoderm
ISBN:9780878932504
mesoderma paraxiale
TODO - add grouping class for the anterior end of the neural tube at all stages
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]
AAO:0011012
TAO:0007038
VHOG:0001384
XAO:0000307
ZFA:0007038
uberon
UBERON:0003080
anterior neural tube
lexical
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]
2012-09-17
VHOG:0001384
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28
Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP].
Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO]
The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]
A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG]
subclass of mesoderm in ZFA.
UBERON:0006258
AAO:0010574
EHDAA2:0000919
EHDAA:379
EMAPA:16179
FMA:293149
NCIT:C34199
TAO:0000121
UMLS:C1517749
VHOG:0000118
XAO:0000311
ZFA:0000121
LPM
lateral mesoderm
uberon
lateral plate
lateral plate mesenchyme
mesoderma laminae lateralis
UBERON:0003081
lateral plate mesoderm
http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png
EHDAA2
EHDAA2
VHOG
Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP].
MP:0010117
Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO]
2012-06-20
AAO:0010574
AAO
AAO:EJS
The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]
2012-09-17
VHOG:0000118
VHOG
A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG]
2012-09-17
VHOG:0000118
VHOG
DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)
subclass of mesoderm in ZFA.
ZFA
UMLS:C1517749
ncithesaurus:Lateral_Mesoderm
LPM
ZFA:0000121
lateral mesoderm
GO:0048368
lateral plate mesenchyme
EHDAA2:0000919
mesoderma laminae lateralis
A transitional population of migrating mesenchymal cells that derive from somites and that will become muscle cells.
The term 'myotome' is also used to describe the muscles served by a single nerve root / spinal segment - consider adding new class, myomere.
Portion of the somites giving rise to body wall muscle masses. Kimmel et al, 1995.[TAO]
In all vertebrates, the skeletal muscle of the body axis is chiefly derived from an early embryonic compartment, known as the myotome.[well established][VHOG]
AAO:0011067
AEO:0001018
BTO:0000742
EHDAA2_RETIRED:0003431
EHDAA:1721
EHDAA:1727
EHDAA:1733
EHDAA:1739
EMAPA:32841
FMA:295658
NCIT:C34214
TAO:0001056
UMLS:C1513802
VHOG:0001244
XAO:0000315
ZFA:0001056
myomeres
uberon
muscle plate
myomere
myotome region
myotomes
myotomus
UBERON:0003082
myotome
http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png
AEO
EHDAA2-abduced
A transitional population of migrating mesenchymal cells that derive from somites and that will become muscle cells.
AEO:0001018
Portion of the somites giving rise to body wall muscle masses. Kimmel et al, 1995.[TAO]
2012-08-14
TAO:0001056
TAO
ZFIN:curator
In all vertebrates, the skeletal muscle of the body axis is chiefly derived from an early embryonic compartment, known as the myotome.[well established][VHOG]
2012-09-17
VHOG:0001244
VHOG
DOI:10.1038/sj.embor.embor920 Hollway GE, Currie PD, Myotome meanderings. Cellular morphogenesis and the making of muscle. EMBO Rep.(2003)
UMLS:C1513802
ncithesaurus:Myotome_Region
myomeres
TAO:0001056
myotomus
Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone.
should probably be merged with heart rudiment.
Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO]
The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO]
relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO]
AAO:0011044
BTO:0001887
NCIT:C34276
TAO:0000028
UMLS:C1514450
XAO:0000336
ZFA:0000028
uberon
cardiac field
fused heart primordium
UBERON:0003084
heart primordium
Obol
ZFA
ZFA
XAO
Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone.
ZFIN:curator
Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO]
2012-08-14
TAO:0000028
TAO
ZFIN:curator
The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO]
2012-06-20
AAO:0011044
AAO
XAO:curator
relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO]
2012-08-14
TAO:0000028
TAO
UMLS:C1514450
ncithesaurus:Primordium_of_the_Heart
cardiac field
ZFA:0000028
Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP].
Skeletogenic portion of somites.[AAO]
The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG]
part_of somite in XAO
AAO:0010571
AEO:0000212
EHDAA2:0003439
EMAPA:31159
FMA:295652
NCIT:C34287
TAO:0001080
UMLS:C0183176
VHOG:0000680
XAO:0000397
ZFA:0001080
sclerotomes
uberon
sclerotomus
UBERON:0003089
sclerotome
http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png
EHDAA2
EHDAA2
ZFA
Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP].
XB:curator
Skeletogenic portion of somites.[AAO]
2012-06-20
AAO:0010571
AAO
AAO:EJS
The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG]
2012-09-17
VHOG:0000680
VHOG
DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)
part_of somite in XAO
XAO
UMLS:C0183176
ncithesaurus:Sclerotome
sclerotomes
TAO:0001080
sclerotomus
neural crest cells (NCCs) originating in the anterior part of the developing embryo and residing between the mid-diencephalon and the forming hindbrain; cranial NCCs migrate dorsolaterally to form the craniofacial mesenchyme that differentiates into various craniofacial cartilages and bones, cranial neurons, glia, and connective tissues of the face; these cells enter the pharyngeal pouches and arches where they give rise to thymic cells, bones of the middle ear and jaw (mandible), and the odontoblasts of the tooth primordia; like their counterparts in the trunk, cranial NCCs also contribute to the developing peripheral nervous system, along with the pigmented cell (i.e. melanocyte) lineage.
Anterior most portion of the neural crest. Migrates in three highly conserved streams: mandibular, hyoid and branchial.[AAO]
Neural crest that is part of the head.[TAO]
We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]
AAO:0010580
EFO:0003645
EHDAA2:0004420
EMAPA:16091
TAO:0001194
VHOG:0000063
XAO:0001001
ZFA:0001194
CNC
cephalic neural crest
cranial NCC population
head NCC population
uberon
crista neuralis cranialis
head crest
head neural crest
UBERON:0003099
cranial neural crest
neural crest cells (NCCs) originating in the anterior part of the developing embryo and residing between the mid-diencephalon and the forming hindbrain; cranial NCCs migrate dorsolaterally to form the craniofacial mesenchyme that differentiates into various craniofacial cartilages and bones, cranial neurons, glia, and connective tissues of the face; these cells enter the pharyngeal pouches and arches where they give rise to thymic cells, bones of the middle ear and jaw (mandible), and the odontoblasts of the tooth primordia; like their counterparts in the trunk, cranial NCCs also contribute to the developing peripheral nervous system, along with the pigmented cell (i.e. melanocyte) lineage.
MGI:anna
Anterior most portion of the neural crest. Migrates in three highly conserved streams: mandibular, hyoid and branchial.[AAO]
2012-06-20
AAO:0010580
AAO
AAO:EJS
Neural crest that is part of the head.[TAO]
2012-08-14
TAO:0001194
TAO
ZFIN:curator
We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]
2012-09-17
VHOG:0000063
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43
CNC
XAO:0001001
cephalic neural crest
EMAPA:16091
crista neuralis cranialis
Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism.
consider obsoleting. See issue/1305
Organism subdivision which is the collection of anatomical structures on the body surface.[ZFA]
AAO:0010337
AEO_RETIRED:0000010
EHDAA2_RETIRED:0003010
TAO:0000292
VSAO:0000001
XAO:0003028
ZFA:0000292
galen:SurfaceRegion
anatomical surface feature
uberon
surface feature
surface region
surface structures
UBERON:0003102
surface structure
Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism.
Organism subdivision which is the collection of anatomical structures on the body surface.[ZFA]
2012-08-14
TAO:0000292
TAO
ZFIN:curator
anatomical surface feature
EHDAA2:0003010
surface structures
ZFA:0000292
Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types.
this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs
AAO:0010015
AEO:0000024
BILA:0000024
CARO:0000024
EHDAA2:0003024
HAO:0000024
TADS:0000598
TAO:0000496
TGMA:0001837
VHOG:0001723
XAO:0003041
ZFA:0000496
uberon
organ
UBERON:0003103
compound organ
Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types.
CARO:0000024
Portion of tissue composed of mesenchymal cells (motile cells that develop from epthelia via an epithelial to mesenchymal transition) and surrounding extracellular material. Mesenchyme has different embryological origins in different metazoan taxa - in many invertebrates it derives in whole or part from ectoderm. In vertebrates it derives largely from mesoderm, and sometimes the terms are used interchangeably, e.g. lateral plate mesoderm/mesenchyme.
the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense
A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO]
Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO]
mesenchymal
AAO:0010427
AEO:0000145
BTO:0001393
CALOHA:TS-0620
EHDAA2:0003145
EV:0100007
NCIT:C13301
TAO:0000393
UMLS:C0162415
VHOG:0000170
XAO:0003046
ZFA:0000393
mesenchymal tissue
mesenchyme tissue
portion of mesenchymal tissue
portion of mesenchyme tissue
uberon
mesenchyma
UBERON:0003104
mesenchyme
http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg
Portion of tissue composed of mesenchymal cells (motile cells that develop from epthelia via an epithelial to mesenchymal transition) and surrounding extracellular material. Mesenchyme has different embryological origins in different metazoan taxa - in many invertebrates it derives in whole or part from ectoderm. In vertebrates it derives largely from mesoderm, and sometimes the terms are used interchangeably, e.g. lateral plate mesoderm/mesenchyme.
A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO]
2012-08-14
TAO:0000393
TAO
ZFIN:curator
Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO]
2012-06-20
AAO:0010427
AAO
AAO:EJS
UMLS:C0162415
ncithesaurus:Mesenchyme
mesenchyma
Subdivision of skeleton that includes all dermal bones in the cranial skeleton[ZFA,modified].
wikipedia treats skull roof and dermatocranium as synonymous, but some sources treat the roof as being part of the dermatocranium - see UBERONREF:0000007
Anatomical cluster that is part of the cranium and composed of dermally derived bones.[TAO]
Anatomical cluster that is part of the cranium which consists of dermally derived bones.[AAO]
AAO:0010154
TAO:0000863
VHOG:0001665
XAO:0003169
ZFA:0000863
dendrocranium
exocranium
dermal skull roof
dermatocranial cover
roof of skull
skull roof
uberon
dermal bone cranium
dermal part of skull
dermal skull bones
roofing bones of the skull
skull exoskeleton
UBERON:0003113
dermatocranium
Subdivision of skeleton that includes all dermal bones in the cranial skeleton[ZFA,modified].
ZFA:0000863
Anatomical cluster that is part of the cranium and composed of dermally derived bones.[TAO]
2012-08-14
TAO:0000863
TAO
ZFIN:curator
Anatomical cluster that is part of the cranium which consists of dermally derived bones.[AAO]
2012-06-20
AAO:0010154
AAO
AAO:BJB
dendrocranium
TAO:0000863
exocranium
UBERONREF:0000007
dermal skull roof
roof of skull
skull roof
dermal bone cranium
ZFA:0000863
roofing bones of the skull
Upper portion of the skull that excludes the mandible (when present in the organism).
cranial
the inclusion of the FMA class here is probably not quite correct, as this class includes as parts sutures, whereas this is not part of the bones of the cranium
The term cranium can be ambiguous, in that it can refer to the neurocranium, or the neurocranium and the Facial skeleton
BTO:0001328
EFO:0000831
EHDAA:6029
EMAPA:17680
FMA:71325
MA:0000316
MAT:0000340
MIAA:0000340
OpenCyc:Mx4rvVlEyJwpEbGdrcN5Y29ycA
VHOG:0000334
bones of cranium
ossa cranii
set of bones of cranium
skull minus mandible
upper part of skull
uberon
calvarium
epicranial plate
skeletal system of head
UBERON:0003128
cranium
FMA-inferred
Upper portion of the skull that excludes the mandible (when present in the organism).
the inclusion of the FMA class here is probably not quite correct, as this class includes as parts sutures, whereas this is not part of the bones of the cranium
FMA
The term cranium can be ambiguous, in that it can refer to the neurocranium, or the neurocranium and the Facial skeleton
WP
bones of cranium
FMA:71325
ossa cranii
FMA:71325
FMA:TA
set of bones of cranium
FMA:71325
calvarium
BTO:0001328
Anatomical structure that is part of the head consisting entirely of cranium and mandible[WP].
in FMA the skull is divided into orbit, neurocranium (8 parts), viscerocranium (26 parts). Here we have a separate overlapping division into cranium and mandible.
in many ontologies, the structure called the cranium is inclusive of the mandible/lower jaw skeleton
A skull that is missing a mandible is only a cranium; this is the source of a very commonly made error in terminology. Those animals having skulls are called craniates
BTO:0001295
CALOHA:TS-2344
EHDAA2:0000325
EMAPA:17680
FMA:46565
GAID:82
MESH:D012886
NCIT:C12789
OpenCyc:Mx4rvVjOsZwpEbGdrcN5Y29ycA
UMLS:C0037303
WikipediaCategory:Skull
galen:Skull
uberon
cranial skeleton
skeletal system of head
UBERON:0003129
skull
FMA
Anatomical structure that is part of the head consisting entirely of cranium and mandible[WP].
in FMA the skull is divided into orbit, neurocranium (8 parts), viscerocranium (26 parts). Here we have a separate overlapping division into cranium and mandible.
FMA
A skull that is missing a mandible is only a cranium; this is the source of a very commonly made error in terminology. Those animals having skulls are called craniates
WP
UMLS:C0037303
ncithesaurus:Skull
An organ involved in reproduction
GO uses genitalia for the singular organ
EMAPA:17381
EMAPA:37731
MA:0001752
MESH:D005835
NCIT:C25177
OpenCyc:Mx4rwO39aJwpEbGdrcN5Y29ycA
TGMA:0000591
UMLS:C0017420
WBbt:0008422
genital organ
reproductive system organ
sex organ
uberon
genitalia
UBERON:0003133
reproductive organ
An organ involved in reproduction
UBERON:xp
GO uses genitalia for the singular organ
GO
EMAPA:37731
MA:th
UMLS:C0017420
ncithesaurus:Genitalia
genitalia
An epithelium that is part of a lower jaw [Automatically generated definition].
EHDAA2:0001019
EHDAA:7999
EMAPA:35516
VHOG:0000802
epithelial tissue of lower jaw
epithelial tissue of ventral mandibular arch
epithelium of ventral mandibular arch
lower jaw epithelial tissue
lower jaw epithelium
ventral mandibular arch epithelial tissue
ventral mandibular arch epithelium
uberon
UBERON:0003236
epithelium of lower jaw
An epithelium that is part of a lower jaw [Automatically generated definition].
OBOL:automatic
epithelial tissue of lower jaw
OBOL:automatic
epithelial tissue of ventral mandibular arch
OBOL:automatic
epithelium of ventral mandibular arch
OBOL:automatic
lower jaw epithelial tissue
OBOL:automatic
lower jaw epithelium
OBOL:automatic
ventral mandibular arch epithelial tissue
OBOL:automatic
ventral mandibular arch epithelium
OBOL:automatic
An endoderm that is part of a foregut [Automatically generated definition].
TODO - check
EHDAA2:0004568
EHDAA:524
foregut endoderm
uberon
UBERON:0003258
endoderm of foregut
An endoderm that is part of a foregut [Automatically generated definition].
OBOL:automatic
foregut endoderm
OBOL:automatic
A portion of skeletal muscle tissue that is part of a eye [Automatically generated definition].
EHDAA2:0000486
EHDAA:2923
EMAPA:17844
eye skeletal muscle
eye skeletal muscle tissue
skeletal muscle tissue of eye
uberon
eye skeletal muscle group
UBERON:0003269
skeletal muscle tissue of eye
A portion of skeletal muscle tissue that is part of a eye [Automatically generated definition].
OBOL:automatic
eye skeletal muscle
OBOL:automatic
eye skeletal muscle tissue
OBOL:automatic
skeletal muscle tissue of eye
OBOL:automatic
eye skeletal muscle group
EHDAA2:0000486
A subdivision of the skeleton that corresponds to the lower part of the mouth. The lower jaw skeleton includes the following elements, when present: lower jaw teeth, the mandible and other lower jaw bones, and Meckel's cartilage.
The ventral portion of the first pharyngeal arch, comprising the lower jaw.[TAO]
The jaw joint of all jawed vertebrates, except for mammals, involves the quadrate and articular bones, or the posterior ends of the palatoquadrate and mandibular cartilages; A correlate of the conversion of the articular and quadrate bones to the malleus and incus is that all adult mammals have a jaw joint that lies between the dentary of the lower jaw and the squamosal bone of the skull roof.[well established][VHOG]
Inclusion of the FMA class 'lower jaw' is debatable - this mostly corresponds to the lower jaw skeleton (with 'maxillary part of mouth' corresponding to the upper jaw region); however, the FMA class also includes gingiva. See also: https://github.com/obophenotype/mouse-anatomy-ontology/issues/102
lower jaw
mandible
AAO:0000274
EHDAA2:0004606
EHDAA:8005
EMAPA:17906
EMAPA:17910
FMA:54398
MA:0001906
TAO:0001273
VHOG:0000428
XAO:0003084
ZFA:0001273
lower jaw skeleton
uberon
mandibles
mandibular series
UBERON:0003278
skeleton of lower jaw
EHDAA2
VHOG-modified
A subdivision of the skeleton that corresponds to the lower part of the mouth. The lower jaw skeleton includes the following elements, when present: lower jaw teeth, the mandible and other lower jaw bones, and Meckel's cartilage.
The ventral portion of the first pharyngeal arch, comprising the lower jaw.[TAO]
2012-08-14
TAO:0001273
TAO
ZFIN:curator
The jaw joint of all jawed vertebrates, except for mammals, involves the quadrate and articular bones, or the posterior ends of the palatoquadrate and mandibular cartilages; A correlate of the conversion of the articular and quadrate bones to the malleus and incus is that all adult mammals have a jaw joint that lies between the dentary of the lower jaw and the squamosal bone of the skull roof.[well established][VHOG]
2012-09-17
VHOG:0000428
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.241 and p.101
Inclusion of the FMA class 'lower jaw' is debatable - this mostly corresponds to the lower jaw skeleton (with 'maxillary part of mouth' corresponding to the upper jaw region); however, the FMA class also includes gingiva. See also: https://github.com/obophenotype/mouse-anatomy-ontology/issues/102
FMA
lower jaw
MA:0001906
lower jaw
ZFA:0001273
mandible
ZFA:0001273
lower jaw skeleton
AAO:0000274
mandibles
TAO:0001273
mandibular series
ZFA:0001273
A gland that is part of a foregut [Automatically generated definition].
EHDAA2:0000567
EHDAA:950
EMAPA:16557
VHOG:0000650
foregut gland
uberon
UBERON:0003294
gland of foregut
A gland that is part of a foregut [Automatically generated definition].
OBOL:automatic
foregut gland
OBOL:automatic
Racemose mucous glands beneath the mucous membrane of the pharynx.
BTO:0004849
EHDAA2:0001461
EHDAA:2967
FMA:55075
pharynx gland
uberon
glandulae pharyngeae
UBERON:0003295
pharyngeal gland
BTO
Racemose mucous glands beneath the mucous membrane of the pharynx.
pharynx gland
EHDAA2:0001461
glandulae pharyngeae
BTO:0004849
A gland that is part of a integumental system [Automatically generated definition].
EHDAA2:0000837
EHDAA:6522
EMAPA:17758
MA:0000144
VHOG:0000654
integumental gland
integumental system gland
integumentary gland
uberon
UBERON:0003297
gland of integumental system
A gland that is part of a integumental system [Automatically generated definition].
OBOL:automatic
integumental gland
integumental system gland
integumentary gland
A blood island that is part of a mesoderm.
in EHDAA2, gives rise to blood and dorsal aorta
UBERON:0003305
EHDAA2:0003241
EHDAA:170
EMAPA:16115
mesoderm blood islands
uberon
mesenchyme blood island
UBERON:0003304
mesoderm blood island
EHDAA2
EHDAA2
A blood island that is part of a mesoderm.
OBOL:automatic
in EHDAA2, gives rise to blood and dorsal aorta
EHDAA2
mesoderm blood islands
EHDAA2:0003241
mesenchyme blood island
OBOL:automatic
Mesenchyme that is part of a developing camera-type eye.
TODO - change mesenchyme relationships to precursor_of
EHDAA2:0000485
EHDAA:2910
EMAPA:16673
VHOG:0001084
mesenchyme of eye
uberon
UBERON:0003314
eye mesenchyme
EHDAA2
Mesenchyme that is part of a developing camera-type eye.
OBOL:automatic
mesenchyme of eye
OBOL:automatic
Mesenchyme that is part of a developing lower jaw [Automatically generated definition].
EHDAA2:0001024
EHDAA:8003
EMAPA:17916
VHOG:0001069
lower jaw mesenchyme
mesenchyme of ventral mandibular arch
ventral mandibular arch mesenchyme
uberon
UBERON:0003324
mesenchyme of lower jaw
EHDAA2
Mesenchyme that is part of a developing lower jaw [Automatically generated definition].
OBOL:automatic
lower jaw mesenchyme
OBOL:automatic
mesenchyme of ventral mandibular arch
OBOL:automatic
ventral mandibular arch mesenchyme
OBOL:automatic
A mucosa that is part of a oral opening [Automatically generated definition].
EMAPA:26937
mucosa of oral opening
mucosa of oral part of face
mucosa of organ of oral opening
mucosa of organ of oral part of face
mucosa of organ of oral region
mucosa of organ of subdivision of mouth
mucosa of subdivision of mouth
mucous membrane of oral opening
mucous membrane of oral part of face
mucous membrane of oral region
mucous membrane of subdivision of mouth
oral opening mucosa
oral opening mucosa of organ
oral opening mucous membrane
oral opening organ mucosa
oral part of face mucosa
oral part of face mucosa of organ
oral part of face mucous membrane
oral part of face organ mucosa
oral region mucosa
oral region mucosa of organ
oral region mucous membrane
oral region organ mucosa
organ mucosa of oral opening
organ mucosa of oral part of face
organ mucosa of oral region
organ mucosa of subdivision of mouth
subdivision of mouth mucosa
subdivision of mouth mucosa of organ
subdivision of mouth mucous membrane
subdivision of mouth organ mucosa
uberon
UBERON:0003343
mucosa of oral region
A mucosa that is part of a oral opening [Automatically generated definition].
OBOL:automatic
mucosa of oral opening
OBOL:automatic
mucosa of oral part of face
OBOL:automatic
mucosa of organ of oral opening
OBOL:automatic
mucosa of organ of oral part of face
OBOL:automatic
mucosa of organ of oral region
OBOL:automatic
mucosa of organ of subdivision of mouth
OBOL:automatic
mucosa of subdivision of mouth
OBOL:automatic
mucous membrane of oral opening
OBOL:automatic
mucous membrane of oral part of face
OBOL:automatic
mucous membrane of oral region
OBOL:automatic
mucous membrane of subdivision of mouth
OBOL:automatic
oral opening mucosa
OBOL:automatic
oral opening mucosa of organ
OBOL:automatic
oral opening mucous membrane
OBOL:automatic
oral opening organ mucosa
OBOL:automatic
oral part of face mucosa
OBOL:automatic
oral part of face mucosa of organ
OBOL:automatic
oral part of face mucous membrane
OBOL:automatic
oral part of face organ mucosa
OBOL:automatic
oral region mucosa
OBOL:automatic
oral region mucosa of organ
OBOL:automatic
oral region mucous membrane
OBOL:automatic
oral region organ mucosa
OBOL:automatic
organ mucosa of oral opening
OBOL:automatic
organ mucosa of oral part of face
OBOL:automatic
organ mucosa of oral region
OBOL:automatic
organ mucosa of subdivision of mouth
OBOL:automatic
subdivision of mouth mucosa
OBOL:automatic
subdivision of mouth mucosa of organ
OBOL:automatic
subdivision of mouth mucous membrane
OBOL:automatic
subdivision of mouth organ mucosa
OBOL:automatic
A layer of epithelial cells on the surface of the mucosa.
BTO:0003752
uberon
lamina epithelialis mucosa
lamina epithelialis mucosae
UBERON:0003350
lies on top of lamina propria
epithelium of mucosa
A layer of epithelial cells on the surface of the mucosa.
BTO:0003752
lamina epithelialis mucosa
BTO:0003752
lamina epithelialis mucosae
BTO:0003752
An epithelium that is part of a pharynx [Automatically generated definition].
Epithelium lining the pharynx consisting largely of simple columnar epithelium with a short segment (1mm) of stratified squamous epithelium on the ventral side. Chen et al, 2007.[TAO]
BSA:0000112
BTO:0005240
EMAPA:16708
MA:0002725
RETIRED_EHDAA2:0001460
TAO:0001174
XAO:0003202
ZFA:0001174
epithelial tissue of pharynx
epithelium of pharynx
pharynx epithelial tissue
pharynx epithelium
uberon
UBERON:0003351
pharyngeal epithelium
ZFA
ZFA
An epithelium that is part of a pharynx [Automatically generated definition].
OBOL:automatic
Epithelium lining the pharynx consisting largely of simple columnar epithelium with a short segment (1mm) of stratified squamous epithelium on the ventral side. Chen et al, 2007.[TAO]
2012-08-14
TAO:0001174
TAO
ZFIN:curator
epithelial tissue of pharynx
OBOL:automatic
epithelium of pharynx
OBOL:automatic
pharynx epithelial tissue
OBOL:automatic
pharynx epithelium
OBOL:automatic
A portion of skeletal muscle tissue that is part of a pharynx [Automatically generated definition].
EMAPA:18963
pharynx skeletal muscle
pharynx skeletal muscle tissue
skeletal muscle tissue of pharynx
uberon
UBERON:0003384
skeletal muscle tissue of pharynx
A portion of skeletal muscle tissue that is part of a pharynx [Automatically generated definition].
OBOL:automatic
pharynx skeletal muscle
OBOL:automatic
pharynx skeletal muscle tissue
OBOL:automatic
skeletal muscle tissue of pharynx
OBOL:automatic
any of the striated muscles that move the eye and include: superior rectus, inferior rectus, medial rectus, lateral rectus, superior oblique, inferior oblique, retractor bulbi
Not clear if we need this and intra-ocular muscle. See issue #331. MA includes ciliary and iris smooth muscle
EMAPA:18807
MA:0001268
ocular smooth muscle
uberon
UBERON:0003386
smooth muscle of eye
any of the striated muscles that move the eye and include: superior rectus, inferior rectus, medial rectus, lateral rectus, superior oblique, inferior oblique, retractor bulbi
MGI:cwg
MP:0005247
ocular smooth muscle
MA:0001268
A mesothelium that is part of a pericardium [Automatically generated definition].
RETIRED_EHDAA2:0001436
cavity of pericardial sac meso-epithelium
cavity of pericardial sac mesothelium
meso-epithelium of cavity of pericardial sac
meso-epithelium of pericardial cavity
mesothelium of cavity of pericardial sac
pericardial cavity meso-epithelium
pericardial cavity mesothelium
uberon
UBERON:0003388
mesothelium of pericardial cavity
A mesothelium that is part of a pericardium [Automatically generated definition].
OBOL:automatic
cavity of pericardial sac meso-epithelium
OBOL:automatic
cavity of pericardial sac mesothelium
OBOL:automatic
meso-epithelium of cavity of pericardial sac
OBOL:automatic
meso-epithelium of pericardial cavity
OBOL:automatic
mesothelium of cavity of pericardial sac
OBOL:automatic
pericardial cavity meso-epithelium
OBOL:automatic
pericardial cavity mesothelium
OBOL:automatic
A cartilage element that is part of a respiratory system [Automatically generated definition].
EMAPA:18694
MA:0001818
apparatus respiratorius cartilage
cartilage of apparatus respiratorius
respiratory system cartilage
uberon
UBERON:0003406
cartilage of respiratory system
A cartilage element that is part of a respiratory system [Automatically generated definition].
OBOL:automatic
apparatus respiratorius cartilage
OBOL:automatic
cartilage of apparatus respiratorius
OBOL:automatic
respiratory system cartilage
OBOL:automatic
A gland that is part of a digestive tract [Automatically generated definition].
EMAPA:18815
MA:0003202
digestive tract gland
gland of digestive tract
gland of lower gastrointestinal tract
gut gland
lower gastrointestinal tract gland
uberon
UBERON:0003408
gland of digestive tract
A gland that is part of a digestive tract [Automatically generated definition].
OBOL:automatic
digestive tract gland
OBOL:automatic
gland of digestive tract
OBOL:automatic
gland of lower gastrointestinal tract
OBOL:automatic
gut gland
MA:0003202
lower gastrointestinal tract gland
OBOL:automatic
An adipose tissue that is part of a dermis [Automatically generated definition].
MA:0000798
adipose tissue of dermis
dermis fat tissue
dermis fatty tissue
fat tissue of dermis
fatty tissue of dermis
uberon
UBERON:0003426
dermis adipose tissue
An adipose tissue that is part of a dermis [Automatically generated definition].
OBOL:automatic
adipose tissue of dermis
OBOL:automatic
dermis fat tissue
OBOL:automatic
dermis fatty tissue
OBOL:automatic
fat tissue of dermis
OBOL:automatic
fatty tissue of dermis
OBOL:automatic
A bone that is part of a head [Automatically generated definition].
EMAPA:35996
MA:0000576
adult head bone
adult head bone organ
bone of adult head
bone of head
bone organ of adult head
bone organ of head
head bone organ
uberon
craniofacial bone
UBERON:0003457
Different sources vary regarding which bones are craniofacial; e.g. hyoid bone
head bone
A bone that is part of a head [Automatically generated definition].
OBOL:automatic
adult head bone
OBOL:automatic
adult head bone organ
OBOL:automatic
bone of adult head
OBOL:automatic
bone of head
OBOL:automatic
bone organ of adult head
OBOL:automatic
bone organ of head
OBOL:automatic
head bone organ
OBOL:automatic
craniofacial bone
A bone that is part of a neck [Automatically generated definition].
EMAPA:37246
MA:0000584
OpenCyc:Mx4rvnpJSJwpEbGdrcN5Y29ycA
bone of neck
bone of neck (volume)
bone organ of neck
bone organ of neck (volume)
neck (volume) bone
neck (volume) bone organ
neck bone organ
uberon
UBERON:0003458
neck bone
A bone that is part of a neck [Automatically generated definition].
OBOL:automatic
EMAPA:37246
MA:th
bone of neck
OBOL:automatic
bone of neck (volume)
OBOL:automatic
bone organ of neck
OBOL:automatic
bone organ of neck (volume)
OBOL:automatic
neck (volume) bone
OBOL:automatic
neck (volume) bone organ
OBOL:automatic
neck bone organ
OBOL:automatic
A bone that is part of a facial skeleton [Automatically generated definition].
test whether 'facial bone' is an exact synonym
EMAPA:19019
EMAPA:35924
MA:0001482
MA:0003159
NCIT:C63706
UMLS:C0015455
bone of facial skeleton
facial bone
facial skeleton bone
uberon
bone of viscerocranium
viscerocranium bone
UBERON:0003462
facial bone
MA
A bone that is part of a facial skeleton [Automatically generated definition].
OBOL:automatic
UMLS:C0015455
ncithesaurus:Facial_Bone
bone of facial skeleton
OBOL:automatic
facial bone
EMAPA:19019
facial skeleton bone
OBOL:automatic
bone of viscerocranium
OBOL:automatic
viscerocranium bone
OBOL:automatic
A bone that is part of a trunk [Automatically generated definition].
EMAPA:36583
MA:0000512
bone of torso
bone of trunk
bone organ of torso
bone organ of trunk
torso bone
torso bone organ
trunk bone organ
uberon
UBERON:0003463
trunk bone
A bone that is part of a trunk [Automatically generated definition].
OBOL:automatic
bone of torso
OBOL:automatic
bone of trunk
OBOL:automatic
bone organ of torso
OBOL:automatic
bone organ of trunk
OBOL:automatic
torso bone
OBOL:automatic
torso bone organ
OBOL:automatic
trunk bone organ
OBOL:automatic
An artery that is part of a respiratory system [Automatically generated definition].
EMAPA:37569
MA:0001804
uberon
UBERON:0003469
respiratory system artery
An artery that is part of a respiratory system [Automatically generated definition].
OBOL:automatic
EMAPA:37569
MA:th
An artery that is part of a thoracic cavity[cjm].
in MA, aorta is classified here - but this is problematic because the abdominal aorta is not in the thoracic cavity
EMAPA:37241
MA:0001902
MESH:D013895
uberon
thoracic artery
UBERON:0003473
thoracic cavity artery
An artery that is part of a thoracic cavity[cjm].
in MA, aorta is classified here - but this is problematic because the abdominal aorta is not in the thoracic cavity
MA
EMAPA:37241
MA:th
thoracic artery
MESH:A07.231.114.891
A vein that is part of a respiratory system [Automatically generated definition].
EMAPA:37584
MA:0001809
MA:0001810
apparatus respiratorius vein
respiratory system vein
vein of apparatus respiratorius
vein of respiratory system
uberon
UBERON:0003476
respiratory system venous blood vessel
A vein that is part of a respiratory system [Automatically generated definition].
OBOL:automatic
EMAPA:37584
MA:th
apparatus respiratorius vein
OBOL:automatic
respiratory system vein
OBOL:automatic
vein of apparatus respiratorius
OBOL:automatic
vein of respiratory system
OBOL:automatic
The inferior labial vein is the vein receiving blood from the lower lip.
EMAPA:37202
FMA:52541
MA:0002253
inferior labial vein
lower lip vein
vena labialis inferior
uberon
venae labiales inferiores
UBERON:0003478
vein of lower lip
http://upload.wikimedia.org/wikipedia/commons/8/8c/Gray557.png
The inferior labial vein is the vein receiving blood from the lower lip.
EMAPA:37202
MA:th
inferior labial vein
FMA:52541
lower lip vein
OBOL:automatic
vena labialis inferior
venae labiales inferiores
A vein that is part of a thoracic cavity [Automatically generated definition].
EMAPA:37242
MA:0001903
cavity of chest vein
cavity of thorax vein
chest cavity vein
pectoral cavity vein
vein of cavity of chest
vein of cavity of thorax
vein of chest cavity
vein of pectoral cavity
vein of thoracic cavity
uberon
UBERON:0003479
thoracic cavity vein
A vein that is part of a thoracic cavity [Automatically generated definition].
OBOL:automatic
EMAPA:37242
MA:th
cavity of chest vein
OBOL:automatic
cavity of thorax vein
OBOL:automatic
chest cavity vein
OBOL:automatic
pectoral cavity vein
OBOL:automatic
vein of cavity of chest
OBOL:automatic
vein of cavity of thorax
OBOL:automatic
vein of chest cavity
OBOL:automatic
vein of pectoral cavity
OBOL:automatic
vein of thoracic cavity
OBOL:automatic
An endothelium of capillary that is part of a respiratory system [Automatically generated definition].
EMAPA:37575
MA:0001808
apparatus respiratorius blood capillary endothelium
apparatus respiratorius capillary endothelium
apparatus respiratorius capillary vessel endothelium
apparatus respiratorius endothelium of blood capillary
apparatus respiratorius endothelium of capillary
apparatus respiratorius endothelium of capillary vessel
blood capillary endothelium of apparatus respiratorius
blood capillary endothelium of respiratory system
capillary endothelium of apparatus respiratorius
capillary endothelium of respiratory system
capillary vessel endothelium of apparatus respiratorius
capillary vessel endothelium of respiratory system
endothelium of blood capillary of apparatus respiratorius
endothelium of blood capillary of respiratory system
endothelium of capillary of apparatus respiratorius
endothelium of capillary of respiratory system
endothelium of capillary vessel of apparatus respiratorius
endothelium of capillary vessel of respiratory system
respiratory system blood capillary endothelium
respiratory system capillary vessel endothelium
respiratory system endothelium of blood capillary
respiratory system endothelium of capillary
respiratory system endothelium of capillary vessel
uberon
UBERON:0003489
respiratory system capillary endothelium
true
An endothelium of capillary that is part of a respiratory system [Automatically generated definition].
OBOL:automatic
EMAPA:37575
MA:th
apparatus respiratorius blood capillary endothelium
OBOL:automatic
apparatus respiratorius capillary endothelium
OBOL:automatic
apparatus respiratorius capillary vessel endothelium
OBOL:automatic
apparatus respiratorius endothelium of blood capillary
OBOL:automatic
apparatus respiratorius endothelium of capillary
OBOL:automatic
apparatus respiratorius endothelium of capillary vessel
OBOL:automatic
blood capillary endothelium of apparatus respiratorius
OBOL:automatic
blood capillary endothelium of respiratory system
OBOL:automatic
capillary endothelium of apparatus respiratorius
OBOL:automatic
capillary endothelium of respiratory system
OBOL:automatic
capillary vessel endothelium of apparatus respiratorius
OBOL:automatic
capillary vessel endothelium of respiratory system
OBOL:automatic
endothelium of blood capillary of apparatus respiratorius
OBOL:automatic
endothelium of blood capillary of respiratory system
OBOL:automatic
endothelium of capillary of apparatus respiratorius
OBOL:automatic
endothelium of capillary of respiratory system
OBOL:automatic
endothelium of capillary vessel of apparatus respiratorius
OBOL:automatic
endothelium of capillary vessel of respiratory system
OBOL:automatic
respiratory system blood capillary endothelium
OBOL:automatic
respiratory system capillary vessel endothelium
OBOL:automatic
respiratory system endothelium of blood capillary
OBOL:automatic
respiratory system endothelium of capillary
OBOL:automatic
respiratory system endothelium of capillary vessel
OBOL:automatic
A venule that is part of a respiratory system [Automatically generated definition].
EMAPA:37587
MA:0001813
apparatus respiratorius venule
venule of apparatus respiratorius
venule of respiratory system
uberon
UBERON:0003494
respiratory system venule
A venule that is part of a respiratory system [Automatically generated definition].
OBOL:automatic
EMAPA:37587
MA:th
apparatus respiratorius venule
OBOL:automatic
venule of apparatus respiratorius
OBOL:automatic
venule of respiratory system
OBOL:automatic
An arteriole that is part of a respiratory system [Automatically generated definition].
EMAPA:37568
MA:0001803
uberon
UBERON:0003495
respiratory system arteriole
true
An arteriole that is part of a respiratory system [Automatically generated definition].
OBOL:automatic
EMAPA:37568
MA:th
A blood vessel that is part of a head [Automatically generated definition].
EMAPA:36610
MA:0000575
adult head blood vessel
blood vessel of adult head
blood vessel of head
uberon
UBERON:0003496
head blood vessel
true
A blood vessel that is part of a head [Automatically generated definition].
OBOL:automatic
adult head blood vessel
OBOL:automatic
blood vessel of adult head
OBOL:automatic
blood vessel of head
OBOL:automatic
A blood vessel that is part of a heart [Automatically generated definition].
EMAPA:35397
MA:0002483
blood vessel of heart
uberon
cardiac blood vessel
UBERON:0003498
heart blood vessel
A blood vessel that is part of a heart [Automatically generated definition].
OBOL:automatic
blood vessel of heart
OBOL:automatic
cardiac blood vessel
EMAPA:35397
A blood vessel that is part of a brain [Automatically generated definition].
EMAPA:35182
MA:0002769
blood vessel of brain
uberon
UBERON:0003499
brain blood vessel
A blood vessel that is part of a brain [Automatically generated definition].
OBOL:automatic
blood vessel of brain
OBOL:automatic
A blood vessel that is part of a cornea [Automatically generated definition].
follow up on tracker item
EMAPA:36611
MA:0001241
blood vessel of cornea
cornea blood vessel
uberon
UBERON:0003500
corneal blood vessel
A blood vessel that is part of a cornea [Automatically generated definition].
blood vessel of cornea
OBOL:automatic
cornea blood vessel
OBOL:automatic
A blood vessel that is part of a retina [Automatically generated definition].
EMAPA:36520
GAID:509
MA:0001317
MESH:D012171
XAO:0004153
blood vessel of inner layer of eyeball
blood vessel of retina
blood vessel of tunica interna of eyeball
inner layer of eyeball blood vessel
retinal blood vessel
tunica interna of eyeball blood vessel
uberon
UBERON:0003501
retina blood vessel
A blood vessel that is part of a retina [Automatically generated definition].
OBOL:automatic
blood vessel of inner layer of eyeball
OBOL:automatic
blood vessel of retina
OBOL:automatic
blood vessel of tunica interna of eyeball
OBOL:automatic
inner layer of eyeball blood vessel
OBOL:automatic
retinal blood vessel
OBOL:automatic
tunica interna of eyeball blood vessel
OBOL:automatic
A blood vessel that is part of a neck [Automatically generated definition].
EMAPA:37236
MA:0000583
blood vessel of neck
blood vessel of neck (volume)
neck (volume) blood vessel
uberon
UBERON:0003502
neck blood vessel
A blood vessel that is part of a neck [Automatically generated definition].
OBOL:automatic
EMAPA:37236
MA:th
blood vessel of neck
OBOL:automatic
blood vessel of neck (volume)
OBOL:automatic
neck (volume) blood vessel
OBOL:automatic
A blood vessel that is part of a respiratory system [Automatically generated definition].
EMAPA:35731
EMAPA:35995
MA:0001799
apparatus respiratorius blood vessel
blood vessel of apparatus respiratorius
blood vessel of respiratory system
uberon
UBERON:0003504
respiratory system blood vessel
A blood vessel that is part of a respiratory system [Automatically generated definition].
OBOL:automatic
apparatus respiratorius blood vessel
OBOL:automatic
blood vessel of apparatus respiratorius
OBOL:automatic
blood vessel of respiratory system
OBOL:automatic
A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta.
EMAPA:35144
MA:0000061
uberon
UBERON:0003509
only in MA - supertype of artery, arteriole, aorta.
arterial blood vessel
A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta.
A blood vessel that is part of a iris [Automatically generated definition].
EMAPA:37387
MA:0001290
ZFA:0005568
blood vessel of iris
uberon
UBERON:0003511
iris blood vessel
A blood vessel that is part of a iris [Automatically generated definition].
OBOL:automatic
EMAPA:37387
MA:th
blood vessel of iris
OBOL:automatic
A blood vessel that is part of a trunk [Automatically generated definition].
EMAPA:37237
MA:0000511
blood vessel of torso
blood vessel of trunk
torso blood vessel
uberon
UBERON:0003513
trunk blood vessel
A blood vessel that is part of a trunk [Automatically generated definition].
OBOL:automatic
EMAPA:37237
MA:th
blood vessel of torso
OBOL:automatic
blood vessel of trunk
OBOL:automatic
torso blood vessel
OBOL:automatic
A blood vessel that is part of a thoracic cavity [Automatically generated definition].
EMAPA:37240
MA:0000554
blood vessel of cavity of chest
blood vessel of cavity of thorax
blood vessel of chest cavity
blood vessel of pectoral cavity
blood vessel of thoracic cavity
cavity of chest blood vessel
cavity of thorax blood vessel
chest cavity blood vessel
pectoral cavity blood vessel
uberon
UBERON:0003519
thoracic cavity blood vessel
A blood vessel that is part of a thoracic cavity [Automatically generated definition].
OBOL:automatic
EMAPA:37240
MA:th
blood vessel of cavity of chest
OBOL:automatic
blood vessel of cavity of thorax
OBOL:automatic
blood vessel of chest cavity
OBOL:automatic
blood vessel of pectoral cavity
OBOL:automatic
blood vessel of thoracic cavity
OBOL:automatic
cavity of chest blood vessel
OBOL:automatic
cavity of thorax blood vessel
OBOL:automatic
chest cavity blood vessel
OBOL:automatic
pectoral cavity blood vessel
OBOL:automatic
A capillary that is part of a respiratory system [Automatically generated definition].
EMAPA:37574
MA:0001807
apparatus respiratorius blood capillary
apparatus respiratorius capillary
apparatus respiratorius capillary vessel
blood capillary of apparatus respiratorius
blood capillary of respiratory system
capillary of apparatus respiratorius
capillary of respiratory system
capillary vessel of apparatus respiratorius
capillary vessel of respiratory system
respiratory system blood capillary
respiratory system capillary vessel
uberon
UBERON:0003526
respiratory system capillary
A capillary that is part of a respiratory system [Automatically generated definition].
OBOL:automatic
EMAPA:37574
MA:th
apparatus respiratorius blood capillary
OBOL:automatic
apparatus respiratorius capillary
OBOL:automatic
apparatus respiratorius capillary vessel
OBOL:automatic
blood capillary of apparatus respiratorius
OBOL:automatic
blood capillary of respiratory system
OBOL:automatic
capillary of apparatus respiratorius
OBOL:automatic
capillary of respiratory system
OBOL:automatic
capillary vessel of apparatus respiratorius
OBOL:automatic
capillary vessel of respiratory system
OBOL:automatic
respiratory system blood capillary
OBOL:automatic
respiratory system capillary vessel
OBOL:automatic
A gray matter that is part of a brain [Automatically generated definition].
EMAPA:35184
MA:0000810
NCIT:C49333
UMLS:C1707348
brain grey matter
brain grey substance
gray matter of brain
grey matter of brain
grey substance of brain
uberon
UBERON:0003528
brain gray matter
A gray matter that is part of a brain [Automatically generated definition].
OBOL:automatic
UMLS:C1707348
ncithesaurus:Cerebral_Gray_Matter
brain grey matter
MA:0000810
brain grey substance
OBOL:automatic
gray matter of brain
OBOL:automatic
grey matter of brain
OBOL:automatic
grey substance of brain
OBOL:automatic
A portion of connective tissue that is part of a head [Automatically generated definition].
EMAPA:16098
MA:0000577
adult head connective tissue
adult head portion of connective tissue
adult head textus connectivus
connective tissue of adult head
connective tissue of head
head portion of connective tissue
head textus connectivus
portion of connective tissue of adult head
portion of connective tissue of head
textus connectivus of adult head
textus connectivus of head
uberon
UBERON:0003566
head connective tissue
A portion of connective tissue that is part of a head [Automatically generated definition].
OBOL:automatic
adult head connective tissue
OBOL:automatic
adult head portion of connective tissue
OBOL:automatic
adult head textus connectivus
OBOL:automatic
connective tissue of adult head
OBOL:automatic
connective tissue of head
OBOL:automatic
head portion of connective tissue
OBOL:automatic
head textus connectivus
OBOL:automatic
portion of connective tissue of adult head
OBOL:automatic
portion of connective tissue of head
OBOL:automatic
textus connectivus of adult head
OBOL:automatic
textus connectivus of head
OBOL:automatic
A portion of connective tissue that is part of a neck [Automatically generated definition].
EMAPA:37250
MA:0000585
connective tissue of neck
connective tissue of neck (volume)
neck (volume) connective tissue
neck (volume) portion of connective tissue
neck (volume) textus connectivus
neck portion of connective tissue
neck textus connectivus
portion of connective tissue of neck
portion of connective tissue of neck (volume)
textus connectivus of neck
textus connectivus of neck (volume)
uberon
UBERON:0003568
neck connective tissue
A portion of connective tissue that is part of a neck [Automatically generated definition].
OBOL:automatic
EMAPA:37250
MA:th
connective tissue of neck
OBOL:automatic
connective tissue of neck (volume)
OBOL:automatic
neck (volume) connective tissue
OBOL:automatic
neck (volume) portion of connective tissue
OBOL:automatic
neck (volume) textus connectivus
OBOL:automatic
neck portion of connective tissue
OBOL:automatic
neck textus connectivus
OBOL:automatic
portion of connective tissue of neck
OBOL:automatic
portion of connective tissue of neck (volume)
OBOL:automatic
textus connectivus of neck
OBOL:automatic
textus connectivus of neck (volume)
OBOL:automatic
A portion of connective tissue that is part of a respiratory system [Automatically generated definition].
EMAPA:35968
EMAPA:35977
MA:0001814
apparatus respiratorius connective tissue
apparatus respiratorius portion of connective tissue
apparatus respiratorius textus connectivus
connective tissue of apparatus respiratorius
connective tissue of respiratory system
portion of connective tissue of apparatus respiratorius
portion of connective tissue of respiratory system
respiratory system portion of connective tissue
respiratory system textus connectivus
textus connectivus of apparatus respiratorius
textus connectivus of respiratory system
uberon
UBERON:0003570
respiratory system connective tissue
A portion of connective tissue that is part of a respiratory system [Automatically generated definition].
OBOL:automatic
apparatus respiratorius connective tissue
OBOL:automatic
apparatus respiratorius portion of connective tissue
OBOL:automatic
apparatus respiratorius textus connectivus
OBOL:automatic
connective tissue of apparatus respiratorius
OBOL:automatic
connective tissue of respiratory system
OBOL:automatic
portion of connective tissue of apparatus respiratorius
OBOL:automatic
portion of connective tissue of respiratory system
OBOL:automatic
respiratory system portion of connective tissue
OBOL:automatic
respiratory system textus connectivus
OBOL:automatic
textus connectivus of apparatus respiratorius
OBOL:automatic
textus connectivus of respiratory system
OBOL:automatic
A portion of connective tissue that is part of a dermis [Automatically generated definition].
EMAPA:36509
MA:0000799
connective tissue of dermis
dermis portion of connective tissue
dermis textus connectivus
portion of connective tissue of dermis
textus connectivus of dermis
uberon
UBERON:0003585
dermis connective tissue
A portion of connective tissue that is part of a dermis [Automatically generated definition].
OBOL:automatic
connective tissue of dermis
OBOL:automatic
dermis portion of connective tissue
OBOL:automatic
dermis textus connectivus
OBOL:automatic
portion of connective tissue of dermis
OBOL:automatic
textus connectivus of dermis
OBOL:automatic
A portion of connective tissue that is part of a trunk [Automatically generated definition].
EMAPA:37252
MA:0000513
connective tissue of torso
connective tissue of trunk
portion of connective tissue of torso
portion of connective tissue of trunk
textus connectivus of torso
textus connectivus of trunk
torso connective tissue
torso portion of connective tissue
torso textus connectivus
trunk portion of connective tissue
trunk textus connectivus
uberon
UBERON:0003586
trunk connective tissue
A portion of connective tissue that is part of a trunk [Automatically generated definition].
OBOL:automatic
EMAPA:37252
MA:th
connective tissue of torso
OBOL:automatic
connective tissue of trunk
OBOL:automatic
portion of connective tissue of torso
OBOL:automatic
portion of connective tissue of trunk
OBOL:automatic
textus connectivus of torso
OBOL:automatic
textus connectivus of trunk
OBOL:automatic
torso connective tissue
OBOL:automatic
torso portion of connective tissue
OBOL:automatic
torso textus connectivus
OBOL:automatic
trunk portion of connective tissue
OBOL:automatic
trunk textus connectivus
OBOL:automatic
A portion of connective tissue that is part of a thoracic cavity [Automatically generated definition].
EMAPA:37255
MA:0000555
cavity of chest connective tissue
cavity of chest portion of connective tissue
cavity of chest textus connectivus
cavity of thorax connective tissue
cavity of thorax portion of connective tissue
cavity of thorax textus connectivus
chest cavity connective tissue
chest cavity portion of connective tissue
chest cavity textus connectivus
connective tissue of cavity of chest
connective tissue of cavity of thorax
connective tissue of chest cavity
connective tissue of pectoral cavity
connective tissue of thoracic cavity
pectoral cavity connective tissue
pectoral cavity portion of connective tissue
pectoral cavity textus connectivus
portion of connective tissue of cavity of chest
portion of connective tissue of cavity of thorax
portion of connective tissue of chest cavity
portion of connective tissue of pectoral cavity
portion of connective tissue of thoracic cavity
textus connectivus of cavity of chest
textus connectivus of cavity of thorax
textus connectivus of chest cavity
textus connectivus of pectoral cavity
textus connectivus of thoracic cavity
thoracic cavity portion of connective tissue
thoracic cavity textus connectivus
uberon
UBERON:0003593
thoracic cavity connective tissue
A portion of connective tissue that is part of a thoracic cavity [Automatically generated definition].
OBOL:automatic
EMAPA:37255
MA:th
cavity of chest connective tissue
OBOL:automatic
cavity of chest portion of connective tissue
OBOL:automatic
cavity of chest textus connectivus
OBOL:automatic
cavity of thorax connective tissue
OBOL:automatic
cavity of thorax portion of connective tissue
OBOL:automatic
cavity of thorax textus connectivus
OBOL:automatic
chest cavity connective tissue
OBOL:automatic
chest cavity portion of connective tissue
OBOL:automatic
chest cavity textus connectivus
OBOL:automatic
connective tissue of cavity of chest
OBOL:automatic
connective tissue of cavity of thorax
OBOL:automatic
connective tissue of chest cavity
OBOL:automatic
connective tissue of pectoral cavity
OBOL:automatic
connective tissue of thoracic cavity
OBOL:automatic
pectoral cavity connective tissue
OBOL:automatic
pectoral cavity portion of connective tissue
OBOL:automatic
pectoral cavity textus connectivus
OBOL:automatic
portion of connective tissue of cavity of chest
OBOL:automatic
portion of connective tissue of cavity of thorax
OBOL:automatic
portion of connective tissue of chest cavity
OBOL:automatic
portion of connective tissue of pectoral cavity
OBOL:automatic
portion of connective tissue of thoracic cavity
OBOL:automatic
textus connectivus of cavity of chest
OBOL:automatic
textus connectivus of cavity of thorax
OBOL:automatic
textus connectivus of chest cavity
OBOL:automatic
textus connectivus of pectoral cavity
OBOL:automatic
textus connectivus of thoracic cavity
OBOL:automatic
thoracic cavity portion of connective tissue
OBOL:automatic
thoracic cavity textus connectivus
OBOL:automatic
A cartilage that is part of a neck [Automatically generated definition].
EMAPA:37251
MA:0000586
cartilage of neck
cartilage of neck (volume)
neck (volume) cartilage
uberon
UBERON:0003601
neck cartilage
A cartilage that is part of a neck [Automatically generated definition].
OBOL:automatic
EMAPA:37251
MA:th
cartilage of neck
OBOL:automatic
cartilage of neck (volume)
OBOL:automatic
neck (volume) cartilage
OBOL:automatic
A skin gland that is part of a camera-type eye [Automatically generated definition].
EMAPA:37530
MA:0002451
camera-type eye skin gland
camera-type eye skin glands
camera-type eye skin glands set
skin gland of camera-type eye
skin gland of vertebrate eye
skin glands of camera-type eye
skin glands of vertebrate eye
skin glands set of camera-type eye
skin glands set of vertebrate eye
vertebrate eye skin gland
vertebrate eye skin glands
vertebrate eye skin glands set
uberon
UBERON:0003605
eye skin gland
A skin gland that is part of a camera-type eye [Automatically generated definition].
OBOL:automatic
EMAPA:37530
MA:th
camera-type eye skin gland
OBOL:automatic
camera-type eye skin glands
OBOL:automatic
camera-type eye skin glands set
OBOL:automatic
skin gland of camera-type eye
OBOL:automatic
skin gland of vertebrate eye
OBOL:automatic
skin glands of camera-type eye
OBOL:automatic
skin glands of vertebrate eye
OBOL:automatic
skin glands set of camera-type eye
OBOL:automatic
skin glands set of vertebrate eye
OBOL:automatic
vertebrate eye skin gland
OBOL:automatic
vertebrate eye skin glands
OBOL:automatic
vertebrate eye skin glands set
OBOL:automatic
The type of heart connective tissue found in the endocardial layer that consists mainly of elastic fibers.
MA:0002858
cardiac elastic tissue
elastic connective tissue of heart
elastic tissue of heart
heart elastic connective tissue
heart textus connectivus elasticus
textus connectivus elasticus of heart
uberon
UBERON:0003610
heart elastic tissue
The type of heart connective tissue found in the endocardial layer that consists mainly of elastic fibers.
MP:0009863
cardiac elastic tissue
MP:0009863
elastic connective tissue of heart
OBOL:automatic
elastic tissue of heart
OBOL:automatic
heart elastic connective tissue
OBOL:automatic
heart textus connectivus elasticus
OBOL:automatic
textus connectivus elasticus of heart
OBOL:automatic
An elastic tissue that is part of a respiratory system [Automatically generated definition].
EMAPA:37579
MA:0001820
apparatus respiratorius elastic connective tissue
apparatus respiratorius elastic tissue
apparatus respiratorius textus connectivus elasticus
elastic connective tissue of apparatus respiratorius
elastic connective tissue of respiratory system
elastic tissue of apparatus respiratorius
elastic tissue of respiratory system
respiratory system elastic connective tissue
respiratory system textus connectivus elasticus
textus connectivus elasticus of apparatus respiratorius
textus connectivus elasticus of respiratory system
uberon
UBERON:0003611
respiratory system elastic tissue
An elastic tissue that is part of a respiratory system [Automatically generated definition].
OBOL:automatic
EMAPA:37579
MA:th
apparatus respiratorius elastic connective tissue
OBOL:automatic
apparatus respiratorius elastic tissue
OBOL:automatic
apparatus respiratorius textus connectivus elasticus
OBOL:automatic
elastic connective tissue of apparatus respiratorius
OBOL:automatic
elastic connective tissue of respiratory system
OBOL:automatic
elastic tissue of apparatus respiratorius
OBOL:automatic
elastic tissue of respiratory system
OBOL:automatic
respiratory system elastic connective tissue
OBOL:automatic
respiratory system textus connectivus elasticus
OBOL:automatic
textus connectivus elasticus of apparatus respiratorius
OBOL:automatic
textus connectivus elasticus of respiratory system
OBOL:automatic
An elastic tissue that is part of a circulatory system [Automatically generated definition].
MA:0002857
cardiovascular system elastic connective tissue
cardiovascular system textus connectivus elasticus
circulatory system elastic connective tissue
circulatory system elastic tissue
circulatory system textus connectivus elasticus
elastic connective tissue of cardiovascular system
elastic connective tissue of circulatory system
elastic tissue of cardiovascular system
elastic tissue of circulatory system
textus connectivus elasticus of cardiovascular system
textus connectivus elasticus of circulatory system
uberon
UBERON:0003613
cardiovascular system elastic tissue
An elastic tissue that is part of a circulatory system [Automatically generated definition].
OBOL:automatic
cardiovascular system elastic connective tissue
OBOL:automatic
cardiovascular system textus connectivus elasticus
OBOL:automatic
circulatory system elastic connective tissue
OBOL:automatic
circulatory system elastic tissue
OBOL:automatic
circulatory system textus connectivus elasticus
OBOL:automatic
elastic connective tissue of cardiovascular system
OBOL:automatic
elastic connective tissue of circulatory system
OBOL:automatic
elastic tissue of cardiovascular system
OBOL:automatic
elastic tissue of circulatory system
OBOL:automatic
textus connectivus elasticus of cardiovascular system
OBOL:automatic
textus connectivus elasticus of circulatory system
OBOL:automatic
Elastic tissue layer that lines a blood vessel layer.
elastic lamina
elastic laminae
EMAPA:36300
MA:0002856
blood vessel elastic connective tissue
blood vessel textus connectivus elasticus
elastic connective tissue of blood vessel
elastic tissue of blood vessel
textus connectivus elasticus of blood vessel
vascular elastic lamina
vascular elastic laminae
vascular elastic tissue
uberon
UBERON:0003614
blood vessel elastic tissue
Elastic tissue layer that lines a blood vessel layer.
elastic lamina
MP:0006083
elastic laminae
MP:0006083
blood vessel elastic connective tissue
OBOL:automatic
blood vessel textus connectivus elasticus
OBOL:automatic
elastic connective tissue of blood vessel
OBOL:automatic
elastic tissue of blood vessel
OBOL:automatic
textus connectivus elasticus of blood vessel
OBOL:automatic
vascular elastic lamina
vascular elastic laminae
vascular elastic tissue
MP:0006083
An arterial blood vessel that is part of a respiratory system [Automatically generated definition].
EMAPA:37565
MA:0001800
uberon
UBERON:0003643
respiratory system arterial blood vessel
An arterial blood vessel that is part of a respiratory system [Automatically generated definition].
OBOL:automatic
EMAPA:37565
MA:th
In anatomy, in the occipital bone, the foramen magnum is one of the several oval or circular apertures in the base of the skull, through which the medulla oblongata (an extension of the spinal cord) enters and exits the skull vault. Apart from the transmission of the medulla oblongata and its membranes, the foramen magnum transmits the Spinal Accessory nerve, vertebral arteries, the anterior and posterior spinal arteries, the membrana tectoria and alar ligaments. [WP,unvetted].
Foramen in the occipital region of neurocranium to allow passage of spinal cord.[TAO]
AAO:0010826
EMAPA:37868
FMA:75306
GAID:228
MESH:D005539
NCIT:C12495
OpenCyc:Mx4rwOm-FpwpEbGdrcN5Y29ycA
TAO:0002045
UMLS:C0016519
ZFA:0005387
uberon
UBERON:0003687
Design pattern notes: check whether this fits the foramen design pattern
foramen magnum
http://upload.wikimedia.org/wikipedia/commons/3/39/Gray130.png
In anatomy, in the occipital bone, the foramen magnum is one of the several oval or circular apertures in the base of the skull, through which the medulla oblongata (an extension of the spinal cord) enters and exits the skull vault. Apart from the transmission of the medulla oblongata and its membranes, the foramen magnum transmits the Spinal Accessory nerve, vertebral arteries, the anterior and posterior spinal arteries, the membrana tectoria and alar ligaments. [WP,unvetted].
Foramen in the occipital region of neurocranium to allow passage of spinal cord.[TAO]
2012-08-14
TAO:0002045
TAO
TAO:wd
EMAPA:37868
MA:th
UMLS:C0016519
ncithesaurus:Foramen_Magnum
Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature.
One of the four types of tissue in traditional classifications. Cells forming the brain, spinal cord and peripheral nervous system.[AAO]
FMA definition includes vasculature
AAO:0000325
AEO:0000123
EHDAA2:0003123
FMA:9642
GAID:609
MESH:D009417
NCIT:C13052
OpenCyc:Mx4rVmfYCsQ_QdeM_bFAeS8NRQ
UMLS:C0027757
nerve tissue
nervous tissue
portion of neural tissue
uberon
UBERON:0003714
neural tissue
Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature.
FMA:9642
One of the four types of tissue in traditional classifications. Cells forming the brain, spinal cord and peripheral nervous system.[AAO]
2012-06-20
AAO:0000325
AAO
AAO:LAP
FMA definition includes vasculature
FMA
UMLS:C0027757
ncithesaurus:Nervous_Tissue
nerve tissue
FMA:9642
nervous tissue
FMA:9642
portion of neural tissue
FMA:9642
A mucous membrane that lines the mouth.
this is defined as any mucous membrane of the mouth - including palate, lips, uvula, etc. ncit split mouth/oral mucosa into lip and buccal. In future we may split into masticatory/keratinized (gingiva + hard palate) vs lining/non-keratinized (lips, cheeks, floor of mouth, soft palate). FMA distinguishes between mucosa of mouth and region of mouth (the latter including the buccal mucosa)
the mucous membrane epithelium of the mouth. It can be divided into three categories: masticatory, lining, and specialized[Wikipedia:Oral_mucosa].
BTO:0002860
CALOHA:TS-0716
EMAPA:26937
FMA:59660
GAID:951
MA:0002794
MESH:D009061
NCIT:C77637
UMLS:C0026639
mouth mucosa
mouth mucous membrane
mouth organ mucosa
mucosa of mouth
mucous membrane of mouth
oral mucous membrane
oral part of viscerocranial mucosa
tunica mucosa oris
uberon
buccal mucosa
mucosal lining of mouth
oral mucosa
tunica mucosa oris
UBERON:0003729
mouth mucosa
A mucous membrane that lines the mouth.
the mucous membrane epithelium of the mouth. It can be divided into three categories: masticatory, lining, and specialized[Wikipedia:Oral_mucosa].
UMLS:C0026639
ncithesaurus:Oral_Mucosa
mouth mucosa
FMA:59660
mouth mucous membrane
OBOL:accepted
mouth organ mucosa
OBOL:accepted
mucosa of mouth
OBOL:accepted
mucous membrane of mouth
FMA:59660
oral part of viscerocranial mucosa
FMA:59660
tunica mucosa oris
FMA:59660
FMA:TA
buccal mucosa
GAID:951
mucosal lining of mouth
MA:0002794
oral mucosa
GAID:951
tunica mucosa oris
A bone that is part of a thorax [Automatically generated definition].
EMAPA:37247
MA:0000559
bone of thorax
bone organ of thorax
thorax bone
thorax bone organ
uberon
upper body bone
UBERON:0003827
thoracic segment bone
A bone that is part of a thorax [Automatically generated definition].
OBOL:automatic
EMAPA:37247
MA:th
bone of thorax
OBOL:automatic
bone organ of thorax
OBOL:automatic
thorax bone
OBOL:automatic
thorax bone organ
OBOL:automatic
upper body bone
MA:0000559
Any muscle organ that is part of a thorax [Automatically generated definition].
MA:0000561
muscle organ of thorax
thorax muscle organ
uberon
upper body muscle
UBERON:0003830
thoracic segment muscle
prolog
Any muscle organ that is part of a thorax [Automatically generated definition].
OBOL:automatic
muscle organ of thorax
OBOL:automatic
thorax muscle organ
OBOL:automatic
upper body muscle
MA:0000561
Any muscle organ that is part of a respiratory system [Automatically generated definition].
EMAPA:35733
MA:0001828
apparatus respiratorius muscle organ
muscle organ of apparatus respiratorius
muscle organ of respiratory system
respiratory system muscle organ
uberon
UBERON:0003831
respiratory system muscle
Any muscle organ that is part of a respiratory system [Automatically generated definition].
OBOL:automatic
apparatus respiratorius muscle organ
OBOL:automatic
muscle organ of apparatus respiratorius
OBOL:automatic
muscle organ of respiratory system
OBOL:automatic
respiratory system muscle organ
OBOL:automatic
A blood vessel that is part of a thorax [Automatically generated definition].
EMAPA:37238
MA:0000558
blood vessel of thorax
thorax blood vessel
uberon
upper body blood vessel
UBERON:0003834
thoracic segment blood vessel
A blood vessel that is part of a thorax [Automatically generated definition].
OBOL:automatic
EMAPA:37238
MA:th
blood vessel of thorax
OBOL:automatic
thorax blood vessel
OBOL:automatic
upper body blood vessel
MA:0000558
A portion of connective tissue that is part of a thorax [Automatically generated definition].
EMAPA:37253
MA:0000560
connective tissue of thorax
portion of connective tissue of thorax
textus connectivus of thorax
thorax connective tissue
thorax portion of connective tissue
thorax textus connectivus
uberon
upper body connective tissue
UBERON:0003837
thoracic segment connective tissue
A portion of connective tissue that is part of a thorax [Automatically generated definition].
OBOL:automatic
EMAPA:37253
MA:th
connective tissue of thorax
OBOL:automatic
portion of connective tissue of thorax
OBOL:automatic
textus connectivus of thorax
OBOL:automatic
thorax connective tissue
OBOL:automatic
thorax portion of connective tissue
OBOL:automatic
thorax textus connectivus
OBOL:automatic
upper body connective tissue
MA:0000560
An anatomical space that surrounded_by a neural tube.
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]
UBERON:0005713
AAO:0011073
EHDAA2:0001269
EHDAA:2889
EHDAA:914
EMAPA:16167
VHOG:0001119
XAO:0000252
cavity of neural tube
lumen of neural tube
neural tube neural lumen
prosencoel
uberon
central lumen
neural lumen
neurocoel
UBERON:0003842
neural tube lumen
An anatomical space that surrounded_by a neural tube.
OBOL:automatic
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]
2012-09-17
VHOG:0001119
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28
cavity of neural tube
lumen of neural tube
neural tube neural lumen
EHDAA2:0001269
neural lumen
EHDAA:2889
neurocoel
VHOG:0001119
In medicine, gonadal vein refers to the blood vessel that carrying blood away from the gonad (testis, ovary) toward the heart. Females : ovarian vein Males : testicular vein [WP,unvetted].
EHDAA2:0000719
EHDAA:8703
OpenCyc:Mx4rvlWYh5wpEbGdrcN5Y29ycA
VHOG:0001340
gonad vein
gonada vein
vein of gonad
vein of gonada
uberon
UBERON:0003848
gonadal vein
http://upload.wikimedia.org/wikipedia/commons/d/da/Gray1120.png
In medicine, gonadal vein refers to the blood vessel that carrying blood away from the gonad (testis, ovary) toward the heart. Females : ovarian vein Males : testicular vein [WP,unvetted].
gonad vein
OBOL:automatic
gonada vein
OBOL:automatic
vein of gonad
OBOL:automatic
vein of gonada
OBOL:automatic
A neural crest that has_potential_to_developmentally_contribute_to a midbrain.
We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]
EFO:0003591
EHDAA2:0001101
EHDAA:360
TAO:0000935
VHOG:0000796
ZFA:0000935
mesencephalic neural crest
neural crest midbrain
uberon
UBERON:0003849
mesencephalic neural crest
ZFA
A neural crest that has_potential_to_developmentally_contribute_to a midbrain.
OBOL:automatic
We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]
2012-09-17
VHOG:0000796
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43
mesencephalic neural crest
ZFA:0000935
neural crest midbrain
ZFA:0000935
A neural crest that has_potential_to_developmentally_contribute_to a hindbrain.
Cranial neural crest that is part of the hindbrain.[TAO]
We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]
EHDAA2:0001628
EHDAA:362
EMAPA:35747
TAO:0007063
VHOG:0001210
ZFA:0007063
neural crest hindbrain
rhombencephalic neural crest
uberon
rhombomere neural crest
UBERON:0003852
rhombencephalon neural crest
ZFA
A neural crest that has_potential_to_developmentally_contribute_to a hindbrain.
OBOL:automatic
Cranial neural crest that is part of the hindbrain.[TAO]
2012-08-14
TAO:0007063
TAO
ZFIN:curator
We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]
2012-09-17
VHOG:0001210
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43
neural crest hindbrain
ZFA:0007063
rhombencephalic neural crest
ZFA:0007063
rhombomere neural crest
EMAPA:35747
A neural crest that has_potential_to_developmentally_contribute_to a spinal cord.
We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)[well established][VHOG]
EHDAA:696
EMAPA:16163
EMAPA:16881
VHOG:0001006
neural crest spinal cord
uberon
spinal neural crest
UBERON:0003853
spinal cord neural crest
A neural crest that has_potential_to_developmentally_contribute_to a spinal cord.
OBOL:automatic
We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)[well established][VHOG]
2012-09-17
VHOG:0001006
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43
neural crest spinal cord
VHOG:0001006
spinal neural crest
VHOG:0001006
A neural plate that develops_from a future spinal cord.
Neural plate that is part of the spinal cord. [Bgee_curator][VHOG]
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...)[well established][VHOG]
FMA:312957
TAO:0007021
VHOG:0000439
ZFA:0007021
neural plate of spinal cord
uberon
UBERON:0003854
spinal cord neural plate
ZFA
A neural plate that develops_from a future spinal cord.
OBOL:automatic
Neural plate that is part of the spinal cord. [Bgee_curator][VHOG]
2012-09-17
VHOG:0000439
VHOG
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...)[well established][VHOG]
2012-09-17
VHOG:0000439
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28
neural plate of spinal cord
OBOL:automatic
Mesenchyme that is part of a developing gonad [Automatically generated definition].
EHDAA:5012
EMAPA:16858
EMAPA:17385
VHOG:0001090
gonada mesenchyme
mesenchyme of gonad
mesenchyme of gonada
uberon
UBERON:0003855
gonad mesenchyme
Mesenchyme that is part of a developing gonad [Automatically generated definition].
OBOL:automatic
gonada mesenchyme
OBOL:automatic
mesenchyme of gonad
OBOL:automatic
mesenchyme of gonada
OBOL:automatic
An anatomical cavity that has the potential to develop into a coelemic cavity lumen.
uberon
body cavity precursor
UBERON:0003886
future coelemic cavity lumen
An anatomical cavity that has the potential to develop into a coelemic cavity lumen.
OBOL:automatic
The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom
consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults
(...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG]
EHDAA:251
EMAPA:16088
NCIT:C34195
UMLS:C1512940
VHOG:0000316
somatic coelom
uberon
UBERON:0003887
intraembryonic coelom
Wikipedia
The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom
MGI:anna
MP:0012187
(...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG]
2012-09-17
VHOG:0000316
VHOG
ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.166
UMLS:C1512940
ncithesaurus:Intraembryonic_Coelom
somatic coelom
One of the skeletal muscles of the head and neck, spine, and ribs.
EHDAA:5982
EMAPA:18167
MA:0003153
RETIRED_EHDAA2:0000160
TAO:0001954
uberon
UBERON:0003897
axial muscle
One of the skeletal muscles of the head and neck, spine, and ribs.
HP:0003327
A portion of skeletal muscle tissue in the trunk.
skeletal muscle of torso
skeletal muscle tissue of torso
skeletal muscle tissue of trunk
torso skeletal muscle
torso skeletal muscle tissue
trunk skeletal muscle
trunk skeletal muscle tissue
uberon
UBERON:0003898
skeletal muscle tissue of trunk
A portion of skeletal muscle tissue in the trunk.
skeletal muscle of torso
OBOL:automatic
skeletal muscle tissue of torso
OBOL:automatic
skeletal muscle tissue of trunk
OBOL:automatic
torso skeletal muscle
OBOL:automatic
torso skeletal muscle tissue
OBOL:automatic
trunk skeletal muscle
OBOL:automatic
trunk skeletal muscle tissue
OBOL:automatic
The part of the retina that contains neurons and photoreceptor cells[GO].
(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]
AAO:0011095
BTO:0000929
CALOHA:TS-0685
EHDAA2:0001253
EHDAA:4763
EMAPA:17171
EMAPA:18590
FMA:58628
MA:0000277
NCIT:C33166
TAO:0000046
UMLS:C1518263
VHOG:0000535
XAO:0003216
ZFA:0000046
neural layer of retina
neural retina
neuroretina
stratum nervosum (retina)
stratum nervosum retinae
uberon
neural retinal epithelium
UBERON:0003902
retinal neural layer
Bgee:AN
The part of the retina that contains neurons and photoreceptor cells[GO].
GO:0003407
(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]
2012-09-17
VHOG:0000535
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429
UMLS:C1518263
ncithesaurus:Neural_Retina
neural layer of retina
FMA:58628
neural retina
XAO:0003216
ZFA:0000046
neuroretina
ZFA:0000046
stratum nervosum (retina)
FMA:58628
stratum nervosum retinae
FMA:58628
FMA:TA
neural retinal epithelium
MA:000027
Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system.
contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers
AEO:0000114
EHDAA2:0003114
FBbt:00007474
epithelial or endothelial tube
uberon
UBERON:0003914
epithelial tube
Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system.
GO:0060562
Any endothelium that has the quality of being cylindrical [Automatically generated definition].
uberon
UBERON:0003915
endothelial tube
Any endothelium that has the quality of being cylindrical [Automatically generated definition].
OBOL:automatic
A blood vessel that carries blood from the capillaries toward the heart
EMAPA:35932
FMA:86188
MA:0000066
segment of venous tree organ
venous tree organ segment
uberon
UBERON:0003920
Compare to: vein
venous blood vessel
A blood vessel that carries blood from the capillaries toward the heart
segment of venous tree organ
FMA:86188
venous tree organ segment
FMA:86188
A duct that is part of a digestive system [Automatically generated definition].
TAO:0005162
ZFA:0005162
duct of digestive system
duct of gastrointestinal system
gastrointestinal system duct
uberon
UBERON:0003928
digestive system duct
A duct that is part of a digestive system [Automatically generated definition].
OBOL:automatic
duct of digestive system
OBOL:automatic
duct of gastrointestinal system
OBOL:automatic
gastrointestinal system duct
OBOL:automatic
An epithelium that lines the lumen of the digestive tract.
Epithelium lining the lumen of the gut.[TAO]
BTO:0000956
EHDAA2:0004567
EMAPA:32928
MA:0003201
NCIT:C12963
TAO:0005123
UMLS:C0836205
XAO:0003200
ZFA:0005123
digestive tract epithelial tissue
epithelial tissue of digestive tract
epithelial tissue of gut
epithelium of digestive tract
epithelium of gut
gastrodermis
gut epithelial tissue
gut epithelium
uberon
alimentary tract epithelium
UBERON:0003929
digestive tract epithelium
An epithelium that lines the lumen of the digestive tract.
Epithelium lining the lumen of the gut.[TAO]
2012-08-14
TAO:0005123
TAO
ZFIN:curator
UMLS:C0836205
ncithesaurus:Gut_Epithelium
digestive tract epithelial tissue
OBOL:automatic
epithelial tissue of digestive tract
OBOL:automatic
epithelial tissue of gut
OBOL:automatic
epithelium of digestive tract
OBOL:automatic
epithelium of gut
OBOL:automatic
gastrodermis
BGEE:ANN
NCBITaxon:6073
gut epithelial tissue
OBOL:automatic
gut epithelium
EHDAA2:0004567
MA:0003201
ZFA:0005123
alimentary tract epithelium
OBOL:automatic
A cartilage element of chondrocranium. Example: neurocranial trabecula.
EFO:0003690
TAO:0001461
ZFA:0001461
cartilage of chondrocranium
cartilaginous element of chondrocranium
chondrocranium cartilage
neurocranium cartilage
uberon
UBERON:0003932
cartilage element of chondrocranium
A cartilage element of chondrocranium. Example: neurocranial trabecula.
cartilage of chondrocranium
OBOL:accepted
cartilaginous element of chondrocranium
OBOL:accepted
chondrocranium cartilage
ZFA:0001461
neurocranium cartilage
ZFA:0001461
A cartilage element that is part of the cranial skeleton.
Cartilage which is part of the cranium.[TAO]
TAO:0001458
ZFA:0001458
cartilage of cranium
cranium cartilage
uberon
cranial cartilages
UBERON:0003933
cranial cartilage
A cartilage element that is part of the cranial skeleton.
ZFA:0001458
Cartilage which is part of the cranium.[TAO]
2012-08-14
TAO:0001458
TAO
ZFIN:curator
cartilage of cranium
OBOL:automatic
cranium cartilage
OBOL:automatic
cranial cartilages
ZFA:0001458
Any of the organized aggregations of cells that function as secretory or excretory organs and are associated with reproduction.
MA:0001751
genitalia gland
gland of genitalia
gland of reproductive system
reproductive gland
reproductive system gland
sex gland
uberon
UBERON:0003937
reproductive gland
Any of the organized aggregations of cells that function as secretory or excretory organs and are associated with reproduction.
MP:0000653
genitalia gland
OBOL:automatic
gland of genitalia
MP:0000653
gland of reproductive system
OBOL:automatic
reproductive gland
MA:0001751
reproductive system gland
OBOL:automatic
sex gland
MP:0000653
The slender connective tissue fiber in the extracellular matrix of skin tissue that is composed of microfibrils and amorphous elastin and is characterized by great elasticity
EMAPA:37841
cutaneous elastic fiber
dermal elastic fiber
uberon
UBERON:0003967
cutaneous elastic tissue
The slender connective tissue fiber in the extracellular matrix of skin tissue that is composed of microfibrils and amorphous elastin and is characterized by great elasticity
MP:0008418
EMAPA:37841
MA:th
cutaneous elastic fiber
MP:0008418
dermal elastic fiber
MP:0008418
The connection between the embryo proper and extraembryonic tissues
uberon
UBERON:0004015
embryonic-extraembryonic boundary
The connection between the embryo proper and extraembryonic tissues
MP:0003890
A transitional population of migrating mesenchymal cells that derive from somites and that will become dermal cells.
Not to be confused with 'dermatome segment of skin'.
AAO:0011028
AEO:0001017
EHDAA2_RETIRED:0003428
EHDAA:1719
EHDAA:1725
EHDAA:1731
EHDAA:1737
EMAPA:32838
FMA:295656
NCIT:C61572
UMLS:C0180383
XAO:0000220
cutis plate
dermatomal mesenchyme
uberon
epimere mesoderm
mesenchyma dermatomiale
UBERON:0004016
dermatome
http://upload.wikimedia.org/wikipedia/commons/f/f3/Gray64.png
AEO
EHDAA2-abduced
A transitional population of migrating mesenchymal cells that derive from somites and that will become dermal cells.
AEO:0001017
AEO:JB
UMLS:C0180383
ncithesaurus:Dermatome
cutis plate
dermatomal mesenchyme
mesenchyma dermatomiale
The single layer of epithelial cells that lines the early neural tube and develops into the nervous system and into the neural crest cells
As the cells adjacent to the lumen continue to divide, the migrating cells form a second layer around the original neural tube. This layer becomes progressively thicker as more cells are added to it from the germinal neuroepithelium. This new layer is called the mantle (or intermediate) zone, and the germinal epithelium is now called the ventricular zone (and, later, the ependyma)[NCBIBook:NBK10047]
germinal neuroepithelial layer
germinal neuroepithelium
original neural tube
uberon
UBERON:0004022
germinal neuroepithelium
NCBIBook:NBK10047
The single layer of epithelial cells that lines the early neural tube and develops into the nervous system and into the neural crest cells
MP:0004261
germinal neuroepithelial layer
germinal neuroepithelium
NCBIBook:NBK10047
original neural tube
NCBIBook:NBK10047
The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium
consider merging with 'ventricular zone'; note that the MA class probably does not belong here, as this is an embryonic structure
The layer of undifferentiated, proliferating cells that line the neural tube lumen
ependymal layer
EMAPA:17152
EMAPA:35362
EMAPA_RETIRED:16783
MA:0003193
neural tube ependymal layer
neural tube ventricular germinal zone
neural tube ventricular zone
neural tube ependymal zone
uberon
UBERON:0004060
neural tube ventricular layer
NCBIBook:NBK10047
NCBIBook:NBK10047
The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium
MP:0009689
The layer of undifferentiated, proliferating cells that line the neural tube lumen
MP:0009689
ependymal layer
NCBIBook:NBK10047
neural tube ependymal layer
NCBIBook:NBK10047
neural tube ventricular germinal zone
NCBIBook:NBK10047
neural tube ventricular zone
MP:0009689
neural tube ependymal zone
MP:0009689
The layer of glia and differentiating neurons that forms as a second layer around the germinal neuroepithium; as this develops it comes to lie between the ventricular and marginal layers and includes the basal and alar plates. Develops into neurons and glia forming a gray matter layer.
EMAPA:17148
EMAPA:35360
neural tube intermediate zone
uberon
future brain marginal layer
UBERON:0004061
neural tube mantle layer
NCBIBook:NBK10047
by division
NCBIBook:NBK10047
The layer of glia and differentiating neurons that forms as a second layer around the germinal neuroepithium; as this develops it comes to lie between the ventricular and marginal layers and includes the basal and alar plates. Develops into neurons and glia forming a gray matter layer.
MP:0009690
neural tube intermediate zone
MP:0009690
future brain marginal layer
EMAPA:35360
The outermost layer of the neural tube that consists of axons from the developing mantle layer and will form the white matter
EMAPA:17151
neural tube marginal zone
uberon
brain marginal zone
UBERON:0004062
neural tube marginal layer
forms from axons
The outermost layer of the neural tube that consists of axons from the developing mantle layer and will form the white matter
MP:0009691
neural tube marginal zone
MP:0009691
The subdivision of the face that includes the eye (eyeball plus adnexa such as eyelids) and the orbit of the skull and associated parts of the face such as the eyebrows, if present
note the FMA class is more narrow though, and is more like eye + muscles + vasculature. The FMA also has FMA:72951 orbital part of eye
in HP covers eyelid, eyebrow.
FMA:260119
content of orbital part of eye
eye region
orbital part of face
uberon
ocular and peri-ocular region
ocular region
orbital content
orbital part of eye
UBERON:0004088
orbital region
The subdivision of the face that includes the eye (eyeball plus adnexa such as eyelids) and the orbit of the skull and associated parts of the face such as the eyebrows, if present
in HP covers eyelid, eyebrow.
HP:0000284
content of orbital part of eye
FMA:260119
eye region
orbital part of face
orbital content
FMA:260119
orbital part of eye
FMA:72951
2
2
Any tube, opening or passage that connects two distinct anatomical spaces.
FMA has both conduit and conduit space. In EHDAA2 this is a surface feature
AEO:0000080
EHDAA2:0003080
FMA:242873
foramen
foramina
uberon
opening
ostia
ostium
UBERON:0004111
anatomical conduit
Any tube, opening or passage that connects two distinct anatomical spaces.
FMA has both conduit and conduit space. In EHDAA2 this is a surface feature
FMA
foramen
EHDAA2:0003080
foramina
ostia
A vasculature that is part of a iris [Automatically generated definition].
ZFA:0005568
iris blood vessels
iris vascular network
iris vasculature
vascular network of iris
uberon
UBERON:0004118
vasculature of iris
A vasculature that is part of a iris [Automatically generated definition].
OBOL:automatic
iris blood vessels
ZFA:0005568
iris vascular network
OBOL:automatic
vascular network of iris
OBOL:automatic
An anatomical structure that develops (entirely or partially) from the endoderm.
Grouping term for query purposes
uberon
UBERON:0004119
endoderm-derived structure
An anatomical structure that develops (entirely or partially) from the endoderm.
An anatomical structure that develops (entirely or partially) from the mesoderm.
Grouping term for query purposes
FBbt:00025998
mesodermal derivative
uberon
UBERON:0004120
mesoderm-derived structure
An anatomical structure that develops (entirely or partially) from the mesoderm.
mesodermal derivative
FBbt:00025998
An anatomical structure that develops (entirely or partially) from the ectoderm.
Grouping term for query purposes
FBbt:00025990
ectodermal deriviative
uberon
UBERON:0004121
ectoderm-derived structure
An anatomical structure that develops (entirely or partially) from the ectoderm.
ectodermal deriviative
FBbt:00025990
The optic vesicle is the evagination of neurectoderm that precedes formation of the optic cup[GO]. Portion of tissue that is comprised of neuroepitheium which has pinched off from the anterior neural keel and will form the optic cup[ZFA].
(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles.[well established][VHOG]
AAO:0011039
EHDAA2:0001320
EMAPA:16540
FMA:293357
NCIT:C34236
TAO:0000050
UMLS:C0231106
VHOG:0000165
XAO:0000228
ZFA:0000050
uberon
evagination
eye vesicle
ocular vesicle
optic vesicles
UBERON:0004128
Genes: Six3, Pax6, Rx1 are expressed together in the tip of the neural plate [ISBN:9780878932504 "Developmental Biology"]. Development notes: During subsequent develop- ment, the optic vesicle invaginates and becomes a two-layered structure with an inner neural retina and outer retinal pigment epithelium. As soon as the developing optic vesicle makes contact with the overlying ectoderm, it induces the ectoderm to thicken and form the lens placode [PMID:16496288]
optic vesicle
http://upload.wikimedia.org/wikipedia/commons/e/e0/Gray863.png
ZFA
GO-def
ZFA
The optic vesicle is the evagination of neurectoderm that precedes formation of the optic cup[GO]. Portion of tissue that is comprised of neuroepitheium which has pinched off from the anterior neural keel and will form the optic cup[ZFA].
GO:0003404
(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles.[well established][VHOG]
2012-09-17
VHOG:0000165
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429
UMLS:C0231106
ncithesaurus:Optic_Vesicle
eye vesicle
XAO:0000228
ocular vesicle
VHOG:0000165
optic vesicles
ZFA:0000050
The first recognizable structure derived from the heart field
TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO
(In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG]
EHDAA2:0000215
EMAPA:16106
VHOG:0000975
myocardial plate
uberon
cardiac crescent
cardiogenic crescent
heart rudiment
UBERON:0004139
cardiogenic plate
The first recognizable structure derived from the heart field
GO:0003142
(In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG]
2012-09-17
VHOG:0000975
VHOG
PMID:15611355 Gittenberger-de Groot AC, Bartelings MM, Deruiter MC, Poelmann RE, Basics of cardiac development for the understanding of congenital heart malformations. Pediatric Research (2005)
myocardial plate
EHDAA2:0000215
cardiac crescent
EMAPA:16106
cardiogenic crescent
GO:0003142
A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle.
this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138]
XAO:0004185
first heart field
primary heart field
uberon
FHF
PHF
heart field
UBERON:0004140
primary heart field
GO:0003128
BGEE:ann
A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle.
GO:0003138
GOC:mtg_heart
GOC:rl
this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138]
GO
first heart field
XAO:0004185
primary heart field
XAO:0004185
FHF
XAO:0004185
PHF
XAO:0004185
heart field
XAO:0004185
An epithelial tube that will give rise to the mature heart.
the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube.
AAO:0010411
EFO:0003526
EMAPA:32685
NCIT:C34161
TAO:0000360
XAO:0000337
ZFA:0000360
embryonic heart tube
endocardial heart tube
endocardial tube
uberon
UBERON:0004141
heart tube
ZFA-modified
An epithelial tube that will give rise to the mature heart.
GO:0003143
GOC:mtg_heart
the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube.
MP:0012700
embryonic heart tube
GO:0003143
endocardial heart tube
MP:0012700
endocardial tube
XAO:0000337
Vein of heart that drains the myocardium
EHDAA2:0004507
EMAPA:37137
FMA:12846
NCIT:C12878
NCIT:C12882
UMLS:C0226654
UMLS:C0226737
ZFA:0005814
galen:CoronaryVein
cardiac vein
coronary vein
heart vein
vein of heart
uberon
coronary vein
UBERON:0004148
cardiac vein
FMA
Vein of heart that drains the myocardium
EMAPA:37137
MA:th
UMLS:C0226654
ncithesaurus:Cardiac_Vein
UMLS:C0226737
ncithesaurus:Coronary_Vein
cardiac vein
FMA:12846
coronary vein
ZFA:0005814
heart vein
OBOL:automatic
vein of heart
OBOL:automatic
coronary vein
A cardiac chamber surrounds an enclosed cavity within the heart
FMA:7095
OpenCyc:Mx4rmexpjPdAEduAAAAOpmP6tw
chamber of heart
heart chamber
uberon
UBERON:0004151
generic enough to cover FBbt:00003156 heart chamber but this is a cavity. GO defines it as the cavity. TODO - move subclasses. Note this also includes sinus venosus
cardiac chamber
A cardiac chamber surrounds an enclosed cavity within the heart
GO:0003205
An embryonic group of progenitor cells that forms from an outpouching of the septum transversum near the venous pole of the heart and gives rise to the epicardium
propepicardial
Proepicardial clusters in Zebrafish form on the pericardial wall, adjacent to the atrioventricular (AV) junction and near the venous pole[ZFA]
EMAPA:36025
ZFA:0005808
proepicardial cluster
proepicardial organ
uberon
UBERON:0004160
proepicardium
todo check other taxa
ZFA
An embryonic group of progenitor cells that forms from an outpouching of the septum transversum near the venous pole of the heart and gives rise to the epicardium
GO:0003342
proepicardial cluster
ZFA:0005808
proepicardial organ
ZFIN:ZDB-PUB-080218-16
A thick plate of mesodermal tissue that occupies the space between the thoracic cavity and yolk stalk in the early embryo, forming a transverse partition partially separating the coelomic cavity into thoracic and abdominal portions. It gives rise to the central tendon of the diaphragm[VHOG].
A thick plate of mesodermal tissue that occupies the space between the thoracic cavity and yolk stalk in the early embryo, forming a transverse partition partially separating the coelomic cavity into thoracic and abdominal portions. It gives rise to the central tendon of the diaphragm. [TFD][VHOG]
In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart (of other tetrapods) is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes) Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG]
The cranial part of the septum transversum gives rise to the central tendon of the diaphragm and is the origin of the myoblasts that invade the pleuroperitoneal folds resulting in the formation of the muscular diaphragm. The caudal part of the septum transversum is invaded by the hepatic diverticulum which divides within it to form the liver and thus gives rise to the ventral mesentery of the foregut.
in EHDAA2 this is divided into mesenchymal portion and hepatic diverticulum
EHDAA2:0001829
EHDAA:736
EMAPA:16318
FMA:295593
NCIT:C34296
UMLS:C0231004
VHOG:0000019
transverse septum
uberon
UBERON:0004161
septum transversum
A thick plate of mesodermal tissue that occupies the space between the thoracic cavity and yolk stalk in the early embryo, forming a transverse partition partially separating the coelomic cavity into thoracic and abdominal portions. It gives rise to the central tendon of the diaphragm[VHOG].
VHOG:0000019
A thick plate of mesodermal tissue that occupies the space between the thoracic cavity and yolk stalk in the early embryo, forming a transverse partition partially separating the coelomic cavity into thoracic and abdominal portions. It gives rise to the central tendon of the diaphragm. [TFD][VHOG]
2012-09-17
VHOG:0000019
VHOG
In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart (of other tetrapods) is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes) Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG]
2012-09-17
VHOG:0000019
VHOG
ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206
in EHDAA2 this is divided into mesenchymal portion and hepatic diverticulum
EHDAA2
UMLS:C0231004
ncithesaurus:Septum_Transversum
transverse septum
The internal genitalia are the internal sex organs such as the uterine tube, the uterus and the vagina in female mammals, and the testis, seminal vesicle, ejaculatory duct and prostate in male mammals
FMA:45652
internal genitalia
internal genitals
uberon
internal reproductive organ
internal sex organ
UBERON:0004175
TODO: make a subdivision of reproductive system. Relabel. See https://github.com/obophenotype/uberon/issues/547
internal genitalia
internal genitalia
The internal genitalia are the internal sex organs such as the uterine tube, the uterus and the vagina in female mammals, and the testis, seminal vesicle, ejaculatory duct and prostate in male mammals
GO:0035260
Organ that is part of the hematopoietic system.
consider splitting out lymph organ, compare with lymph node
the organs in which the formed elements of the blood and lymph are produced[http://encyclopedia2.thefreedictionary.com/Hematopoietic+Organs].
the FMA class 'lymphoid organ' is a general anatomical term
BTO:0004605
EMAPA:37665
FMA:7143
MA:0000747
haematological system organ
haemopoietic system organ
hematopoeitic organ
hematopoietic system organ
organ of haematological system
organ of haemopoietic system
organ of hematopoietic system
organ of organa haemopoietica
organa haemopoietica organ
hematopoeitic or lymphoid organ
lymph organ
lymphoid organ
uberon
UBERON:0004177
hemopoietic organ
Organ that is part of the hematopoietic system.
GOC:Obol
the organs in which the formed elements of the blood and lymph are produced[http://encyclopedia2.thefreedictionary.com/Hematopoietic+Organs].
the FMA class 'lymphoid organ' is a general anatomical term
FMA
EMAPA:37665
MA:th
haematological system organ
OBOL:automatic
haemopoietic system organ
OBOL:automatic
hematopoietic system organ
OBOL:automatic
organ of haematological system
OBOL:automatic
organ of haemopoietic system
OBOL:automatic
organ of hematopoietic system
OBOL:automatic
organ of organa haemopoietica
OBOL:automatic
organa haemopoietica organ
OBOL:automatic
lymph organ
MA:0000747
lymphoid organ
BTO:0004605
FMA:7143
A portions of the gut that is derived from endoderm.
EMAPA:32930
endodermal gut
gut endoderm
uberon
UBERON:0004185
endodermal part of digestive tract
A portions of the gut that is derived from endoderm.
GO:0061031
gut endoderm
EMAPA:32930
A portion of smooth muscle tissue that is part of a respiratory system [Automatically generated definition].
BTO:0001660
EMAPA:35734
MA:0001830
respiratory smooth muscle
smooth muscle of respiratory system
uberon
airway smooth muscle
airway smooth muscle cell
UBERON:0004225
respiratory system smooth muscle
A portion of smooth muscle tissue that is part of a respiratory system [Automatically generated definition].
OBOL:automatic
respiratory smooth muscle
BTO:0001660
smooth muscle of respiratory system
OBOL:automatic
airway smooth muscle
BTO:0001660
airway smooth muscle cell
BTO:0001660
A portion of smooth muscle tissue that is part of a iris [Automatically generated definition].
see notes for muscle of iris.
BTO:0000655
EMAPA:35448
FMA:312338
MA:0001270
involuntary muscle of iris
iridial smooth muscle
iris involuntary muscle
iris non-striated muscle
iris smooth muscle tissue
non-striated muscle of iris
smooth muscle of iris
smooth muscle tissue of iris
uberon
UBERON:0004234
iris smooth muscle
MA
A portion of smooth muscle tissue that is part of a iris [Automatically generated definition].
OBOL:automatic
involuntary muscle of iris
OBOL:automatic
iridial smooth muscle
iris involuntary muscle
OBOL:automatic
iris non-striated muscle
OBOL:automatic
iris smooth muscle tissue
OBOL:automatic
non-striated muscle of iris
OBOL:automatic
smooth muscle of iris
OBOL:automatic
smooth muscle tissue of iris
OBOL:automatic
A portion of smooth muscle tissue that is part of an arteriole [Automatically generated definition].
EMAPA:36287
FMA:312251
MA:0000706
uberon
UBERON:0004236
arteriole smooth muscle
A portion of smooth muscle tissue that is part of an arteriole [Automatically generated definition].
OBOL:automatic
smooth muscle found within, and composing the majority of the wall of blood vessels.
Vascular smooth muscle contracts or relaxes to both change the volume of blood vessels and the local blood pressure, a mechanism that is responsible for the redistribution of the blood within the body to areas where it is needed (i.e. areas with temporarily enhanced oxygen consumption). Thus the main function of vascular smooth muscle tonus is to regulate the caliber of the blood vessels in the body. Excessive vasoconstriction leads to hypertension, while excessive vasodilation as in shock leads to hypotension.
UBERON:0010508
BTO:0001431
CALOHA:TS-1107
EMAPA:35177
MA:0000710
MESH:D009131
NCIT:C33853
TAO:0005321
UMLS:C1519956
ZFA:0005321
blood vessel involuntary muscle
blood vessel non-striated muscle
blood vessel smooth muscle tissue
involuntary muscle of blood vessel
non-striated muscle of blood vessel
smooth muscle of blood vessel
smooth muscle tissue of blood vessel
vascular smooth muscle
vascular smooth muscle tissue
uberon
UBERON:0004237
blood vessel smooth muscle
smooth muscle found within, and composing the majority of the wall of blood vessels.
UMLS:C1519956
ncithesaurus:Vascular_Smooth_Muscle_Tissue
blood vessel involuntary muscle
OBOL:automatic
blood vessel non-striated muscle
OBOL:automatic
blood vessel smooth muscle tissue
OBOL:automatic
involuntary muscle of blood vessel
OBOL:automatic
non-striated muscle of blood vessel
OBOL:automatic
smooth muscle of blood vessel
OBOL:automatic
smooth muscle tissue of blood vessel
OBOL:automatic
vascular smooth muscle
ZFA:0005321
A bone that is part of the dorsal region of an animal.
this class may be obsoleted. See: https://github.com/obophenotype/mouse-anatomy-ontology/issues/93
https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern
EMAPA:37248
MA:0000494
uberon
back bone
bone of back
dorsal region bone
UBERON:0004247
bone of dorsum
A bone that is part of the dorsal region of an animal.
EMAPA:37248
MA:th
back bone
MA:0000494
bone of back
OBOL:automatic
dorsal region bone
Any muscle organ that is part of a skin of body [Automatically generated definition].
review as part of general integumentary system review - part of skin, or more generally, integumental system
in MA, the only skin muscle is arrector pili. The only integumental muscle is panniculus carnosus. In EMAPA, the arrector pili only
UBERON:0015797
EMAPA:18187
EMAPA:35776
MA:0002710
MA:0003139
integumental system muscle
muscle of integumental system
muscle organ of skin
skin muscle organ
uberon
UBERON:0004253
skin muscle
Any muscle organ that is part of a skin of body [Automatically generated definition].
OBOL:automatic
in MA, the only skin muscle is arrector pili. The only integumental muscle is panniculus carnosus. In EMAPA, the arrector pili only
MA
integumental system muscle
MA:0003139
muscle of integumental system
EMAPA:18187
muscle organ of skin
OBOL:automatic
skin muscle organ
OBOL:automatic
A blood vessel that is part of a back [Automatically generated definition].
EMAPA:37243
MA:0000493
blood vessel of back
uberon
UBERON:0004258
back blood vessel
A blood vessel that is part of a back [Automatically generated definition].
OBOL:automatic
EMAPA:37243
MA:th
blood vessel of back
OBOL:automatic
A portion of connective tissue that is part of a back [Automatically generated definition].
EMAPA:37256
MA:0000495
uberon
mesenchyne of back
UBERON:0004267
back connective tissue
A portion of connective tissue that is part of a back [Automatically generated definition].
OBOL:automatic
EMAPA:37256
MA:th
mesenchyne of back
OBOL:automatic
A muscle that is part of the eye region.
AAO:0000156
EMAPA:35335
MA:0000271
OpenCyc:Mx8Ngx4rwKSh9pwpEbGdrcN5Y29ycB4rvViTvpwpEbGdrcN5Y29ycB4rvYA8cJwpEbGdrcN5Y29ycA
uberon
UBERON:0004277
eye muscle
MA
A muscle that is part of the eye region.
OBOL:automatic
Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.
Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO]
skeletal
AEO:0000168
EHDAA2:0001843
EHDAA:5047
EMAPA:17213
FMA:23875
GAID:177
MA:0003006
MAT:0000032
MESH:D012863
MIAA:0000032
OpenCyc:Mx4rvVi1rpwpEbGdrcN5Y29ycA
VSAO:0000026
XAO:0004053
galen:Skeleton
set of all bones
set of bones of body
uberon
UBERON:0004288
skeleton
https://github.com/obophenotype/uberon/wiki/The-skeletal-system
Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.
VSAO:0000026
Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO]
2012-08-14
VSAO:0000026
VSAO
GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070
The bilaminar epithelium formed from the myotome and dermatome.
Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis. Within the dermomyotome there is also a medio-lateral difference. The central region makes dermis, the mesenchymal connective tissue of the back skin. The medial region (closest to neural tube) makes epaxial muscle, and the lateral region (furthest from neural tube) makes hypaxial muscle[http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768].
Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis.[TAO]
Portion of somites that gives rise to dermis and muscles.[AAO]
all but the sclerotome of a mesodermal somite; the primordium of skeletal muscle and, perhaps, of the dermis.
Thus, representatives of the agnathan vertebrates, chondrichthyans, and sarcopterygians all have a layer of undifferentiated cells external to the embryonic myotome. In the amniotes, this external cell layer is the dermomyotome. The simplest interpretation of the similar position, morphology, and lack of myosin labeling is that a dermomyotome epithelium is a shared, ancestral vertebrate characteristic.[well established][VHOG]
AAO:0010572
AEO:0000214
EHDAA2:0003259
EMAPA:31109
FMA:295654
NCIT:C34140
TAO:0001513
UMLS:C1511786
VHOG:0000676
ZFA:0001513
uberon
dermamyotome
dermomyotomes
UBERON:0004290
dermomyotome
AEO
AEO
EHDAA2
ZFA
The bilaminar epithelium formed from the myotome and dermatome.
AEO:0000214
Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis. Within the dermomyotome there is also a medio-lateral difference. The central region makes dermis, the mesenchymal connective tissue of the back skin. The medial region (closest to neural tube) makes epaxial muscle, and the lateral region (furthest from neural tube) makes hypaxial muscle[http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768].
Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis.[TAO]
2012-08-14
TAO:0001513
TAO
ZFIN:curator
Portion of somites that gives rise to dermis and muscles.[AAO]
2012-06-20
AAO:0010572
AAO
AAO:EJS
all but the sclerotome of a mesodermal somite; the primordium of skeletal muscle and, perhaps, of the dermis.
Thus, representatives of the agnathan vertebrates, chondrichthyans, and sarcopterygians all have a layer of undifferentiated cells external to the embryonic myotome. In the amniotes, this external cell layer is the dermomyotome. The simplest interpretation of the similar position, morphology, and lack of myosin labeling is that a dermomyotome epithelium is a shared, ancestral vertebrate characteristic.[well established][VHOG]
2012-09-17
VHOG:0000676
VHOG
DOI:10.1111/j.1525-142X.2006.05079.x Devoto SH, Stoiber W, Hammond CL, Steinbacher P, Haslett JR, Barresi MJF, Patterson SE, Adiarte EG and Hughes SM, Generality of vertebrate developmental patterns: evidence for a dermomyotome in fish. Evolution and Development (2006)
UMLS:C1511786
ncithesaurus:Dermomyotome
dermamyotome
VHOG:0000676
dermomyotomes
VHOG:0000676
A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube.
The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO]
TAO:0000115
ZFA:0000115
heart cone
rudimentary heart
uberon
UBERON:0004291
heart rudiment
A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube.
GO:0003313
The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO]
2012-08-14
TAO:0000115
TAO
ZFIN:curator
heart cone
GO:0003313
rudimentary heart
ZFA:0000115
Dense connective tissue that separates the atria from the ventricles and provides physical support for the heart.
It is not a true skeleton, but it does provide structure and support for the heart, as well as isolating the atria from the ventricles. This allows the AV node and AV bundle to delay the wave of depolarisation such that the atria can contract and assist in ventricular filling before the ventricles themselves depolarise and contract (the AV bundle is the only part of the conduction system that passes from the atria to the ventricles in a normal heart). It also allows the valves (bicuspid, tricuspid, semilunar) to keep open by giving them structural support[WP]
EMAPA:36645
FMA:9496
cardiac fibrous skeleton
fibrous skeleton of heart
heart fibrous skeleton
skeleton of heart
uberon
anulus fibrosus dexter cordis
anulus fibrosus sinister cordis
trigona fibrosa
trigonum fibrosum dextrum cordis
trigonum fibrosum sinistrum cordis
UBERON:0004292
cardiac skeleton
http://upload.wikimedia.org/wikipedia/commons/5/50/Gray495.png
Dense connective tissue that separates the atria from the ventricles and provides physical support for the heart.
GO:0003204
cardiac fibrous skeleton
EMAPA:36645
heart fibrous skeleton
GO:0003204
skeleton of heart
FMA:9496
anulus fibrosus dexter cordis
anulus fibrosus sinister cordis
trigona fibrosa
trigonum fibrosum dextrum cordis
trigonum fibrosum sinistrum cordis
A blood vessel smooth muscle that is part of a respiratory system [Automatically generated definition].
EMAPA:37573
MA:0001806
smooth muscle tissue of blood vessel of respiratory system
uberon
UBERON:0004297
respiratory system blood vessel smooth muscle
A blood vessel smooth muscle that is part of a respiratory system [Automatically generated definition].
OBOL:automatic
EMAPA:37573
MA:th
smooth muscle tissue of blood vessel of respiratory system
OBOL:automatic
The embryonic structure that gives rise to the corneal ectoderm
EHDAA:938
EMAPA:16322
RETIRED_EHDAA2:0001308
VHOG:0001296
uberon
UBERON:0004348
optic eminence
The embryonic structure that gives rise to the corneal ectoderm
MP:0006305
The first of the series of pharyngeal arches that develop into jaw bones or their homologs, and their associated nerves and arteries
The first of the series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO]
the first arch which contributes to development of mastication muscles, maxilla, mandible, incus, malleus, Meckel's cartilage, trigeminal nerve, and maxillary artery
A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG]
1
AAO:0010364
CALOHA:TS-2089
EHDAA2:0000006
EHDAA:573
EMAPA:16118
FMA:293019
MFMO:0000095
NCIT:C34175
TAO:0001595
UMLS:C1517197
VHOG:0000296
XAO:0000097
ZFA:0001612
1st pharyngeal arch
branchial arch 1
first branchial arch
first pharyngeal arch
first visceral arch
mandibular arch
visceral arch 1
uberon
1st arch
1st visceral arch
arcus pharyngeus primus
UBERON:0004362
pharyngeal arch 1
http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray48.png
The first of the series of pharyngeal arches that develop into jaw bones or their homologs, and their associated nerves and arteries
The first of the series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO]
2012-06-20
AAO:0010364
AAO
XAO:EJS
the first arch which contributes to development of mastication muscles, maxilla, mandible, incus, malleus, Meckel's cartilage, trigeminal nerve, and maxillary artery
MP:0006337,MGI:smb
A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG]
2012-09-17
VHOG:0000296
VHOG
DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)
UMLS:C1517197
ncithesaurus:First_Pharyngeal_Arch
branchial arch 1
first branchial arch
first visceral arch
visceral arch 1
1st arch
EHDAA2:0000006
1st visceral arch
VHOG:0000296
arcus pharyngeus primus
A transparent homogeneous acellular layer, 6 to 9 um thick, lying between the basal lamina of the outer layer of stratified epithelium and the substantia propria of the cornea; it is considered to be a basement membrane.
Acellular anatomical structure that is the zone of collagen fibers adjacent the basement membrane of the corneal epithelium.[TAO]
Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals
FMA:58273
MA:0001240
NCIT:C32226
TAO:0002155
UMLS:C0229127
ZFA:0001684
Bowman's anterior elastic lamina
Bowman's layer
Bowman's membrane
anterior elastic lamina
anterior limiting lamina
anterior limiting lamina of cornea
lamina limitans anterior (cornea)
lamina limitans anterior corneae
uberon
Reichert's membrane
anterior limiting membrane
UBERON:0004370
anterior limiting lamina of cornea
A transparent homogeneous acellular layer, 6 to 9 um thick, lying between the basal lamina of the outer layer of stratified epithelium and the substantia propria of the cornea; it is considered to be a basement membrane.
ncithesaurus:Bowman_s_Membrane
Acellular anatomical structure that is the zone of collagen fibers adjacent the basement membrane of the corneal epithelium.[TAO]
2012-08-14
TAO:0002155
TAO
ZFIN:ZDB-PUB-061010-3
UMLS:C0229127
ncithesaurus:Bowman_s_Membrane
Bowman's anterior elastic lamina
FMA:58273
Bowman's layer
FMA:58273
Bowman's membrane
FMA:58273
anterior elastic lamina
ZFA:0001684
anterior limiting lamina
MA:0001240
anterior limiting lamina of cornea
FMA:58273
lamina limitans anterior (cornea)
FMA:58273
lamina limitans anterior corneae
FMA:58273
FMA:TA
Reichert's membrane
anterior limiting membrane
ZFA:0001684
An embryo at the neurula stage.
UBERON:0007013
BILA:0000061
BTO:0001766
NCIT:C34229
UMLS:C1518306
neurula
uberon
UBERON:0004455
neurula embryo
An embryo at the neurula stage.
UMLS:C1518306
ncithesaurus:Neurula
neurula
BTO:0001766
Sum of all sensory systems in an organism.
note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs
FMA:78499
sense organ system
uberon
UBERON:0004456
entire sense organ system
Sum of all sensory systems in an organism.
sense organ system
FMA:78499
Any collection of skeletal muscles that is part of a head [Automatically generated definition].
EMAPA:18171
FMA:71287
head musculature
muscle group of head
muscles of head
musculi capitis
set of muscles of head
uberon
UBERON:0004461
This class is restricted to skeletal muscles that attach to the cranial skeleton. This seems to be consistent with FMA and EMAPA usage. Note that by definition this excludes invertebrate head musculature. It corresponds to the individual muscle organ term UBERON:0002376
skeletal musculature of head
https://github.com/obophenotype/mouse-anatomy-ontology/issues/4
https://github.com/obophenotype/uberon/issues/1405
Any collection of skeletal muscles that is part of a head [Automatically generated definition].
OBOL:automatic
head musculature
FMA:71287
muscle group of head
FMA:71287
muscles of head
FMA:71287
musculi capitis
FMA:71287
FMA:TA
set of muscles of head
FMA:71287
Any collection of muscles that is part of a thorax [Automatically generated definition].
BTO and FMA do not mean precisely the same thing here. BTO thorax muscle is a pectoral muscle or diaphragm
BTO:0000508
EMAPA:37260
FMA:71293
muscle group of thorax
muscles of thorax
musculi thoracis
set of muscles of thorax
thoracic musculature
uberon
UBERON:0004464
musculature of thorax
Any collection of muscles that is part of a thorax [Automatically generated definition].
OBOL:automatic
BTO and FMA do not mean precisely the same thing here. BTO thorax muscle is a pectoral muscle or diaphragm
BTO
EMAPA:37260
MA:th
muscle group of thorax
FMA:71293
muscles of thorax
FMA:71293
musculi thoracis
FMA:71293
FMA:TA
set of muscles of thorax
FMA:71293
thoracic musculature
FMA:71293
Any collection of muscles that is part of a neck [Automatically generated definition].
AAO:0000091
EMAPA:36050
FMA:71290
MESH:D009334
cervical muscles
muscle group of neck
muscles of neck
musculi cervicis
musculi colli
neck musculature
set of muscles of neck
uberon
UBERON:0004465
musculature of neck
Any collection of muscles that is part of a neck [Automatically generated definition].
OBOL:automatic
cervical muscles
AAO:0000091
muscle group of neck
FMA:71290
muscles of neck
FMA:71290
musculi cervicis
FMA:71290
FMA:TA
musculi colli
FMA:71290
FMA:TA
neck musculature
FMA:71290
set of muscles of neck
FMA:71290
Any collection of muscles that is part of a back [Automatically generated definition].
FMA:71291
muscle group of back
muscles of back
musculi dorsi
set of muscles of back
uberon
UBERON:0004469
musculature of back
Any collection of muscles that is part of a back [Automatically generated definition].
OBOL:automatic
muscle group of back
FMA:71291
muscles of back
FMA:71291
musculi dorsi
FMA:71291
FMA:TA
set of muscles of back
FMA:71291
Any collection of muscles that is part of a face.
originally created to reflect the distinction drawn in FMA between a facial muscle and the entire musculature of the face. However, naming both does not serve any particular purpose
FMA:71288
entire facial musculature
facial muscles
muscle group of face
musculi faciei
uberon
set of facial muscles
set of muscles of face
UBERON:0004473
musculature of face
Any collection of muscles that is part of a face.
OBOL:automatic
entire facial musculature
facial muscles
FMA:71288
muscle group of face
FMA:71288
musculi faciei
FMA:71288
FMA:TA
set of facial muscles
FMA:71288
set of muscles of face
FMA:71288
Any collection of muscles that is part of a trunk [Automatically generated definition].
currently defined by location rather than attachment
AAO:0011572
EFO:0003531
FMA:50187
muscle group of trunk
set of muscles of trunk
uberon
muscular system of trunk
UBERON:0004479
musculature of trunk
Any collection of muscles that is part of a trunk [Automatically generated definition].
OBOL:automatic
muscle group of trunk
FMA:50187
set of muscles of trunk
FMA:50187
muscular system of trunk
FMA:50187
A portion of cardiac muscle tissue that is part of an atrium [Automatically generated definition].
in GO, this is equivalent to the atrial myocardium, but FMA distinguishes these two. Consider merging.
FMA:7283
atrial cardiac muscle tissue
atrial heart muscle
cardiac atrium muscle
uberon
atrial myocardium
UBERON:0004490
cardiac muscle tissue of atrium
A portion of cardiac muscle tissue that is part of an atrium [Automatically generated definition].
OBOL:automatic
in GO, this is equivalent to the atrial myocardium, but FMA distinguishes these two. Consider merging.
GO
atrial cardiac muscle tissue
GO:0055009
atrial heart muscle
GO:0055009
cardiac atrium muscle
GO:0055009
atrial myocardium
GO:0055009
GOC:mtg_heart
A portion of cardiac muscle tissue that is part of a cardiac septum [Automatically generated definition].
FMA:226279
cardiac septum cardiac muscle tissue
cardiac septum heart muscle
cardiac septum muscle
cardiac septum myocardium
uberon
UBERON:0004492
cardiac muscle tissue of cardiac septum
A portion of cardiac muscle tissue that is part of a cardiac septum [Automatically generated definition].
OBOL:automatic
cardiac septum cardiac muscle tissue
cardiac septum heart muscle
cardiac septum muscle
cardiac septum myocardium
A portion of cardiac muscle tissue that is part of a myocardium [Automatically generated definition].
Note placement of MA class based on parthood relationship
EMAPA:32688
FMA:261726
MA:0002441
uberon
UBERON:0004493
cardiac muscle tissue of myocardium
MA
A portion of cardiac muscle tissue that is part of a myocardium [Automatically generated definition].
OBOL:automatic
A vasculature that is part of a muscle organ [Automatically generated definition].
FMA:87123
muscular organ vasculature
uberon
UBERON:0004521
vasculature of muscle organ
A vasculature that is part of a muscle organ [Automatically generated definition].
OBOL:automatic
muscular organ vasculature
FMA:87123
A vasculature that is part of a musculoskeletal system [Automatically generated definition].
FMA:239607
uberon
UBERON:0004522
vasculature of musculoskeletal system
A vasculature that is part of a musculoskeletal system [Automatically generated definition].
OBOL:automatic
Anatomical system that has as its parts the heart and blood vessels.
we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph.
The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG]
AAO:0011001
BILA:0000016
BTO:0000088
CALOHA:TS-1297
EFO:0000791
EHDAA2:0000216
EHDAA:394
EMAPA:16104
EMAPA:16370
EV:0100017
FMA:7161
GAID:467
MA:0000010
MAT:0000016
MESH:D002319
MIAA:0000016
NCIT:C12686
OpenCyc:Mx4rvVjzG5wpEbGdrcN5Y29ycA
TAO:0000010
UMLS:C0007226
VHOG:0000302
WikipediaCategory:Cardiovascular_system
XAO:0000100
XAO:0001010
ZFA:0000010
uberon
CV system
Herz und Gefaesssystem
UBERON:0004535
cardiovascular system
Anatomical system that has as its parts the heart and blood vessels.
BTO:0000088
The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG]
2012-09-17
VHOG:0000302
VHOG
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.451
UMLS:C0007226
ncithesaurus:Cardiovascular_System
CV system
BTO:0000088
Herz und Gefaesssystem
BTO:0000088
A vascular network consisting of blood vessels.
TAO:0001079
ZFA:0001079
blood vascular network
set of blood vessels
uberon
blood system
blood vessel system
blood vessels
UBERON:0004537
blood vasculature
A vascular network consisting of blood vessels.
blood vessels
TAO:0001079
The part of the cardiovascular system consisting of all arteries.
The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]
BTO:0004690
EHDAA2:0000143
EHDAA:396
EMAPA:16201
EMAPA:16371
MA:0002719
VHOG:0000273
uberon
UBERON:0004572
arterial system
MA
The part of the cardiovascular system consisting of all arteries.
The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]
2012-09-17
VHOG:0000273
VHOG
DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005)
The part of the venous system that drains the general body tissues[Kardong]
In human anatomy, the systemic venous system refers to veins that drain into the right atrium without passing through two vascular beds (i.e. they originate from a set of capillaries and do not pass through a second set of capillaries before reaching the right side of the heart). The term systemic venous system is often used to differentiate veins from veins that drain the pulmonary system (the pulmonary venous system) and veins that drain the digestive tract (the portal venous system). Large veins that are considered part of the systemic venous system are the: Superior vena cava; Inferior vena cava[WP]
Subdivision of cardiovascular system which has as its parts the right side of heart, the superior vena cava and the inferior vena cava[FMA]
The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]
FMA:45626
systemic venous circulatory system
uberon
UBERON:0004581
systemic venous system
The part of the venous system that drains the general body tissues[Kardong]
ISBN:0073040584
In human anatomy, the systemic venous system refers to veins that drain into the right atrium without passing through two vascular beds (i.e. they originate from a set of capillaries and do not pass through a second set of capillaries before reaching the right side of the heart). The term systemic venous system is often used to differentiate veins from veins that drain the pulmonary system (the pulmonary venous system) and veins that drain the digestive tract (the portal venous system). Large veins that are considered part of the systemic venous system are the: Superior vena cava; Inferior vena cava[WP]
Subdivision of cardiovascular system which has as its parts the right side of heart, the superior vena cava and the inferior vena cava[FMA]
FMA
FMA:45626
The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]
2012-09-17
VHOG:0000277
VHOG
DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005)
systemic venous circulatory system
FMA:45626
The part of the cardiovascular system consisting of all venous vessels. In vertebrates with a double circulation, this can be divided into systemic and pulmonary portions.
The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]
BTO:0004692
EHDAA2:0002171
EHDAA:486
EMAPA:16240
MA:0002720
NCIT:C33858
UMLS:C1267406
VHOG:0000277
vein system
uberon
UBERON:0004582
venous system
MA
The part of the cardiovascular system consisting of all venous vessels. In vertebrates with a double circulation, this can be divided into systemic and pulmonary portions.
The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]
2012-09-17
VHOG:0000277
VHOG
DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005)
UMLS:C1267406
ncithesaurus:Venous_System
An endothelium that lines the blood vasculature. Other endothelia may line lymph vessels, the heart
BTO:0000766
CALOHA:TS-2155
EMAPA:35176
MA:0000709
NCIT:C53395
TAO:0005257
UMLS:C1706972
ZFA:0005257
uberon
UBERON:0004638
blood vessel endothelium
An endothelium that lines the blood vasculature. Other endothelia may line lymph vessels, the heart
UMLS:C1706972
ncithesaurus:Blood_Vessel_Endothelium
The costocervical trunk arises from the upper and back part of the subclavian artery, behind the scalenus anterior on the right side, and medial to that muscle on the left side. Passing backward, it splits into the deep cervical artery and the supreme intercostal artery (or the Highest intercostal artery), which descends behind the pleura in front of the necks of the first and second ribs, and anastomoses with the first aortic intercostal (3rd posterior intercostal artery). As it crosses the neck of the first rib it lies medial to the anterior division of the first thoracic nerve, and lateral to the first thoracic ganglion of the sympathetic trunk. In the first intercostal space, it gives off a branch which is distributed in a manner similar to the distribution of the aortic intercostals. The branch for the second intercostal space usually joins with one from the highest aortic intercostal artery. This branch is not constant, but is more commonly found on the right side; when absent, its place is supplied by an intercostal branch from the aorta. Each intercostal gives off a posterior branch which goes to the posterior vertebral muscles, and sends a small spinal branch through the corresponding intervertebral foramen to the medulla spinalis and its membranes. [WP,unvetted].
EMAPA:37496
FMA:10636
MA:0001939
costocervical trunk
trunk of costocervical artery
uberon
truncus costocervicalis
UBERON:0004688
costo-cervical trunk
http://upload.wikimedia.org/wikipedia/commons/b/b3/Costocervical_trunk_with_branches.png
The costocervical trunk arises from the upper and back part of the subclavian artery, behind the scalenus anterior on the right side, and medial to that muscle on the left side. Passing backward, it splits into the deep cervical artery and the supreme intercostal artery (or the Highest intercostal artery), which descends behind the pleura in front of the necks of the first and second ribs, and anastomoses with the first aortic intercostal (3rd posterior intercostal artery). As it crosses the neck of the first rib it lies medial to the anterior division of the first thoracic nerve, and lateral to the first thoracic ganglion of the sympathetic trunk. In the first intercostal space, it gives off a branch which is distributed in a manner similar to the distribution of the aortic intercostals. The branch for the second intercostal space usually joins with one from the highest aortic intercostal artery. This branch is not constant, but is more commonly found on the right side; when absent, its place is supplied by an intercostal branch from the aorta. Each intercostal gives off a posterior branch which goes to the posterior vertebral muscles, and sends a small spinal branch through the corresponding intervertebral foramen to the medulla spinalis and its membranes. [WP,unvetted].
EMAPA:37496
MA:th
costocervical trunk
FMA:10636
trunk of costocervical artery
FMA:10636
truncus costocervicalis
A portion of smooth muscle tissue that is part of an arterial system [Automatically generated definition].
EMAPA:36503
MA:0000704
uberon
UBERON:0004695
arterial system smooth muscle
A portion of smooth muscle tissue that is part of an arterial system [Automatically generated definition].
OBOL:automatic
A portion of smooth muscle tissue that is part of a venous system [Automatically generated definition].
EMAPA:36613
MA:0000715
uberon
UBERON:0004696
venous system smooth muscle
A portion of smooth muscle tissue that is part of a venous system [Automatically generated definition].
OBOL:automatic
An endothelium that is part of an arterial system [Automatically generated definition].
EMAPA:35145
MA:0000703
NCIT:C49329
UMLS:C1706849
uberon
UBERON:0004700
arterial system endothelium
An endothelium that is part of an arterial system [Automatically generated definition].
OBOL:automatic
UMLS:C1706849
ncithesaurus:Arterial_System_Endothelium
An endothelium that is part of a venous system [Automatically generated definition].
EMAPA:35907
MA:0000714
NCIT:C49320
UMLS:C1710626
uberon
UBERON:0004701
venous system endothelium
An endothelium that is part of a venous system [Automatically generated definition].
OBOL:automatic
UMLS:C1710626
ncithesaurus:Venous_System_Endothelium
A blood vessel endothelium that is part of a respiratory system [Automatically generated definition].
EMAPA:35732
MA:0001805
uberon
UBERON:0004702
respiratory system blood vessel endothelium
A blood vessel endothelium that is part of a respiratory system [Automatically generated definition].
OBOL:automatic
The jugular veins are veins that bring deoxygenated blood from the head back to the heart via the superior vena cava.
BTO:0001744
CALOHA:TS-0497
EMAPA:18638
GAID:536
MA:0002154
MESH:D007601
NCIT:C12738
UMLS:C0022427
uberon
jugular
vena jugularis
UBERON:0004711
jugular vein
http://upload.wikimedia.org/wikipedia/commons/f/f8/Gray558.png
The jugular veins are veins that bring deoxygenated blood from the head back to the heart via the superior vena cava.
UMLS:C0022427
ncithesaurus:Jugular_Vein
vena jugularis
BTO:0001744
The embryo and its adnexa (appendages or adjunct parts) or associated membranes (i.e. the products of conception) The conceptus includes all structures that develop from the zygote, both embryonic and extraembryonic. It includes the embryo as well as the embryonic part of the placenta and its associated membranes - amnion, chorion (gestational sac), and yolk sac[WP].
EHDAA2 places this as a subtype of organism. This leads to the inference that a conceptus is an embryo (if an embryo is defined as an organism at embryo stage), which eliminates the embryonic + extra-embryonic = conceptus
AEO:0000194
BTO:0003834
EHDAA2:0000001
EHDAA2:0003235
EMAPA:36040
NCIT:C34131
UMLS:C1516779
embryo plus adnexa
uberon
UBERON:0004716
conceptus
The embryo and its adnexa (appendages or adjunct parts) or associated membranes (i.e. the products of conception) The conceptus includes all structures that develop from the zygote, both embryonic and extraembryonic. It includes the embryo as well as the embryonic part of the placenta and its associated membranes - amnion, chorion (gestational sac), and yolk sac[WP].
BTO:0003834
UMLS:C1516779
ncithesaurus:Conceptus
A transverse unitary subdivision of the neural tube that shares a common dorsoventral structure (floor, basal, alar, and roof plates), but each having differential molecular identities and fates; they comprise the secondary prosencephalon, diencephalon (prosomeres), the midbrain (mesomeres), and the hindbrain (rhombomeres).
We take the definition of neuromere from Puelles et al, although the existence of mesomeres and prosomeres may not be widely accepted
A metameric segment of the central nervous system.[ZFA]
Melissa Haendel
2009-06-18T09:00:04Z
NLX:147842
TAO:0001328
ZFA:0001328
neural tube metameric segment
neural tube segment
neuromere
neuromeres
uberon
neural metamere
neural segment
UBERON:0004731
neuromere
A transverse unitary subdivision of the neural tube that shares a common dorsoventral structure (floor, basal, alar, and roof plates), but each having differential molecular identities and fates; they comprise the secondary prosencephalon, diencephalon (prosomeres), the midbrain (mesomeres), and the hindbrain (rhombomeres).
A metameric segment of the central nervous system.[ZFA]
2012-08-14
TAO:0001328
TAO
ZFIN:curator
neural tube metameric segment
neuromeres
TAO:0001328
Any segmental subdivision of a nervous system. Includes metameric developmental segments, such as vertebrates neuromeres.
revisit this after CARO is revised and/or we have defined metameric segment; note that with the additional of an A/P axis constraint this corresponds to what Richter at al call a neuromere (PMID:21062451)
FBbt:00005140
uberon
neuromere
UBERON:0004732
segmental subdivision of nervous system
Any segmental subdivision of a nervous system. Includes metameric developmental segments, such as vertebrates neuromeres.
FBbt:00005140
neuromere
FBbt:00005140
An organ subunit that is part of a hindbrain [Automatically generated definition].
FMA:61998
hindbrain segment
segment of hindbrain
uberon
UBERON:0004733
segmental subdivision of hindbrain
An organ subunit that is part of a hindbrain [Automatically generated definition].
OBOL:automatic
hindbrain segment
FMA:61998
segment of hindbrain
FMA:61998
Organism at the gastrula stage.
We explicitly merge the NCITA terms here
UBERON:0007012
BILA:0000060
BTO:0001403
FBbt:00005317
FMA:293108
GAID:1302
MESH:A16.254.412
MIAA:0000179
NCIT:C34057
NCIT:C34058
UMLS:C0017199
UMLS:C1284022
gastrula embryo
uberon
blastocystis trilaminaris
tri-laminar disc
tri-laminar disk
trilaminar blastocyst
trilaminar blastoderm
trilaminar disc
trilaminar disk
trilaminar germ
UBERON:0004734
gastrula
Organism at the gastrula stage.
We explicitly merge the NCITA terms here
NCIT
UMLS:C0017199
ncithesaurus:Gastrula
UMLS:C1284022
ncithesaurus:Trilaminar_Embryonic_Disc
gastrula embryo
BILA:0000060
blastocystis trilaminaris
tri-laminar disc
tri-laminar disk
trilaminar blastocyst
trilaminar blastoderm
trilaminar disc
trilaminar disk
trilaminar germ
A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]
A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]
EMAPA:37744
MA:0003047
VSAO:0000015
XAO:0004038
ZFA:0005619
uberon
UBERON:0004755
Four classes of mineralized tissues are found in vertebrates: bone, cartilage, dentine, and enamel. We think of cartilage and bone as skeletal tissues and of enamel and dentine as dental tissues, but enamel and dentine arose evolutionarily together with bone as skeletal tissues in the dermal skeleton (exoskeleton) of early vertebrates. Scales and teeth of sharks are examples of dermal skeletal elements that are still composed of the three ancient components-enamel, dentine, and bone. Cartilage, on the other hand, provided the basis for the second vertebrate skeletal system, the endoskeleton (Smith and Hall, 1990; Hall, 1998a,b). some invertebrate skeletal tissues have surprisingly bone-like features. Examples include chondrocytes interconnected by cell processes in cephalopod cartilages (Cole and Hall, 2004a,b), and the calcium phosphate layer in the shells of brachiopods (Rodland et al., 2003). However, neither bone nor mineralized cartilage have been found in invertebrates. Editors notes: TODO - develops_from
skeletal tissue
VSAO
A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]
GO_REF:0000034
PSPUB:0000170
VSAO:0000015
A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]
2012-08-14
VSAO:0000015
taken from version of VSAO used in TAO and used directly in Uberon
VSAO
GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070
PSPUB:0000170
EMAPA:37744
MA:th
dermis-derived entity that is made of skeletal tissue.
dermal element
uberon
UBERON:0004756
dermal skeletal element
dermis-derived entity that is made of skeletal tissue.
dermal element
VSAO:curator
The primitive cartilagionous skeletal structure of the fetal skull that grows to envelop the rapidly growing embyonic brain. In humans, the chondrocranium begins forming at 28 days from mesenchymal condensations and is fully formed between week 7 and 9 of fetal development. While the majority of the chondrocranium is succeeded by the bony skull in most higher vertebrates, some components do persist into adulthood.[1] In Cartilagious fishes and Agnathans, the chondrocranium persist throughout life.[2] Embryologically, the chondrocranium represent the basal cranial structure, and lay the base for the formation of the endocranium in higher vertebrates[WP].
in contrast to chondrocranium, this structure is entirely cartiliginous. In Chondricthyes this is the same as the neurocranium. FMA:76621 is an undefined fetal structure, so we assume the correct placement is here. Note that this is distinct from MA:0000317 which is the uberon:neurocranium (the part of the cranium that encloses the brain)
AAO:0000094
AAO:0010153
EHDAA:6031
FMA:76621
NCIT:C34121
UMLS:C1516496
XAO:0003059
cartilaginous chondocranium
cartiligionous skeletal structure of skull
uberon
cartilaginous skull
chondocranium
embryonic chondocranium
neurocranium
UBERON:0004761
cartilaginous neurocranium
FMA
PMC1571569
The primitive cartilagionous skeletal structure of the fetal skull that grows to envelop the rapidly growing embyonic brain. In humans, the chondrocranium begins forming at 28 days from mesenchymal condensations and is fully formed between week 7 and 9 of fetal development. While the majority of the chondrocranium is succeeded by the bony skull in most higher vertebrates, some components do persist into adulthood.[1] In Cartilagious fishes and Agnathans, the chondrocranium persist throughout life.[2] Embryologically, the chondrocranium represent the basal cranial structure, and lay the base for the formation of the endocranium in higher vertebrates[WP].
in contrast to chondrocranium, this structure is entirely cartiliginous. In Chondricthyes this is the same as the neurocranium. FMA:76621 is an undefined fetal structure, so we assume the correct placement is here. Note that this is distinct from MA:0000317 which is the uberon:neurocranium (the part of the cranium that encloses the brain)
FMA
UMLS:C1516496
ncithesaurus:Chondrocranium
chondocranium
neurocranium
Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles.
Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO]
Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO]
AAO:0011129
TAO:0001890
VSAO:0000128
XAO:0004012
ZFA:0005494
galen:SkeletalStructure
uberon
UBERON:0004765
skeletal element
VSAO
Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles.
Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO]
2012-08-14
VSAO:0000128
VSAO
PSPUB:0000170
Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO]
2012-08-14
TAO:0001890
TAO
TAO:VSAO_workshop
A bone that is part of a cranium.
here cranium = skull - mandible
cranium bone
uberon
UBERON:0004766
cranial bone
A bone that is part of a cranium.
UBERON:automatic
cranium bone
UBERON:automatic
Any bone that is part of the lower jaw skeleton. This includes (when present): the dentary/mandible, the articular, the splenial, the suprangular
Do not manually classify under here - bones are automatically classified
lower jaw bone
uberon
UBERON:0004768
bone of lower jaw
Any bone that is part of the lower jaw skeleton. This includes (when present): the dentary/mandible, the articular, the splenial, the suprangular
Anatomical system that consists of all the joints of the body.
EMAPA:35150
FMA:23878
MA:0003007
VSAO:0000181
joint system
set of all joints of body
uberon
set of all joints
set of joints of body
UBERON:0004770
articular system
FMA
Anatomical system that consists of all the joints of the body.
VSAO:0000181
joint system
FMA:23878
set of all joints of body
FMA:23878
set of joints of body
FMA:23878
A submucosa that is part of a respiratory system [Automatically generated definition].
EMAPA:37578
MA:0001822
apparatus respiratorius submucosa
submucosa of apparatus respiratorius
submucosa of respiratory system
uberon
UBERON:0004777
respiratory system submucosa
A submucosa that is part of a respiratory system [Automatically generated definition].
OBOL:automatic
EMAPA:37578
MA:th
apparatus respiratorius submucosa
OBOL:automatic
submucosa of apparatus respiratorius
OBOL:automatic
submucosa of respiratory system
OBOL:automatic
A lamina propria that is part of a respiratory system [Automatically generated definition].
EMAPA:37576
MA:0001821
apparatus respiratorius lamina propria
apparatus respiratorius lamina propria mucosa
lamina propria mucosa of apparatus respiratorius
lamina propria mucosa of respiratory system
lamina propria of apparatus respiratorius
lamina propria of respiratory system
respiratory system lamina propria mucosa
uberon
UBERON:0004779
respiratory system lamina propria
true
A lamina propria that is part of a respiratory system [Automatically generated definition].
OBOL:automatic
EMAPA:37576
MA:th
apparatus respiratorius lamina propria
OBOL:automatic
apparatus respiratorius lamina propria mucosa
OBOL:automatic
lamina propria mucosa of apparatus respiratorius
OBOL:automatic
lamina propria mucosa of respiratory system
OBOL:automatic
lamina propria of apparatus respiratorius
OBOL:automatic
lamina propria of respiratory system
OBOL:automatic
respiratory system lamina propria mucosa
OBOL:automatic
An anatomical wall that is part of a cardiac ventricle [Automatically generated definition].
FMA:13884
MA:0002791
NCIT:C119295
anatomical wall of cardiac ventricle
anatomical wall of heart ventricle
anatomical wall of lower chamber of heart
anatomical wall of ventricle of heart
cardiac ventricle anatomical wall
cardiac ventricle wall
heart ventricle anatomical wall
lower chamber of heart anatomical wall
lower chamber of heart wall
ventricle of heart anatomical wall
ventricle of heart wall
ventricular wall
wall of cardiac ventricle
wall of heart ventricle
wall of lower chamber of heart
wall of ventricle of heart
uberon
wall of ventricle
UBERON:0004784
heart ventricle wall
An anatomical wall that is part of a cardiac ventricle [Automatically generated definition].
OBOL:automatic
anatomical wall of cardiac ventricle
OBOL:automatic
anatomical wall of heart ventricle
OBOL:automatic
anatomical wall of lower chamber of heart
OBOL:automatic
anatomical wall of ventricle of heart
OBOL:automatic
cardiac ventricle anatomical wall
OBOL:automatic
cardiac ventricle wall
OBOL:automatic
heart ventricle anatomical wall
OBOL:automatic
lower chamber of heart anatomical wall
OBOL:automatic
lower chamber of heart wall
OBOL:automatic
ventricle of heart anatomical wall
OBOL:automatic
ventricle of heart wall
OBOL:automatic
ventricular wall
FMA:13884
wall of cardiac ventricle
OBOL:automatic
wall of heart ventricle
OBOL:automatic
wall of lower chamber of heart
OBOL:automatic
wall of ventricle of heart
OBOL:automatic
wall of ventricle
MA:0002791
the mucous membrane lining the respiratory tract
TODO - split respiratory tract mucosa from respiratory system mucosa
BTO:0000973
EMAPA:18334
EMAPA:37577
FMA:302092
GAID:304
MA:0001827
MESH:D020545
apparatus respiratorius mucosa
apparatus respiratorius mucosa of organ
apparatus respiratorius mucous membrane
mucosa of apparatus respiratorius
mucosa of organ of apparatus respiratorius
mucosa of organ of respiratory system
mucosa of respiratory system
mucous membrane of apparatus respiratorius
mucous membrane of respiratory system
respiratory system mucosa of organ
respiratory system mucous membrane
uberon
laryngeal mucous membrane
respiratory mucosa
respiratory tract mucosa
UBERON:0004785
respiratory system mucosa
the mucous membrane lining the respiratory tract
MESH:A04.760
MGI:cwg
MP:0002277
EMAPA:37577
MA:th
apparatus respiratorius mucosa
OBOL:automatic
apparatus respiratorius mucosa of organ
OBOL:automatic
apparatus respiratorius mucous membrane
OBOL:automatic
mucosa of apparatus respiratorius
OBOL:automatic
mucosa of organ of apparatus respiratorius
OBOL:automatic
mucosa of organ of respiratory system
OBOL:automatic
mucosa of respiratory system
OBOL:automatic
mucous membrane of apparatus respiratorius
OBOL:automatic
mucous membrane of respiratory system
OBOL:automatic
respiratory system mucosa of organ
OBOL:automatic
respiratory system mucous membrane
OBOL:automatic
laryngeal mucous membrane
EMAPA:18334
respiratory mucosa
BTO:0000973
Any of the tissue layers that comprise a blood vessel. Examples: tunica media, tunica adventitia.
EMAPA:36296
MA:0002854
uberon
UBERON:0004797
blood vessel layer
Blood:vessels.svg
Any of the tissue layers that comprise a blood vessel. Examples: tunica media, tunica adventitia.
An epithelium that is part of a respiratory system [Automatically generated definition].
CALOHA:TS-0023
EMAPA:32826
MA:0001823
VHOG:0000981
apparatus respiratorius epithelial tissue
apparatus respiratorius epithelium
epithelial tissue of apparatus respiratorius
epithelial tissue of respiratory system
epithelium of apparatus respiratorius
epithelium of respiratory system
respiratory system epithelial tissue
uberon
UBERON:0004807
respiratory system epithelium
An epithelium that is part of a respiratory system [Automatically generated definition].
OBOL:automatic
apparatus respiratorius epithelial tissue
OBOL:automatic
apparatus respiratorius epithelium
OBOL:automatic
epithelial tissue of apparatus respiratorius
OBOL:automatic
epithelial tissue of respiratory system
OBOL:automatic
epithelium of apparatus respiratorius
OBOL:automatic
epithelium of respiratory system
OBOL:automatic
respiratory system epithelial tissue
OBOL:automatic
A portion of skeletal muscle tissue that is part of a respiratory system [Automatically generated definition].
EMAPA:37583
MA:0001829
respiratory system skeletal muscle tissue
skeletal muscle of apparatus respiratorius
skeletal muscle of respiratory system
skeletal muscle tissue of apparatus respiratorius
skeletal muscle tissue of respiratory system
uberon
UBERON:0004830
respiratory system skeletal muscle
A portion of skeletal muscle tissue that is part of a respiratory system [Automatically generated definition].
OBOL:automatic
EMAPA:37583
MA:th
respiratory system skeletal muscle tissue
OBOL:automatic
skeletal muscle of apparatus respiratorius
OBOL:automatic
skeletal muscle of respiratory system
OBOL:automatic
skeletal muscle tissue of apparatus respiratorius
OBOL:automatic
skeletal muscle tissue of respiratory system
OBOL:automatic
A portion of skeletal muscle tissue that is part of a lip [Automatically generated definition].
this class is derived from MA. Consider re-modeling this as being a muscle that acts on the lips. See: Wikipedia:Lip#Muscles_acting_on_the_lips
EMAPA:37642
MA:0001578
lip skeletal muscle tissue
skeletal muscle of lip
skeletal muscle tissue of lip
uberon
UBERON:0004833
lip skeletal muscle
A portion of skeletal muscle tissue that is part of a lip [Automatically generated definition].
OBOL:automatic
EMAPA:37642
MA:th
lip skeletal muscle tissue
OBOL:automatic
skeletal muscle of lip
OBOL:automatic
skeletal muscle tissue of lip
OBOL:automatic
An endothelium of artery that is part of a respiratory system [Automatically generated definition].
EMAPA:37566
MA:0001801
apparatus respiratorius arterial endothelium
apparatus respiratorius artery endothelium
apparatus respiratorius endothelium of artery
arterial endothelium of apparatus respiratorius
arterial endothelium of respiratory system
artery endothelium of apparatus respiratorius
artery endothelium of respiratory system
endothelium of artery of apparatus respiratorius
endothelium of artery of respiratory system
respiratory system artery endothelium
respiratory system endothelium of artery
uberon
UBERON:0004848
respiratory system arterial endothelium
true
An endothelium of artery that is part of a respiratory system [Automatically generated definition].
OBOL:automatic
EMAPA:37566
MA:th
apparatus respiratorius arterial endothelium
OBOL:automatic
apparatus respiratorius artery endothelium
OBOL:automatic
apparatus respiratorius endothelium of artery
OBOL:automatic
arterial endothelium of apparatus respiratorius
OBOL:automatic
arterial endothelium of respiratory system
OBOL:automatic
artery endothelium of apparatus respiratorius
OBOL:automatic
artery endothelium of respiratory system
OBOL:automatic
endothelium of artery of apparatus respiratorius
OBOL:automatic
endothelium of artery of respiratory system
OBOL:automatic
respiratory system artery endothelium
OBOL:automatic
respiratory system endothelium of artery
OBOL:automatic
An endothelium of vein that is part of a respiratory system [Automatically generated definition].
EMAPA:37585
MA:0001811
apparatus respiratorius endothelium of vein
apparatus respiratorius vein endothelium
apparatus respiratorius venous endothelium
endothelium of vein of apparatus respiratorius
endothelium of vein of respiratory system
respiratory system endothelium of vein
respiratory system vein endothelium
vein endothelium of apparatus respiratorius
vein endothelium of respiratory system
venous endothelium of apparatus respiratorius
venous endothelium of respiratory system
uberon
UBERON:0004849
respiratory system venous endothelium
An endothelium of vein that is part of a respiratory system [Automatically generated definition].
OBOL:automatic
EMAPA:37585
MA:th
apparatus respiratorius endothelium of vein
OBOL:automatic
apparatus respiratorius vein endothelium
OBOL:automatic
apparatus respiratorius venous endothelium
OBOL:automatic
endothelium of vein of apparatus respiratorius
OBOL:automatic
endothelium of vein of respiratory system
OBOL:automatic
respiratory system endothelium of vein
OBOL:automatic
respiratory system vein endothelium
OBOL:automatic
vein endothelium of apparatus respiratorius
OBOL:automatic
vein endothelium of respiratory system
OBOL:automatic
venous endothelium of apparatus respiratorius
OBOL:automatic
venous endothelium of respiratory system
OBOL:automatic
An endothelium that is part of the cardiovascular system.
consider merging with 'endothelium'
Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]
BTO:0001853
EMAPA:35201
GAID:519
MA:0000717
MESH:D004730
NCIT:C13053
TAO:0002171
UMLS:C0014261
VHOG:0001217
XAO:0000356
ZFA:0001639
uberon
endothelia
vascular endothelia
UBERON:0004852
cardiovascular system endothelium
An endothelium that is part of the cardiovascular system.
Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]
2012-09-17
VHOG:0001217
VHOG
ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207
UMLS:C0014261
ncithesaurus:Vascular_Endothelium
endothelia
ZFA:0001639
vascular endothelia
XAO:0000356
A connective tissue that surrounds a skeletal muscle tissue.
EMAPA:37743
MA:0002868
connective tissue of skeletal muscle
connective tissue of skeletal muscle tissue
portion of connective tissue of skeletal muscle
portion of connective tissue of skeletal muscle tissue
skeletal muscle portion of connective tissue
skeletal muscle textus connectivus
skeletal muscle tissue connective tissue
skeletal muscle tissue portion of connective tissue
skeletal muscle tissue textus connectivus
textus connectivus of skeletal muscle
textus connectivus of skeletal muscle tissue
uberon
skeletal muscle interstitial tissue
skeletal muscle interstitum
UBERON:0004857
skeletal muscle connective tissue
A connective tissue that surrounds a skeletal muscle tissue.
OBOL:automatic
EMAPA:37743
MA:th
connective tissue of skeletal muscle
OBOL:automatic
connective tissue of skeletal muscle tissue
OBOL:automatic
portion of connective tissue of skeletal muscle
OBOL:automatic
portion of connective tissue of skeletal muscle tissue
OBOL:automatic
skeletal muscle portion of connective tissue
OBOL:automatic
skeletal muscle textus connectivus
OBOL:automatic
skeletal muscle tissue connective tissue
OBOL:automatic
skeletal muscle tissue portion of connective tissue
OBOL:automatic
skeletal muscle tissue textus connectivus
OBOL:automatic
textus connectivus of skeletal muscle
OBOL:automatic
textus connectivus of skeletal muscle tissue
OBOL:automatic
skeletal muscle interstitial tissue
MA:0002868
skeletal muscle interstitum
MA:0002868
A gland that is part of a eye. The eye is a compound unit which depending on the species may consist of an eyeballs plus associated ducts and integumentary structures. Eye glands therefore include the various types of lacrimal gland, the various types of apocrine and sebaceous glands associated with the eyelid.
EMAPA:35334
MA:0000267
eye-associated gland
gland of eye
uberon
UBERON:0004859
Examples: harderian gland, accessory lacrimal gland, gland of Moll, gland of Zeis, nictitating membrane glands
eye gland
A gland that is part of a eye. The eye is a compound unit which depending on the species may consist of an eyeballs plus associated ducts and integumentary structures. Eye glands therefore include the various types of lacrimal gland, the various types of apocrine and sebaceous glands associated with the eyelid.
eye-associated gland
gland of eye
OBOL:automatic
A vasculature that is part of a retina [Automatically generated definition].
FMA:76552
MESH:D012171
XAO:0004153
retina vasculature
retina vasculature of camera-type eye
retinal blood vessels
retinal blood vessels set
retinal vasculature
set of blood vessels of retina
set of retinal blood vessels
vasa sanguinea retinae
uberon
UBERON:0004864
vasculature of retina
A vasculature that is part of a retina [Automatically generated definition].
OBOL:automatic
retina vasculature
GO:0061298
retina vasculature of camera-type eye
GO:0061298
retinal blood vessels
FMA:76552
retinal blood vessels set
FMA:76552
retinal vasculature
OBOL:automatic
set of blood vessels of retina
OBOL:automatic
set of retinal blood vessels
FMA:76552
vasa sanguinea retinae
FMA:76552
FMA:TA
Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP].
We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors
visceral mesoderm
AAO:0011102
BILA:0000044
FMA:295568
XAO:0000276
inner layer of lateral plate mesoderm
uberon
splanchnic mesoderm
UBERON:0004872
splanchnic layer of lateral plate mesoderm
Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP].
We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors
BILA
visceral mesoderm
BILA:0000044
splanchnic mesoderm
ISBN:9780878932504
The central region of trunk mesoderm. This tissue forms the notochord
Notochord rudiment[ZFIN:ZDB-PUB-961014-576].
WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord.
AAO:0000478
EFO:0003426
TAO:0000091
ZFA:0000091
axial chorda mesoderm
chorda mesoderm
dorsal mesoderm
presumptive notochord
uberon
UBERON:0004880
chordamesoderm
The central region of trunk mesoderm. This tissue forms the notochord
Notochord rudiment[ZFIN:ZDB-PUB-961014-576].
ZFIN:ZDB-PUB-961014-576
axial chorda mesoderm
ZFA:0000091
dorsal mesoderm
presumptive notochord
ZFA:0000091
Anatomical cluster that connects two or more adjacent skeletal elements or hardened body parts.
FBbt:00005811
joint
uberon
UBERON:0004905
articulation
Anatomical cluster that connects two or more adjacent skeletal elements or hardened body parts.
A portion of the gut that is derived from ectoderm.
ectodermal gut
gut ectoderm
uberon
UBERON:0004906
ectodermal part of digestive tract
A portion of the gut that is derived from ectoderm.
GO:0007439
gut ectoderm
EMAPA:32930
An epithelium surrounding a gonad.
after reasoning this should subsume the more specific germinal epithelium classes. We include the fly structure here although it is not clear if the sheath is an epithelium or a multi-tissue structure that includes epithelium as parts
EHDAA:4032
EHDAA:5931
FBbt:00004859
NCIT:C32676
UMLS:C1517534
gonad epithelium
gonadal epithelium
uberon
gonadal sheath
UBERON:0004909
epithelium of gonad
An epithelium surrounding a gonad.
OBOL:automatic
UMLS:C1517534
ncithesaurus:Germinal_Epithelium
gonad epithelium
OBOL:automatic
gonadal epithelium
OBOL:automatic
gonadal sheath
FBbt:00004859
A proximal-distal subdivision of the digestive tract.
intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct.
FBbt:00100315
FMA:71131
uberon
alimentary system subdivision
intestinal tract
segment of intestinal tract
subdivision of alimentary system
UBERON:0004921
subdivision of digestive tract
A proximal-distal subdivision of the digestive tract.
alimentary system subdivision
FMA:71131
subdivision of alimentary system
FMA:71131
A part of a wall of an organ that forms a layer.
FMA:82485
uberon
UBERON:0004923
organ component layer
A part of a wall of an organ that forms a layer.
The tissue underlying the tunica mucosa of the pharynx.
BTO:0002113
FMA:75144
pharyngeal submucosa
pharynx submucosa
tela submucosa pharyngea
tela submucosa pharyngis
uberon
pharyngobasilar fascia
submucous coat of pharynx
submucous layer of pharynx
UBERON:0004924
submucosa of pharynx
The tissue underlying the tunica mucosa of the pharynx.
BTO:0002113
pharyngeal submucosa
FMA:75144
pharynx submucosa
OBOL:automatic
tela submucosa pharyngea
FMA:75144
FMA:TA
tela submucosa pharyngis
BTO:0002113
submucous coat of pharynx
BTO:0002113
submucous layer of pharynx
BTO:0002113
A mucosa that is part of a lower lip [Automatically generated definition].
FMA:59833
NCIT:C12225
UMLS:C0226939
lower labial mucosa
lower lip mucosa
lower lip mucosa of organ
lower lip mucous membrane
lower lip organ mucosa
mucosa of organ of lower lip
mucous membrane of lower lip
organ mucosa of lower lip
uberon
UBERON:0005032
mucosa of lower lip
A mucosa that is part of a lower lip [Automatically generated definition].
OBOL:automatic
UMLS:C0226939
ncithesaurus:Mucosa_of_the_Lower_Lip
lower labial mucosa
UBERON:cjm
lower lip mucosa
OBOL:automatic
lower lip mucosa of organ
OBOL:automatic
lower lip mucous membrane
OBOL:automatic
lower lip organ mucosa
OBOL:automatic
mucosa of organ of lower lip
OBOL:automatic
mucous membrane of lower lip
OBOL:automatic
organ mucosa of lower lip
OBOL:automatic
A gland that is part of a hemolymphoid system [Automatically generated definition].
hemopoietic or lymphoid organ
EMAPA:18766
MA:0002962
hemopoietic or lymphoid gland
uberon
haemolymphoid system gland
UBERON:0005058
hemolymphoid system gland
A gland that is part of a hemolymphoid system [Automatically generated definition].
OBOL:automatic
hemopoietic or lymphoid organ
GO:0048534
hemopoietic or lymphoid gland
haemolymphoid system gland
EMAPA:18766
The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds.
The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove].
AAO:0011071
EMAPA:35594
FMA:295624
NCIT:C34224
UMLS:C0814992
XAO:0000248
uberon
UBERON:0005061
neural groove
The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds.
GO:0001842
The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove].
UMLS:C0814992
ncithesaurus:Neural_Groove
One of the two elevated edges of the neural groove[GO,MP].
In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold].
EHDAA2:0001249
FMA:295618
NCIT:C34223
UMLS:C0814993
XAO:0004087
medullary fold
uberon
UBERON:0005062
neural fold
One of the two elevated edges of the neural groove[GO,MP].
GO:0001842
MP:0011256
In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold].
UMLS:C0814993
ncithesaurus:Neural_Fold
medullary fold
MP:0011256
A solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts[GO]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube[ZFIN].
An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO]
EFO:0003498
TAO:0000133
ZFA:0000133
uberon
neural tube rod
UBERON:0005068
neural rod
A solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts[GO]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube[ZFIN].
GO:0014024
ZFA:0000133
An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO]
2012-08-14
TAO:0000133
TAO
ZFIN:curator
neural tube rod
GO:0014027
An anatomical boundary that adjacent_to a hindbrain and adjacent_to a spinal cord.
hindbrain-spinal cord boundary region
uberon
UBERON:0005076
hindbrain-spinal cord boundary
An anatomical boundary that adjacent_to a hindbrain and adjacent_to a spinal cord.
OBOL:automatic
A hole in a tube[GO].
AEO:0000078
EHDAA2:0004618
RETIRED_EHDAA2:0003078
uberon
UBERON:0005082
tube lumen
A hole in a tube[GO].
GO:0060609
An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm[GO]
consder adding placodal ectoderm as a distinct class? Also place placodal ectoderm as develops_from ectoderm; need to check taxon-appropriateness
With the exception of the adenohypophysis, homologues of the nonneurogenic placodes (e.g. placodes giving rise to the teeth, hair follicles and lens), appear to be lacking in invertebrate chordates.
in GO, covers optic, otic, olfactory, mammary, hair, tooth, sebaceous - and also insect structures
AEO:0000218
uberon
epithelial placode
UBERON:0005085
ectodermal placode
An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm[GO]
GO:0060788
in GO, covers optic, otic, olfactory, mammary, hair, tooth, sebaceous - and also insect structures
GO
epithelial placode
AEO:0000112
Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO].
in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila
EMAPA:32715
FBbt:00005073
FMA:30316
musculus
uberon
muscle
muscle element
UBERON:0005090
muscle structure
Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO].
GO:0061061
musculus
FMA:30316
Any anatomical structure that is part of the reproductive system.
reproductive system element
reproductive system structure
uberon
UBERON:0005156
reproductive structure
Any anatomical structure that is part of the reproductive system.
An epithelial sheet bent on a linear axis.
uberon
UBERON:0005157
epithelial fold
An epithelial sheet bent on a linear axis.
GO:0060571
A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part.
we go with the FMA classification rather than the CARO one. FMA def: 'Anatomical cluster which has as direct parts cell parts from two or more cells.'
AAO:0011000
CARO:0001000
FBbt:00007060
FMA:83115
multi-cell-component structure
multi-cell-part structure
uberon
cell part cluster
UBERON:0005162
multi cell part structure
FMA
A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part.
CARO:0001000
we go with the FMA classification rather than the CARO one. FMA def: 'Anatomical cluster which has as direct parts cell parts from two or more cells.'
CARO
FMA
multi-cell-component structure
CARO:0001000
multi-cell-part structure
CARO:0001000
cell part cluster
FMA:83115
An organ or element that part of the dorsum of the organism. Examples: spinal cord, vertebrae, muscles of back.
EMAPA:37274
MA:0001901
back organ
dorsal region organ
uberon
UBERON:0005174
dorsal region element
An organ or element that part of the dorsum of the organism. Examples: spinal cord, vertebrae, muscles of back.
EMAPA:37274
MA:th
back organ
MA:0001901
An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions.
EMAPA:37270
MA:0000516
trunk organ
uberon
UBERON:0005177
trunk region element
An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions.
EMAPA:37270
MA:th
trunk organ
MA:0000516
An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli.
EMAPA:37273
MA:0000557
thoracic cavity organ
uberon
UBERON:0005178
thoracic cavity element
An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli.
EMAPA:37273
MA:th
thoracic cavity organ
MA:0000557
An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions.
EMAPA:37271
MA:0000563
uberon
upper body organ
UBERON:0005181
thoracic segment organ
An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions.
EMAPA:37271
MA:th
upper body organ
MA:0000563
A vein that is part of a thorax [Automatically generated definition].
EMAPA:37197
MA:0002235
NCIT:C53142
UMLS:C0226629
uberon
UBERON:0005194
thoracic vein
A vein that is part of a thorax [Automatically generated definition].
OBOL:automatic
EMAPA:37197
MA:th
UMLS:C0226629
ncithesaurus:Thoracic_Vein
An external ectoderm that is part of a optic eminence [Automatically generated definition].
EMAPA:16539
RETIRED_EHDAA2:0001311
VHOG:0000520
uberon
UBERON:0005216
optic eminence surface ectoderm
true
An external ectoderm that is part of a optic eminence [Automatically generated definition].
OBOL:automatic
An ectoderm that is part of a optic eminence [Automatically generated definition].
EHDAA:940
EMAPA:16539
RETIRED_EHDAA2:0001309
VHOG:0001105
uberon
UBERON:0005234
optic eminence ectoderm
An ectoderm that is part of a optic eminence [Automatically generated definition].
OBOL:automatic
A gland that is part of a stomodeum.
check this
VHOG:0000658
stomatodaeum gland
uberon
UBERON:0005250
stomatodeum gland
A gland that is part of a stomodeum.
OBOL:automatic
stomatodaeum gland
VHOG:0000658
Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells.
Mesoderm that will give rise, along with cranial neural crest cells, to connective tissue, bone and musculature in the head. (Source: BioGlossary, www.Biology-Text.com)[TAO]
EFO:0003492
EHDAA2:0000732
EHDAA:179
EMAPA:16098
EMAPA_RETIRED:16269
FMA:76622
TAO:0000113
VHOG:0000332
ZFA:0000113
cephalic mesenchyme
uberon
cranial mesenchyme
desmocranium
UBERON:0005253
head mesenchyme
EHDAA2
Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells.
ISBN:0683400088
MP:0011260
Mesoderm that will give rise, along with cranial neural crest cells, to connective tissue, bone and musculature in the head. (Source: BioGlossary, www.Biology-Text.com)[TAO]
2012-08-14
TAO:0000113
TAO
ZFIN:curator
cephalic mesenchyme
MP:0011260
cranial mesenchyme
MGI:anna
desmocranium
FMA:76622
Mesenchyme that is part of a developing trunk.
EFO:0003485
EHDAA2:0002092
EHDAA:377
EMAPA:16177
TAO:0000081
VHOG:0000281
ZFA:0000081
uberon
trunk and cervical mesenchyme
UBERON:0005256
trunk mesenchyme
EHDAA2
Mesenchyme that is part of a developing trunk.
OBOL:automatic
trunk and cervical mesenchyme
EHDAA2:0002092
The posterior part of the developing vertebrate hindbrain or the corresponding part of the adult brain composed of the medulla oblongata and a portion of the fourth ventricle; as well as the glossopharyngeal nerve (CN IX), vagus nerve (CN X), accessory nerve (CN XI), hypoglossal nerve (CN XII), and a portion of the vestibulocochlear nerve (CN VIII).[BTO,WP].
The posterior of the two brain vesicles formed by specialization of the rhombencephalon in the developing embryo, it comprises the medulla oblongata. [TFD][VHOG]
The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG]
the terms metencephalon and myelencephalon are only meaningful in mammals and birds - Neuroanatomy of the Zebrafish Brain. Note that its not clear if this refers to the developing medulla oblongata - MA (adult) has two distinct classes
BTO:0000758
CALOHA:TS-0607
CALOHA:TS-2365
DHBA:10662
EHDAA2:0001207
EHDAA:5526
EMAPA:17082
HBA:9512
MA:0000205
VHOG:0000456
uberon
myelencephalon (medulla oblongata)
UBERON:0005290
myelencephalon
http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg
definitional
The posterior part of the developing vertebrate hindbrain or the corresponding part of the adult brain composed of the medulla oblongata and a portion of the fourth ventricle; as well as the glossopharyngeal nerve (CN IX), vagus nerve (CN X), accessory nerve (CN XI), hypoglossal nerve (CN XII), and a portion of the vestibulocochlear nerve (CN VIII).[BTO,WP].
BTO:0000758
The posterior of the two brain vesicles formed by specialization of the rhombencephalon in the developing embryo, it comprises the medulla oblongata. [TFD][VHOG]
2012-09-17
VHOG:0000456
VHOG
The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG]
2012-09-17
VHOG:0000456
VHOG
ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500
myelencephalon (medulla oblongata)
DHBA:10662
A portion of tissue that is part of an embryo.
CALOHA:TS-2100
portion of embryonic tissue
uberon
developing tissue
UBERON:0005291
embryonic tissue
A portion of tissue that is part of an embryo.
OBOL:automatic
portion of embryonic tissue
OBOL:automatic
Portion of tissue that is contiguous with the embryo and is comprised of portions of tissue or cells that will not contribute to the embryo.
BTO:0003360
CALOHA:TS-2119
EFO:0001406
MAT:0000061
MIAA:0000061
extra-embryonic tissue
uberon
UBERON:0005292
extraembryonic tissue
Portion of tissue that is contiguous with the embryo and is comprised of portions of tissue or cells that will not contribute to the embryo.
The endothelial lining of the endocardium.
FMA:83596
endocardium endothelium
endothelium of endocardium
uberon
UBERON:0005316
endocardial endothelium
The endothelial lining of the endocardium.
UBERON:cjm
endocardium endothelium
FMA:83596
endothelium of endocardium
FMA:83596
A lamina propria that is part of a mucosa of oral region.
EMAPA:26947
lamina propria of oral mucosa
uberon
UBERON:0005334
oral lamina propria
A lamina propria that is part of a mucosa of oral region.
OBOL:automatic
An array of photoreceptors and any supporting cells found in an eye.
FBbt:00004200
light-sensitive tissue
uberon
UBERON:0005388
photoreceptor array
An array of photoreceptors and any supporting cells found in an eye.
A transparent structure that is part of a visual sense organ, the function of which is to direct or focus light onto a photoreceptor array.
directing or focusing light onto light receptors
lens
uberon
UBERON:0005389
transparent eye structure
A transparent structure that is part of a visual sense organ, the function of which is to direct or focus light onto a photoreceptor array.
AEO:0000125
CALOHA:TS-2122
EHDAA2:0003125
FBbt:00007006
FMA:292313
MIAA:0000019
uberon
developing structure
developmental structure
developmental tissue
UBERON:0005423
developing anatomical structure
developmental tissue
MIAA:0000019
Portion of tissue that is the inner layer of the optic cup and will become the neural retina.
(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]
EHDAA2:0001304
EMAPA:16675
TAO:0001071
VHOG:0000490
ZFA:0001071
future neural retina
future retinal neural layer
inner layer optic cup
optic cup inner layer
presumptive retinas
uberon
future NR
future neural epithelium
future neural layer
presumptive retina
UBERON:0005425
presumptive neural retina
Portion of tissue that is the inner layer of the optic cup and will become the neural retina.
ZFIN:curator
(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]
2012-09-17
VHOG:0000490
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429
inner layer optic cup
ZFA:0001071
optic cup inner layer
EHDAA2:0001304
presumptive retinas
ZFA:0001071
future neural epithelium
EMAPA:16675
future neural layer
EMAPA:16675
presumptive retina
TAO:0001071
Portion of tissue that gives rise to the lens.
A vesicle formed from the lens pit of the embryo, developing into the crystalline lens. [TFD][VHOG]
(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG]
the lens of zebrafish (and other teleosts) forms from delamination of cells from the lens placode; thus, there is no formation of a hollow lens vesicle, in contrast to the situation in mammals and birds (Glass and Dahm, 2004) [PMID:16496288] The lens of the zebrafish forms by delamination of lens placodal cells and not through invagination. This results in a solid spherical mass as opposed to a hollow lens vesicle. Detachment of the solid lens vesicle of zebrafish at 24b26 hpf is accomplished in part by apoptosis, similar to mammals
EHDAA2:0000983
EHDAA:4737
EMAPA:17163
TAO:0002205
VHOG:0001163
ZFA:0001679
hollow lens vesicle
solid lens vesicle
uberon
immature lens
lens mass
presumptive lens
UBERON:0005426
lens vesicle
Portion of tissue that gives rise to the lens.
ZFIN:curator
A vesicle formed from the lens pit of the embryo, developing into the crystalline lens. [TFD][VHOG]
2012-09-17
VHOG:0001163
VHOG
(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG]
2012-09-17
VHOG:0001163
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429
the lens of zebrafish (and other teleosts) forms from delamination of cells from the lens placode; thus, there is no formation of a hollow lens vesicle, in contrast to the situation in mammals and birds (Glass and Dahm, 2004) [PMID:16496288] The lens of the zebrafish forms by delamination of lens placodal cells and not through invagination. This results in a solid spherical mass as opposed to a hollow lens vesicle. Detachment of the solid lens vesicle of zebrafish at 24b26 hpf is accomplished in part by apoptosis, similar to mammals
ZFA
hollow lens vesicle
solid lens vesicle
ZFA:0001679
immature lens
ZFA:0001679
lens mass
ZFA:0001679
ZFIN:ZDB-PUB-091023-49
presumptive lens
ZFA:0001679
Portion of tissue that is part of the eye and gives rise to the mature, fully layered cornea.
TAO:0002188
ZFA:0001688
uberon
UBERON:0005427
corneal primordium
ZFA
Obol
ZFA
Portion of tissue that is part of the eye and gives rise to the mature, fully layered cornea.
ZFIN:ZDB-PUB-061010-3
Portion of tissue on the side of the lumen of the neural tube.
EHDAA2:0001257
EHDAA:2873
EHDAA:912
EMAPA:16166
TAO:0001435
VHOG:0000513
ZFA:0001435
lateral wall neural tube
uberon
UBERON:0005496
neural tube lateral wall
Portion of tissue on the side of the lumen of the neural tube.
ZFA:0001435
lateral wall neural tube
ZFA:0001435
Multi-tissue structure that arises from the heart rudiment and will become the heart tube.
EHDAA2:0001512
EHDAA:424
EHDAA:436
EMAPA:16215
FMA:321916
TAO:0000149
ZFA:0000149
primitive heart tube
early primitive heart tube
uberon
UBERON:0005498
primitive heart tube
ZFA
Multi-tissue structure that arises from the heart rudiment and will become the heart tube.
ZFA:0000149
primitive heart tube
EMAPA:16215
early primitive heart tube
EMAPA:16208
A neural tube lateral wall that is part of a rhombomere.
EMAPA:32819
EMAPA:35364
uberon
future hindbrain lateral wall
UBERON:0005501
rhombomere lateral wall
A neural tube lateral wall that is part of a rhombomere.
OBOL:automatic
future hindbrain lateral wall
EMAPA:35364
Portion of tissue that gives rise to the immature gonad.
Immature reproductive tissue that has not undergone final maturation into either testis or ovary.[TAO]
this is a very broad grouping class
EFO:0003651
EHDAA:5927
EMAPA:17204
RETIRED_EHDAA2:0002148
TAO:0001262
WBbt:0008366
ZFA:0001262
future gonad
gonadal primordium
primitive gonad
undifferentiated gonad
uberon
immature gonad
UBERON:0005564
gonad primordium
Obol
ZFA
Portion of tissue that gives rise to the immature gonad.
ZFA:0001262
Immature reproductive tissue that has not undergone final maturation into either testis or ovary.[TAO]
2012-08-14
TAO:0001262
TAO
ZFIN:curator
future gonad
gonadal primordium
ZFA:0001262
primitive gonad
undifferentiated gonad
ZFA:0001262
immature gonad
Somite located in the head region, caudal to the otic vesicle
in humans this includes somites 1-4
They provide the epaxial and hypaxial muscles of the neck, the pharyngeal and laryngeal muscles that develop in the caudal branchial arches and the musculature of the tongue. Despite their localisation in the head, myogenic precursors from occipital somites essentially follow the trunk programmes (E. H. Walters and S. D., unpublished). during evolution, have been secondarily incorporated into the head (Gans and Northcutt, 1983)
EHDAA2 has both 'head somite' and 'head somite group', with part_of and develops_from for latter
EHDAA2:0003437
EMAPA:16172
XAO:0000313
occipital somite
uberon
cranial somite
UBERON:0005594
head somite
EHDAA2
EHDAA2
Somite located in the head region, caudal to the otic vesicle
They provide the epaxial and hypaxial muscles of the neck, the pharyngeal and laryngeal muscles that develop in the caudal branchial arches and the musculature of the tongue. Despite their localisation in the head, myogenic precursors from occipital somites essentially follow the trunk programmes (E. H. Walters and S. D., unpublished). during evolution, have been secondarily incorporated into the head (Gans and Northcutt, 1983)
EHDAA2 has both 'head somite' and 'head somite group', with part_of and develops_from for latter
EHDAA2
occipital somite
XAO:0000313
cranial somite
XAO:0000313
A somite that is part of a trunk.
AAO:0010385
EHDAA2:0003438
EMAPA:16184
XAO:0000314
uberon
UBERON:0005598
trunk somite
A somite that is part of a trunk.
OBOL:automatic
A layer of cuboidal epithelial cells bounded anteriorly by the capsule of the lens and posteriorly by the lens cortex.
Cells of the subcapsular epithelium (or anterior lens cells) are mitotically active. In adult individuals they only cover the anterior 'hemisphere' of the lens. As they divide, cells gradually move towards the equator of the lens where they tranform into lens fibres. The apical part of the gradually elongating cell extends between the subcapsular epithelium and adjacent lens fibres towards the anterior pole of the lens. The basal part extends towards the posterior pole. The nucleus remains close to the equatorial plane of the lens - http://www.lab.anhb.uwa.edu.au/mb140/corepages/eye/eye.htm
lens epithelium
EHDAA2:0000984
EHDAA:9059
EMAPA:17304
EMAPA:17839
FMA:70612
MA:0001302
NCIT:C33641
RETIRED_EHDAA2:0000976
UMLS:C1182652
VHOG:0001425
lens subcapsular epithelium
subcapsular lens epithelium
uberon
anterior epithelium of lens vesicle
anterior surface of lens
UBERON:0005614
lens anterior epithelium
A layer of cuboidal epithelial cells bounded anteriorly by the capsule of the lens and posteriorly by the lens cortex.
UMLS:C1182652
ncithesaurus:Subcapsular_Epithelium_of_the_Lens
lens subcapsular epithelium
subcapsular lens epithelium
FMA:70612
anterior epithelium of lens vesicle
EMAPA:17304
anterior surface of lens
FMA:58889
An epithelium that is part of a anterior chamber of eyeball.
EHDAA2:0000130
uberon
UBERON:0005638
anterior chamber epithelium
An epithelium that is part of a anterior chamber of eyeball.
OBOL:automatic
An epithelium that is part of a lens vesicle.
EHDAA2:0000987
EMAPA:17165
VHOG:0000532
uberon
UBERON:0005656
lens vesicle epithelium
An epithelium that is part of a lens vesicle.
OBOL:automatic
An anatomical cavity that is part of a lens vesicle.
(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG]
cavity of lens
lens cavity
EHDAA2:0000986
EMAPA:17164
VHOG:0000531
cavity of lens vesicle
uberon
UBERON:0005688
lens vesicle cavity
An anatomical cavity that is part of a lens vesicle.
OBOL:automatic
(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG]
2012-09-17
VHOG:0000531
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429
lens cavity
EHDAA2:0000986
cavity of lens vesicle
EMAPA:17164
Mesenchyme that is part of a optic eminence.
EHDAA:942
EMAPA:16324
RETIRED_EHDAA2:0001310
VHOG:0001073
uberon
UBERON:0005702
optic eminence mesenchyme
Mesenchyme that is part of a optic eminence.
OBOL:automatic
A venous system that is part of a hindbrain.
EHDAA2:0000776
EMAPA:18632
VHOG:0001322
uberon
rhombencephalon venous system
UBERON:0005720
hindbrain venous system
A venous system that is part of a hindbrain.
OBOL:automatic
rhombencephalon venous system
VHOG:0001322
The outermost layer of a blood vessel, composed mainly of fibrous tissue.
TODO - note terminological problems. WP says tunica external layer of blood vessel. FMA says tunica externa = adventitia, and is FMA adventitia covers other kinds of vessels. Here we opt for a lengthier name that attempts to disambiguate. There is no precise FMA equivalent, as FMA has tunica externa of arteries, veins, genital ducts etc as siblings
The outermost layer of a blood vessel, surrounding the tunica media. It is mainly composed of collagen. The collagen serves to anchor the blood vessel to nearby organs, giving it stability[Wikipedia:Tunica_externa_(vessels)].
BTO:0002010
EMAPA:36299
NCIT:C33818
UMLS:C0225342
adventitia externa
tunica adventitia
tunica adventitia of vessel
uberon
external coat
tunica adventitia vasorum
tunica externa vasorum
UBERON:0005734
tunica adventitia of blood vessel
Illu:artery.jpg
cjm
The outermost layer of a blood vessel, composed mainly of fibrous tissue.
ISBN:0073040584
The outermost layer of a blood vessel, surrounding the tunica media. It is mainly composed of collagen. The collagen serves to anchor the blood vessel to nearby organs, giving it stability[Wikipedia:Tunica_externa_(vessels)].
UMLS:C0225342
ncithesaurus:Tunica_Adventitia
adventitia externa
tunica adventitia
tunica adventitia of vessel
external coat
tunica adventitia vasorum
tunica externa vasorum
A tunica intima that is part of a artery.
EMAPA:36293
EV:0100028
FMA:14272
galen:IntimaOfArtery
arterial intima
tunica interna (intima)(arteriae)
uberon
UBERON:0005740
tunica intima of artery
A tunica intima that is part of a artery.
OBOL:automatic
arterial intima
EV:0100028
tunica interna (intima)(arteriae)
FMA:14272
An outermost connective tissue covering of an organ, vessel, or other structure[WP].
BTO:0002010
FMA:45635
tunica advetitia
tunica externa
uberon
UBERON:0005742
adventitia
http://upload.wikimedia.org/wikipedia/commons/e/e8/Illu_esophageal_layers.jpg
An outermost connective tissue covering of an organ, vessel, or other structure[WP].
tunica advetitia
tunica externa
FMA:45635
Anatomical space that is an opening in a bone, usually for passage of blood vessels or nerves.
in FMA and ZFA this is a conduit space, not a conduit. Note there may be some additional disambiguation required: foramen is used loosely in the sense of any opening (e.g. foramen primum). FMA appears to use cranial conduit (undefined) in the sense of any foramen of the skull (includes mental foramen, which is not in the cranium proper).
foramen
AAO:0010438
TAO:0001736
VHOG:0001760
ZFA:0005386
foramens@fr
foramina@fr
uberon
UBERON:0005744
bone foramen
http://upload.wikimedia.org/wikipedia/commons/8/81/Gray193.png
Anatomical space that is an opening in a bone, usually for passage of blood vessels or nerves.
TAO:curator
in FMA and ZFA this is a conduit space, not a conduit. Note there may be some additional disambiguation required: foramen is used loosely in the sense of any opening (e.g. foramen primum). FMA appears to use cranial conduit (undefined) in the sense of any foramen of the skull (includes mental foramen, which is not in the cranium proper).
FMA
foramen
ZFA:0005386
foramens@fr
TAO:0001736
foramina@fr
TAO:0001736
A acellular anatomical structure that is the bounding layer of a anatomical structure.
FMA:63871
uberon
UBERON:0005764
acellular membrane
A acellular anatomical structure that is the bounding layer of a anatomical structure.
OBOL:automatic
An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina.
this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell.
AAO:0010596
FMA:63872
GAID:915
NCIT:C13191
UMLS:C0004799
basement membrane of connective tissue
membrana basalis
uberon
basement membrane
UBERON:0005769
basement membrane of epithelium
FMA
An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina.
UMLS:C0004799
ncithesaurus:Basement_Membrane
basement membrane of connective tissue
FMA:63872
membrana basalis
basement membrane
FMA:63872
A delimited region of dense mesenchyme within looser mesenchyme.
AEO:0000148
EHDAA2_RETIRED:0003148
EHDAA:8979
mesenchyme condensation
uberon
UBERON:0005856
developing mesenchymal condensation
AEO
cjm
A delimited region of dense mesenchyme within looser mesenchyme.
AEO:0000148
mesenchyme condensation
EMAPA:25351
Cell condensation that is an aggregation of mesenchymal cells that are committed to differentiate into chondroblasts and chondrocytes.
isa cell condensation in VSAO; has_part chondroblast in AEO
AEO:0000147
EHDAA2_RETIRED:0003147
EMAPA:32731
VSAO:0000092
XAO:0004022
cartilage condensation
cartilagenous condensation
chondrogenic condensation
uberon
UBERON:0005863
cartilaginous condensation
AEO
AEO
Cell condensation that is an aggregation of mesenchymal cells that are committed to differentiate into chondroblasts and chondrocytes.
GO:curator
isa cell condensation in VSAO; has_part chondroblast in AEO
VSAO
cartilage condensation
EMAPA:25353
cartilagenous condensation
EHDAA2:0003147
chondrogenic condensation
VSAO:0000092
A delimited region of dense mesenchyme within looser mesenchyme whose cells are committed to become chondroblasts.
A closely packed aggregation of mesenchymal cells just prior to their differentiation into embryonic cartilage.
AEO:0000150
EHDAA2:0003150
EMAPA:32736
pre-chondrogenic condensation
precartilage condensation
precartilagenous condensation
prechondrogenic condensation
uberon
UBERON:0005866
pre-cartilage condensation
AEO
AEO
A delimited region of dense mesenchyme within looser mesenchyme whose cells are committed to become chondroblasts.
AEO:0000150
AEO:JB
A closely packed aggregation of mesenchymal cells just prior to their differentiation into embryonic cartilage.
the paired ventral prominences formed by bifurcation of the first pharyngeal arches in the embryo; the two prominences unite ventrally and fuse to form the mandible and lower lip
check develops_from
EHDAA2:0001061
EHDAA:5871
EMAPA:17355
FMA:293051
NCIT:C34204
UMLS:C1512982
uberon
mandibular process
mandibular swelling
prominentia mandibularis
UBERON:0005867
mandibular prominence
the paired ventral prominences formed by bifurcation of the first pharyngeal arches in the embryo; the two prominences unite ventrally and fuse to form the mandible and lower lip
ISBN:0-683-40008-8
MP:0010939
UMLS:C1512982
ncithesaurus:Mandibular_Prominence
mandibular process
mandibular swelling
prominentia mandibularis
Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occipital condyles.
TODO - check
An anatomical cluster that is located in the posterior region of the neurocranium and forms the margin of the foramen margin and occipital condyles.[AAO]
Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occiptal condyle.[TAO]
AAO:0010199
BTO:0004675
FMA:49187
TAO:0001414
XAO:0003173
ZFA:0001414
basicranial region
occipital part of head
occipital region of head
uberon
back of head
UBERON:0005902
occipital region
Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occipital condyles.
TAO:0001414
UBERONREF:0000007
An anatomical cluster that is located in the posterior region of the neurocranium and forms the margin of the foramen margin and occipital condyles.[AAO]
2012-06-20
AAO:0010199
AAO
AAO:EJS
Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occiptal condyle.[TAO]
2012-08-14
TAO:0001414
TAO
TAO:MAH
basicranial region
ZFA:0001414
occipital part of head
FMA:49187
occipital region of head
FMA:49187
back of head
FMA:49187
Organ with organ cavity, which has as parts a serous membrane and a serous cavity . Examples: pleural sac, pericardial sac, tendon sheath, bursa.[FMA]
EMAPA:16060
FMA:9689
MA:0000005
uberon
UBERON:0005906
See notes for serous membrane
serous sac
Organ with organ cavity, which has as parts a serous membrane and a serous cavity . Examples: pleural sac, pericardial sac, tendon sheath, bursa.[FMA]
FMA:9689
Epithelium that derives from the endoderm. Examples: urothelium, transitional epithelium of ureter, epithelium of prostatic gland.[FMA]
FMA:69065
endoderm-derived epithelium
endoepithelium
uberon
UBERON:0005911
endo-epithelium
Epithelium that derives from the endoderm. Examples: urothelium, transitional epithelium of ureter, epithelium of prostatic gland.[FMA]
FMA:69065
Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified].
Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO]
AAO:0000963
EMAPA:17214
EMAPA:18043
MA:0000308
NCIT:C32172
UMLS:C0222645
VSAO:0000056
XAO:0004011
uberon
skeleton axiale
UBERON:0005944
axial skeleton plus cranial skeleton
http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton
http://upload.wikimedia.org/wikipedia/commons/8/8b/Axial_skeleton_diagram.svg
Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified].
FMA:71221
VSAO:0000056
Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO]
2012-08-14
VSAO:0000056
VSAO
PSPUB:0000170
UMLS:C0222645
ncithesaurus:Axial_Skeleton
skeleton axiale
The laminar structure of the heart
uberon
UBERON:0005983
heart layer
The laminar structure of the heart
MP:0010545
Any of the arteries or veins that supply blood to the heart or return blood from the heart muscles to the circulation
TODO - change relation from part_of
MESH:D003331
uberon
UBERON:0005985
coronary vessel
Any of the arteries or veins that supply blood to the heart or return blood from the heart muscles to the circulation
MP:0010551
Anatomical structure embedded in or located in the integument that is part of the integumental system. Examples: hair, follicles, skin glands, claws, nails, feathers.
add subclasses based on resolution of CARO tracker item. Also check: adnexal gland. Note that MP implicitly includes hypodermis.
the tissue or structures associated with or embedded in the skin such as hair and hair follicles, sweat glands, sebaceous glands and claws or nails[MP:0010678]
EMAPA:37883
body hair or bristle
uberon
adnexae cutis
skin adnexa
skin adnexal structure
skin appendage
UBERON:0006003
integumentary adnexa
Anatomical structure embedded in or located in the integument that is part of the integumental system. Examples: hair, follicles, skin glands, claws, nails, feathers.
the tissue or structures associated with or embedded in the skin such as hair and hair follicles, sweat glands, sebaceous glands and claws or nails[MP:0010678]
MP:0010678
EMAPA:37883
MA:th
body hair or bristle
GO:GO
adnexae cutis
skin adnexa
skin appendage
uberon
UBERON:0006056
posterior surface of head
The thin bilaminar membrane derived from the prechordal plate that is devoid of mesoderm and formed by the apposition of the stomodeal ectoderm with the foregut endoderm; after the embryonic head fold has evolved it lies at the caudal limit of the stomodeum, forming a septum between the primitive mouth and pharynx; the membrane eventually disappears, and thus a communication is established between the mouth and the future pharynx.
EHDAA2:0000189
EHDAA:536
EMAPA:16259
FMA:313607
VHOG:0000380
uberon
oral membrane
oral plate
oropharyngeal membrane
pharyngeal membrane
UBERON:0006211
buccopharyngeal membrane
http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png
EHDAA2
The thin bilaminar membrane derived from the prechordal plate that is devoid of mesoderm and formed by the apposition of the stomodeal ectoderm with the foregut endoderm; after the embryonic head fold has evolved it lies at the caudal limit of the stomodeum, forming a septum between the primitive mouth and pharynx; the membrane eventually disappears, and thus a communication is established between the mouth and the future pharynx.
MP:0012521
oral membrane
MP:0012521
oral plate
MP:0012521
oropharyngeal membrane
pharyngeal membrane
MP:0012521
The embryonic precursor of the brain.
The embryonic precursor of the brain and the set of mature brain structures that derive from it (CUMBO)
BAMS:Enc
BTO:0004726
EFO:0003431
EHDAA:300
EHDAA:830
EMAPA:16089
FMA:312967
RETIRED_EHDAA2:0000591
TAO:0000146
ZFA:0000146
brain rudiment
presumptive brain
encephalon
uberon
embryonic brain
UBERON:0006238
future brain
The embryonic precursor of the brain.
NLX:94995
The embryonic precursor of the brain and the set of mature brain structures that derive from it (CUMBO)
brain rudiment
TAO:0000146
presumptive brain
ZFA:0000146
encephalon
NLX:94995
embryonic brain
BTO:0004726
EFO:0003438
EHDAA2:0000674
EHDAA:898
EMAPA:16092
EMAPA:16755
TAO:0000417
ZFA:0000417
presumptive spinal cord
presumptive spinal cord neural keel
presumptive spinal cord neural plate
presumptive spinal cord neural rod
uberon
UBERON:0006241
future spinal cord
EHDAA2
presumptive spinal cord
ZFA:0000417
presumptive spinal cord neural keel
TAO:0000417
presumptive spinal cord neural plate
TAO:0000417
presumptive spinal cord neural rod
TAO:0000417
An anatomical junctions that overlaps the mouth and foregut.
EHDAA:534
EMAPA:16258
RETIRED_EHDAA2:0001205
VHOG:0000592
uberon
UBERON:0006264
mouth-foregut junction
An anatomical junctions that overlaps the mouth and foregut.
OBOL:automatic
The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord.
TODO - check ordering; awaiting confirmation from JB
The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG]
EHDAA2:0001278
EHDAA:264
EMAPA:16101
NCIT:C34231
UMLS:C1518429
VHOG:0001212
uberon
UBERON:0006267
notochordal plate
EHDAA2
EHDAA2
The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord.
VHOG:0001212
The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG]
2012-09-17
VHOG:0001212
VHOG
UMLS:C1518429
ncithesaurus:Notochordal_Plate
A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot
EHDAA2:0001279
EHDAA:224
EMAPA:16102
FMA:293135
NCIT:C34232
UMLS:C1518430
VHOG:0001213
uberon
chordamesoderm
presumptive notochord
UBERON:0006268
The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus.
notochordal process
EHDAA2
A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot
UMLS:C1518430
ncithesaurus:Notochordal_Process
Multi-tissue structure that is part of the heart tube and will become the cardiac ventricle.
UBERON:0010226
embryonic ventricle
EHDAA2:0001531
EMAPA:16350
FMA:71006
NCIT:C34160
TAO:0002231
ZFA:0001719
early heart ventricle
embryonic heart ventricle
future heart ventricle
presumptive cardiac ventricle heart tube
primitive ventricle
primitive ventricle of heart
primordial cardiac ventricle
primordial ventricle
uberon
UBERON:0006283
The embryonic ventricle or primitive ventricle of the developing heart gives rise to the trabeculated parts of the left and right ventricles. In contrast, the smooth parts of the left and right ventricles originate from the embryological bulbus cordis. The primitive ventricle becomes divided by a septum, the septum inferius or ventricular septum, which grows upward from the lower part of the ventricle, its position being indicated on the surface of the heart by a furrow. Its dorsal part increases more rapidly than its ventral portion, and fuses with the dorsal part of the septum intermedium. For a time an interventricular foramen exists above its ventral portion, but this foramen is ultimately closed by the fusion of the aortic septum with the ventricular septum[WP]
future cardiac ventricle
ZFA
EMAPA
Multi-tissue structure that is part of the heart tube and will become the cardiac ventricle.
ZFA:0001719
presumptive cardiac ventricle heart tube
ZFA:0001719
primitive ventricle
EHDAA2:0001531
primitive ventricle of heart
EMAPA:16350
primordial cardiac ventricle
FMA:71006
primordial ventricle
FMA:71006
A segment of the eyeball that is filled with refractive media
BTO:0002085
EMAPA:37529
FMA:58071
MA:0002459
NCIT:C32301
UMLS:C0459556
eye chamber
eyeball chamber
uberon
chamber of eye
UBERON:0006311
chamber of eyeball
A segment of the eyeball that is filled with refractive media
EMAPA:37529
MA:th
UMLS:C0459556
ncithesaurus:Chamber_of_the_Eye
eye chamber
MA:0002459
eyeball chamber
FMA:58071
chamber of eye
BTO:0002085
Body substance in a liquid or semi-solid state in the eyeball which serves to refract light.
ocular refraction
MA:0001911
uberon
UBERON:0006312
ocular refractive media
Body substance in a liquid or semi-solid state in the eyeball which serves to refract light.
Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not.
fluid
BIRNLEX:20
EMAPA:37441
FMA:280556
GAID:266
MESH:D001826
galen:BodyFluid
body fluid
uberon
UBERON:0006314
bodily fluid
Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not.
MESH:A12.207
EMAPA:37441
MA:th
body fluid
GAID:266
2
2
An artery that connects two larger arteries.
EMAPA:18598
MA:0001938
NCIT:C52851
UMLS:C1707451
uberon
UBERON:0006347
Grouping for anterior and posterior
communicating artery
An artery that connects two larger arteries.
ncithesaurus:Communicating_Artery
UMLS:C1707451
ncithesaurus:Communicating_Artery
A portion of organism substance that secreted_by a zone of skin.
MA:0002537
skin fluid/secretion
uberon
skin fluid
skin substance
UBERON:0006535
skin secretion
A portion of organism substance that secreted_by a zone of skin.
OBOL:automatic
skin fluid/secretion
MA:0002537
A portion of organism substance that secreted_by a respiratory system.
EMAPA:36550
MA:0002533
NCIT:C13722
UMLS:C1514899
uberon
respiratory system fluid
respiratory system secretion
UBERON:0006538
respiratory system fluid/secretion
A portion of organism substance that secreted_by a respiratory system.
OBOL:automatic
UMLS:C1514899
ncithesaurus:Respiratory_System_Fluid_or_Secretion
The pharynx is the part of the digestive system immediately posterior to the mouth[GO].
currently this is an extremely generic class, encompassing both protostomes and deuterostomes.
branchial
pharyngeal
FBbt:00005380
MAT:0000049
MIAA:0000049
uberon
anterior part of foregut
pharyngeal tube
UBERON:0006562
pharynx
The pharynx is the part of the digestive system immediately posterior to the mouth[GO].
GO:0060465
Presumptive structure of the blastula that will develop into endoderm.
AAO:0000471
EFO:0003437
TAO:0000416
ZFA:0000416
uberon
UBERON:0006595
presumptive endoderm
Presumptive structure of the blastula that will develop into endoderm.
AAO:0000468
EFO:0003439
TAO:0000568
ZFA:0000568
future blood
uberon
UBERON:0006596
presumptive blood
Portion of embryonic tissue determined by fate mapping to become a structure.
Consider merging with anlage
AAO:0000479
TAO:0001116
ZFA:0001116
future structure
presumptive structures
uberon
UBERON:0006598
presumptive structure
Portion of embryonic tissue determined by fate mapping to become a structure.
GOC:CVS
GOC:YMB
ZFA:0001116
presumptive structures
ZFA:0001116
Presumptive structure of the blastula that will develop into ectoderm.
AAO:0000470
EFO:0003466
TAO:0001376
XAO:0004132
ZFA:0001376
uberon
presumptive epidermis
UBERON:0006601
presumptive ectoderm
Presumptive structure of the blastula that will develop into ectoderm.
presumptive epidermis
ZFA:0001376
Presumptive structure of the blastula that will develop into mesoderm.
AAO:0000476
EFO:0003467
TAO:0001377
ZFA:0001377
uberon
UBERON:0006603
presumptive mesoderm
Presumptive structure of the blastula that will develop into mesoderm.
An anatomical boundary that adjacent_to a epithelium.
FMA:70997
epithelium surface
uberon
UBERON:0006677
surface of epithelium
An anatomical boundary that adjacent_to a epithelium.
OBOL:automatic
epithelium surface
FMA:70997
the edge of the cornea where it joins the sclera; the limbus is a common site for the occurrence of corneal epithelial neoplasm
EFO:0001403
EMAPA:37835
FMA:58342
GAID:896
MESH:D016850
ZFA:0005570
cornea limbus
corneal limbus
corneal-scleral limbus
corneoscleral junction
limbus corneae
sclerocorneal junction
sclerocorneal limbus
uberon
limbus corneae
UBERON:0006761
This location has parts such as blood vessels etc. See PMC2868485, http://www.ncbi.nlm.nih.gov/pubmed/2695343
corneo-scleral junction
http://upload.wikimedia.org/wikipedia/commons/3/3d/Limbus.png
the edge of the cornea where it joins the sclera; the limbus is a common site for the occurrence of corneal epithelial neoplasm
MP:0013477
EMAPA:37835
MA:th
corneal limbus
FMA:58342
corneal limbus
GAID:896
corneal-scleral limbus
corneoscleral junction
GAID:896
limbus corneae
sclerocorneal junction
FMA:58342
sclerocorneal limbus
GAID:896
limbus corneae
Loose connective tissue located at the outer and inner layers of organs. Examples: submucosal connective tissue, tunica adventitia of artery, papillary dermis, superficial fascia of dorsum of hand.
Also known as loose connective tissue. A pliable, mesh-like tissue with a fluid matrix that functions to cushion and protect body organs.[AAO]
relationship loss: subclass connective tissue proper (AAO:0000099)[AAO]
cushions body organs
AAO:0000027
FMA:63897
loose areolar connective tissue
uberon
areolar tissue
loose connective tissue
UBERON:0006815
areolar connective tissue
FMA
Loose connective tissue located at the outer and inner layers of organs. Examples: submucosal connective tissue, tunica adventitia of artery, papillary dermis, superficial fascia of dorsum of hand.
FMA:63897
Also known as loose connective tissue. A pliable, mesh-like tissue with a fluid matrix that functions to cushion and protect body organs.[AAO]
2012-06-20
AAO:0000027
AAO
AAO:LAP
relationship loss: subclass connective tissue proper (AAO:0000099)[AAO]
2012-06-20
AAO:0000027
AAO
cushions body organs
AAO
loose areolar connective tissue
FMA:63897
loose connective tissue
AAO:0000027
A vasculature that is part of a organ.
FMA:74612
organ vasculature
set of blood vessels of organ
uberon
UBERON:0006876
vasculature of organ
A vasculature that is part of a organ.
OBOL:automatic
organ vasculature
FMA:74612
set of blood vessels of organ
FMA:74612
A head mesenchyme that develops_from a mesoderm.
merged in 'head mesoderm' from XAO/AAO and EFO here. Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme
AAO:0011051
EFO:0003337
EFO:0003603
EHDAA2:0001118
EHDAA:655
EMAPA:16099
EMAPA_RETIRED:16270
FMA:293859
TAO:0000998
VHOG:0000185
XAO:0000053
ZFA:0000998
head mesenchyme derived from mesoderm
head mesenchyme from head mesoderm
head mesenchyme from mesoderm
mesenchyme derived from head mesoderm
mesenchyme from head mesoderm
uberon
cranial mesoderm
head mesoderm
UBERON:0006904
head mesenchyme from mesoderm
ZFA
EHDAA2
XAO
A head mesenchyme that develops_from a mesoderm.
OBOL:automatic
head mesenchyme from head mesoderm
EHDAA2:0001118
mesenchyme derived from head mesoderm
EHDAA:1057
cranial mesoderm
UBERON:0005280
head mesoderm
AAO:0011051
UBERON:0005280
Mesenchyme that is part of a mandibular prominence.
EHDAA2:0001062
EHDAA:5861
EHDAA:5873
EMAPA:17357
mesenchyme of mandibular process
mesenchyme of mandibular prominence
uberon
UBERON:0006905
mandibular process mesenchyme
Mesenchyme that is part of a mandibular prominence.
OBOL:automatic
mesenchyme of mandibular process
EMAPA:17357
mesenchyme of mandibular prominence
An anatomical space that surrounded_by a digestive tract.
BTO:0000349
EMAPA:32908
FMA:45677
digestive tract lumen
gut cavity
gut lumen
lumen of alimentary tract
lumen of digestive tract
lumen of gut
uberon
UBERON:0006909
lumen of digestive tract
An anatomical space that surrounded_by a digestive tract.
OBOL:automatic
digestive tract lumen
gut cavity
BTO:0000349
gut lumen
FMA:45677
lumen of alimentary tract
lumen of digestive tract
lumen of gut
FMA:45677
An epithelium that is part of a lip.
The thick, high squamous-stratified epithelium that covers the lips. It contains abundant melanocytes, many mucous cells and has well differentiated taste buds.[TAO]
BTO:0004468
TAO:0005334
ZFA:0005334
uberon
UBERON:0006913
lip epithelium
An epithelium that is part of a lip.
OBOL:automatic
The thick, high squamous-stratified epithelium that covers the lips. It contains abundant melanocytes, many mucous cells and has well differentiated taste buds.[TAO]
2012-08-14
TAO:0005334
TAO
ZFIN:ZDB-PUB-060921-12
An epithelium characterised by its most superficial layer consisting of squamous epithelial cells.
FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium
BTO:0002072
NCIT:C12848
UMLS:C0221909
uberon
UBERON:0006914
squamous epithelium
An epithelium characterised by its most superficial layer consisting of squamous epithelial cells.
FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium
FBbt
UMLS:C0221909
ncithesaurus:Squamous_Epithelium
The vascular cord is the primordial vasculature that will develop into blood vessels by the process of tubulogenesis[GO]. The vascular cord is composed of angioblast or vascular endothelial cells in a solid linear mass called a cord. The cord then undergoes tubulogenesis to form the lumen of the vessels[ZFA].
EFO:0003709
TAO:0005077
ZFA:0005077
uberon
UBERON:0006965
vascular cord
The vascular cord is the primordial vasculature that will develop into blood vessels by the process of tubulogenesis[GO]. The vascular cord is composed of angioblast or vascular endothelial cells in a solid linear mass called a cord. The cord then undergoes tubulogenesis to form the lumen of the vessels[ZFA].
GO:0072360
ZFA:0005077
A capillary that is part of the coronary system.
ZFA:0005813
heart capillary
uberon
UBERON:0006966
coronary capillary
A capillary that is part of the coronary system.
heart capillary
GO:0003248
A two dimensional anatomical structure that is the boundary between an anatomical structure and an anatomical substance, an anatomical space or the organism's environment. Examples include the surface of your skin, the surface of the lining of your gut; the surface of the endothelium of you aorta that is in contact with blood.n
BILA:0000010
CARO:0001002
EHDAA2_RETIRED:0003192
FMA:24137
NCIT:C34022
UMLS:C1515977
uberon
UBERON:0006984
Old definition: 'Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures.' Note, in the new definition, the space referred to is not necessarily an anatomical space. It may be the outside of an organism.
anatomical surface
via morphological boundary in CARO
A two dimensional anatomical structure that is the boundary between an anatomical structure and an anatomical substance, an anatomical space or the organism's environment. Examples include the surface of your skin, the surface of the lining of your gut; the surface of the endothelium of you aorta that is in contact with blood.n
CARO:0001002
UMLS:C1515977
ncithesaurus:Anatomic_Surface
The splanchnic mesoderm in the cardiogenic region where the heart develops; it gives rise to endocardial heart tubes that fuse to form the primordial cardiac tube, the heart primordium[web]. Two migratory heart primordia that move ventrally during the course of neurulation, and then fuse[XAO].
consider FBbt:00005541 ! cardiogenic mesoderm
review EHDAA2 placement
AAO:0011021
BILA:0000051
EFO:0000315
EHDAA2:0000214
EHDAA:385
FMA:293143
VHOG:0001641
XAO:0000235
cardiogenic splanchnopleure
uberon
cardiac mesoderm
cardiogenic mesoderm
cardiogenic region
heart primordia
UBERON:0007005
cardiogenic splanchnic mesoderm
The splanchnic mesoderm in the cardiogenic region where the heart develops; it gives rise to endocardial heart tubes that fuse to form the primordial cardiac tube, the heart primordium[web]. Two migratory heart primordia that move ventrally during the course of neurulation, and then fuse[XAO].
XAO:0000235
cardiogenic splanchnopleure
EHDAA2:0000214
cardiac mesoderm
XAO:0000235
cardiogenic mesoderm
cardiogenic region
heart primordia
XAO:0000235
Organism at the cleavage stage.
BILA:0000058
uberon
UBERON:0007010
cleaving embryo
Organism at the cleavage stage.
OBOL:automatic
The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis
BILA:0000084
NCIT:C34268
UMLS:C1514442
future digestive tract
future digestive tube
future gut
primitive gut
uberon
embryonic digestive tube
primordial digestive tube
primordial gut
UBERON:0007026
presumptive gut
The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis
NCBIBook:NBK10107
UMLS:C1514442
ncithesaurus:Primordial_Gut
Cranial neural crest that migrates into the mandibular arch.
TAO:0007064
XAO:0000024
ZFA:0007064
uberon
UBERON:0007098
mandibular neural crest
ZFA
ZFA
Cranial neural crest that migrates into the mandibular arch.
ZFA:0007064
A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified].
note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis
FBbt:00003154
SPD:0000130
TADS:0000147
dorsal tube
heart
uberon
adult heart
UBERON:0007100
Gene notes: Bmp, Nkx, Gata
primary circulatory organ
A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified].
GO:0007507
dorsal tube
heart
GO:0007507
adult heart
FBbt:00003154
An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section.
An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO]
EFO:0003497
TAO:0000131
ZFA:0000131
uberon
presumptive central nervous system
UBERON:0007135
neural keel
An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section.
ZFIN:ZDB-PUB-961014-576
An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO]
2012-08-14
TAO:0000131
TAO
ZFIN:curator
presumptive central nervous system
ZFA:0000131
A mesothelium that is part of a serous pericardium.
BTO:0003157
EMAPA:16133
FMA:18149
mesothelium of pericardium
pericardial mesothelium
serous pericardium mesothelium
uberon
UBERON:0007188
mesothelium of serous pericardium
A mesothelium that is part of a serous pericardium.
OBOL:automatic
mesothelium of pericardium
FMA:18149
pericardial mesothelium
FMA:18149
serous pericardium mesothelium
FMA:18149
Mesenchyme that develops_from a cranial neural crest.
EFO:0003572
EHDAA2:0000735
EMAPA:16169
EMAPA:16271
EMAPA_RETIRED:16271
TAO:0000787
ZFA:0000787
head mesenchyme from cranial neural crest
head mesenchyme from neural crest
head neural crest derived mesenchyme
uberon
UBERON:0007213
mesenchyme derived from head neural crest
ZFA
Mesenchyme that develops_from a cranial neural crest.
OBOL:automatic
head mesenchyme from neural crest
EHDAA2:0000735
relationship to Meckel's cartilage to be added
Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG]
EHDAA2:0000031
EHDAA:583
EMAPA:16382
VHOG:0000510
ventral pharyngeal arch 1
uberon
ventral mandibular arch
ventral visceral arch 1
UBERON:0007237
1st arch mandibular component
EHDAA2
Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG]
2012-09-17
VHOG:0000510
VHOG
DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)
ventral pharyngeal arch 1
VHOG:0000510
ventral mandibular arch
VHOG:0000510
ventral visceral arch 1
VHOG:0000510
A tunica media that is part of a artery.
EMAPA:36294
EV:0100029
FMA:14273
NCIT:C49321
UMLS:C1710627
arterial media
tunica media (arteriae)
uberon
UBERON:0007239
tunica media of artery
A tunica media that is part of a artery.
OBOL:automatic
UMLS:C1710627
ncithesaurus:Venous_System_Smooth_Muscle_Tissue
arterial media
EV:0100029
tunica media (arteriae)
FMA:14273
A tunica adventitia that is part of a artery.
EMAPA:36295
EV:0100030
FMA:14274
arterial adventitia
tunica externa (adventitia)(arteriae)
uberon
UBERON:0007240
tunica adventitia of artery
A tunica adventitia that is part of a artery.
OBOL:automatic
arterial adventitia
EV:0100030
tunica externa (adventitia)(arteriae)
FMA:14274
A tunica adventitia that is part of a vein.
EMAPA:36310
EV:0100034
FMA:14355
tunica externa (adventitia)(venae)
venous adventitia
uberon
UBERON:0007241
tunica adventitia of vein
A tunica adventitia that is part of a vein.
OBOL:automatic
tunica externa (adventitia)(venae)
FMA:14355
venous adventitia
EV:0100034
A tunica intima that is part of a vein.
EMAPA:36308
EV:0100032
FMA:14353
tunica interna (intima)(venae)
venous intima
uberon
UBERON:0007242
tunica intima of vein
A tunica intima that is part of a vein.
OBOL:automatic
tunica interna (intima)(venae)
FMA:14353
venous intima
EV:0100032
A tunica media that is part of a vein.
EMAPA:36309
EV:0100033
FMA:14354
tunica media (venae)
venous media
uberon
UBERON:0007243
tunica media of vein
A tunica media that is part of a vein.
OBOL:automatic
tunica media (venae)
FMA:14354
venous media
EV:0100033
The rhombencephalon (or hindbrain) is a developmental categorization of portions of the central nervous system in vertebrates. The rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. In the human embryo eight rhombomeres can be distinguished, from caudal to rostral: Rh7-Rh1 and the isthmus (the most rostral rhombomere). A rare disease of the rhombencephalon, 'rhombencephalosynapsis' is characterized by a missing vermis resulting in a fused cerebellum. Patients generally present with cerebellar ataxia. The caudal rhombencephalon has been generally considered as the initiation site for neural tube closure.
TODO - unify naming conventions
The embryonic rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. Rhombomeres Rh7-Rh4 form the myelencephalon that will give the medulla oblongata. Rhombomeres Rh3-Rh1 form the metencephalon that will form the pons and the cerebellum[NPX:PDR].
BAMS:HB
CALOHA:TS-2118
EFO:0003440
EHDAA2:0001630
FMA:295640
TAO:0000569
ZFA:0000569
presumptive rhombencephalon
uberon
embryonic rhombencephalon
future hindbrain
rhombencephalon
UBERON:0007277
presumptive hindbrain
XAO-abduced
cjm
The rhombencephalon (or hindbrain) is a developmental categorization of portions of the central nervous system in vertebrates. The rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. In the human embryo eight rhombomeres can be distinguished, from caudal to rostral: Rh7-Rh1 and the isthmus (the most rostral rhombomere). A rare disease of the rhombencephalon, 'rhombencephalosynapsis' is characterized by a missing vermis resulting in a fused cerebellum. Patients generally present with cerebellar ataxia. The caudal rhombencephalon has been generally considered as the initiation site for neural tube closure.
The embryonic rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. Rhombomeres Rh7-Rh4 form the myelencephalon that will give the medulla oblongata. Rhombomeres Rh3-Rh1 form the metencephalon that will form the pons and the cerebellum[NPX:PDR].
NPX:PDR
presumptive rhombencephalon
ZFA:0000569
embryonic rhombencephalon
CALOHA:TS-2118
future hindbrain
rhombencephalon
EHDAA2:0001630
A presumptive structure that has the potential to develop into a endocardium.
Portion of tissue that is part of the heart tube and will become the endocardium.[TAO]
TAO:0002233
ZFA:0001724
uberon
UBERON:0007280
presumptive endocardium
A presumptive structure that has the potential to develop into a endocardium.
OBOL:automatic
Portion of tissue that is part of the heart tube and will become the endocardium.[TAO]
2012-08-14
TAO:0002233
TAO
ZFIN:curator
Embryonic structure that gives rise to the midbrain hindbrain boundary.
EFO:0003446
TAO:0001187
XAO:0004086
ZFA:0001187
presumptive MHB
presumptive midbrain-hindbrain boundary
uberon
UBERON:0007281
presumptive midbrain hindbrain boundary
ZFA
Embryonic structure that gives rise to the midbrain hindbrain boundary.
ZFA:0001187
presumptive MHB
presumptive midbrain-hindbrain boundary
ZFA:0001187
A presumptive structure that has the potential to develop into a presomitic mesoderm.
EFO:0003421
TAO:0000053
ZFA:0000053
uberon
presumptive segmental plates
UBERON:0007282
presumptive segmental plate
https://github.com/obophenotype/uberon/wiki/The-neural-crest
EDHAA2
A presumptive structure that has the potential to develop into a presomitic mesoderm.
OBOL:automatic
presumptive segmental plates
ZFA:0000053
A presumptive structure that has the potential to develop into a neural plate.
consider merging
Region of the gastrula which gives rise to the neural plate.[TAO]
EFO:0003424
TAO:0000063
ZFA:0000063
prospective neuroectoderm
prospective vegetal ectoderm
uberon
UBERON:0007284
presumptive neural plate
A presumptive structure that has the potential to develop into a neural plate.
OBOL:automatic
Region of the gastrula which gives rise to the neural plate.[TAO]
2012-08-14
TAO:0000063
TAO
ZFIN:curator
prospective neuroectoderm
ZFA:0000063
prospective vegetal ectoderm
ZFA:0000063
The part of the blastula that has the potential to develop into a paraxial mesoderm.
EFO:0003443
TAO:0000591
XAO:0004134
ZFA:0000591
future paraxial mesenchyme
future paraxial mesoderm
uberon
UBERON:0007285
presumptive paraxial mesoderm
The part of the blastula that has the potential to develop into a paraxial mesoderm.
UBERON:cjm
future paraxial mesenchyme
UBERON:cjm
A vasculature that is part of a chordate pharynx.
TAO:0005003
ZFA:0005003
branchial vasculature
uberon
UBERON:0007303
pharyngeal vasculature
A vasculature that is part of a chordate pharynx.
OBOL:automatic
branchial vasculature
ZFA:0005003
The epidermis is the entire outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species[GO].
this grouping class exists primarily to align with GO - see GO:0008544.
BSA:0000073
BTO:0000313
FBbt:00004993
HAO:0000298
TADS:0000109
WBbt:0005733
epidermis
epidermis (sensu Metazoa)
outer epidermal layer
outer epithelial layer
uberon
hypoderm
hypodermis
UBERON:0007376
outer epithelium
The epidermis is the entire outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species[GO].
GO:0008544
epidermis
GO:0008544
hypoderm
BTO:0000313
hypodermis
GO:0008544
WBbt:0005733
Outermost layer of cells surrounding the embryo.
Outermost monolayer of cells surrounding the embryo that become very flattened in the blastula and give rise to the periderm. Sometimes used synonymously with periderm. Kimmel et al, 1995.[TAO]
relationship loss: develops_from superficial blastomere (TAO:0001484)[TAO]
Originally this tissue is one cell layer thick but in most vertebrates it soon becomes a two layered structure. The outer layer gives rise to the periderm.
EFO:0003425
TAO:0000086
ZFA:0000086
EVL
enveloping layer
uberon
UBERON:0007383
enveloping layer of ectoderm
Outermost layer of cells surrounding the embryo.
Outermost monolayer of cells surrounding the embryo that become very flattened in the blastula and give rise to the periderm. Sometimes used synonymously with periderm. Kimmel et al, 1995.[TAO]
2012-08-14
TAO:0000086
TAO
ZFIN:curator
relationship loss: develops_from superficial blastomere (TAO:0001484)[TAO]
2012-08-14
TAO:0000086
TAO
EVL
ZFA:0000086
enveloping layer
ZFIN:ZDB-PUB-961014-576
Acellular anatomical structure whose predominant constituent is chitin.
EHDAA2:0003100
AEO:0000100
EHDAA2:0003100
uberon
UBERON:0007491
chitin-based acellular structure
Acellular anatomical structure whose predominant constituent is chitin.
AEO:JB
An epithelial tube open at both ends that allows fluid flow.
AEO_RETIRED:0000116
RETIRED_EHDAA2:0003116
uberon
UBERON:0007500
epithelial tube open at both ends
AEO
An epithelial tube open at both ends that allows fluid flow.
AEO:JB
UBERONREF:0000001
A closed epithelium with a lumen.
EHDAA2:0003119
AEO:0000119
EHDAA2:0003119
uberon
UBERON:0007503
epithelial vesicle
AEO
A closed epithelium with a lumen.
AEO:JB
Mesenchyme with little extracellular matrix.
EHDAA2:0003146
AEO:0000146
EHDAA2:0003146
uberon
UBERON:0007524
dense mesenchyme tissue
AEO
Mesenchyme with little extracellular matrix.
AEO:JB
Mesenchymal cells that are migrating.
this class will be an important part of the NC reorganization
EHDAA2:0003152
AEO:0000152
EHDAA2:0003152
uberon
UBERON:0007530
migrating mesenchyme population
Mesenchymal cells that are migrating.
AEO:JB
A thin, loose vascular connective tissue that makes up the membranes surrounding joints and the sheaths protecting tendons (particularly flexor tendons in the hands and feet) where they pass over bony prominences. Synovial tissue contains synovial cells, which secrete a viscous liquid called synovial fluid; this liquid contains protein and hyaluronic acid and serves as a lubricant and nutrient for the joint cartilage surfaces[BTO]. Synovial tissue can be found in tendons (tissues that connect muscle to bone), bursae (fluid-filled, cushioning sacs found in spaces between tendons, ligaments, and bones), and the cavity (hollow enclosed area) that separates the bones of a freely movable joint, such as the knee or elbow[BTO].
BTO:0001338
CALOHA:TS-0998
FMA:66762
synovium
stratum synoviale
synovial layer
synovial membrane
uberon
synovial tissue
UBERON:0007616
layer of synovial tissue
BTO
A thin, loose vascular connective tissue that makes up the membranes surrounding joints and the sheaths protecting tendons (particularly flexor tendons in the hands and feet) where they pass over bony prominences. Synovial tissue contains synovial cells, which secrete a viscous liquid called synovial fluid; this liquid contains protein and hyaluronic acid and serves as a lubricant and nutrient for the joint cartilage surfaces[BTO]. Synovial tissue can be found in tendons (tissues that connect muscle to bone), bursae (fluid-filled, cushioning sacs found in spaces between tendons, ligaments, and bones), and the cavity (hollow enclosed area) that separates the bones of a freely movable joint, such as the knee or elbow[BTO].
BTO:0001338
synovium
CALOHA:TS-0998
stratum synoviale
FMA:TA
synovial layer
FMA:66762
synovial membrane
FMA:66762
synovial tissue
BTO:0001338
An anatomical cavity that surrounded_by a synovial joint.
FMA:11356
articular cavity (synovial joint)
cavitas articularis (junctura synovialis)
cavity of synovial joint
uberon
joint cavity
synovial cavity
UBERON:0007617
synovial cavity of joint
An anatomical cavity that surrounded_by a synovial joint.
OBOL:automatic
articular cavity (synovial joint)
FMA:11356
cavitas articularis (junctura synovialis)
FMA:11356
cavity of synovial joint
FMA:11356
joint cavity
FMA:11356
synovial cavity
FMA:11356
epithelial layer of the retina, ciliary body, or iris composed of cells containing pigment granules.
GAID:907
MESH:D010857
uberon
eye pigment epithelium
UBERON:0007625
pigment epithelium of eye
epithelial layer of the retina, ciliary body, or iris composed of cells containing pigment granules.
MP:0005200
eye pigment epithelium
MESH:A09.371.670
2
An anatomical structure that connects two structures
junction
FMA:5898
anatomical junction
uberon
UBERON:0007651
anatomical junction
FMA
An anatomical structure that connects two structures
Anlagen are populations of contiguous cells, typically arranged in one plane, that are morphologically indistinct, but that already correspond in extent to a later organ/tissue.
field
AEO:0000170
EFO:0001649
EHDAA2:0003170
FBbt:00005426
developmental field
uberon
future organ
organ field
UBERON:0007688
anlage
FBbt
AEO
FBbt
Anlagen are populations of contiguous cells, typically arranged in one plane, that are morphologically indistinct, but that already correspond in extent to a later organ/tissue.
FBbt:00005426
JB:DEF
.
EFO:0003626
EHDAA2:0001457
EHDAA:962
EMAPA:32754
FMA:293087
TAO:0001104
ZFA:0001104
early pharyngeal arch endoderm
uberon
pharyngeal arch endoderm
pharyngeal endoderm
pharyngeal region endoderm
UBERON:0007690
relation conflict: ZFA vs EHDAA2. Note EHDAA2 term renamed to 'early PA endoderm'
early pharyngeal endoderm
cjm
.
early pharyngeal arch endoderm
EHDAA2:0001457
pharyngeal endoderm
ZFA:0001104
pharyngeal region endoderm
EHDAA2:0001456
A bone that is part of a reproductive organ.
baculum
uberon
os penis/os clitoris
UBERON:0007719
bone of reproductive organ
A bone that is part of a reproductive organ.
OBOL:automatic
A gland that is part of a epidermis.
FMA:59153
epidermal gland
gland of epidermis
uberon
UBERON:0007771
epidermis gland
A gland that is part of a epidermis.
OBOL:automatic
gland of epidermis
FMA:59153
Any bodily fluid that has passed through a membrane such as the capillary wall, as a result of unbalanced hydrostatic and osmotic forces
transudative
characteristically low in protein and cellular content (unless there has been secondary concentration)
FMA:12276
GAID:1195
MESH:D005122
ncithesaurus:Transudate
uberon
plasma ultrafiltrate
UBERON:0007779
transudate
Any bodily fluid that has passed through a membrane such as the capillary wall, as a result of unbalanced hydrostatic and osmotic forces
Any fluid produced by a serous gland.
serous fluid
serosal fluid
serous gland fluid
uberon
UBERON:0007794
secretion of serous gland
Any fluid produced by a serous gland.
UBERON:cjm
serosal fluid
Anatomical system that consists of all blood and lymph vessels.
consider merging with vasculature
The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System].
in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system
BTO:0001085
CALOHA:TS-2053
EHDAA2:0004520
EMAPA:35905
MA:0002718
NCIT:C33854
UMLS:C0489903
uberon
Gefaesssystem@de
UBERON:0007798
vascular system
MA
Anatomical system that consists of all blood and lymph vessels.
The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System].
ncithesaurus:Vascular_System
in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system
MA
UMLS:C0489903
ncithesaurus:Vascular_System
Gefaesssystem@de
BTO:0001085
The anteriormost subdivision of the body that includes the head, jaws, pharyngeal region and the neck (if present). In vertebrates this is the subdivision that includes the cervical vertebrae.
CALOHA:TS-2356
EV:0100009
FMA:280881
MA:0000006
NCIT:C12418
UMLS:C0460004
WikipediaCategory:Head_and_neck
galen:HeadAndNeck
uberon
cephalic area
cephalic part of animal
cephalic region
head and neck
head or neck
UBERON:0007811
craniocervical region
MA
The anteriormost subdivision of the body that includes the head, jaws, pharyngeal region and the neck (if present). In vertebrates this is the subdivision that includes the cervical vertebrae.
UMLS:C0460004
ncithesaurus:Head_and_Neck
cephalic area
cephalic part of animal
cephalic region
head and neck
FMA:280881
Bone element that arises as a result of intramembranous ossification.
Bone element that arises as a result of intramembranous ossification.[VSAO]
Intramembranous bone that forms deep in the organism.[TAO]
AEO:0000085
EHDAA2:0003085
TAO:0001645
VSAO:0000023
XAO:0004014
ZFA:0001636
uberon
membrane bones
UBERON:0007842
membrane bone
VSAO
Bone element that arises as a result of intramembranous ossification.
GO_REF:0000034
VSAO:0000023
Bone element that arises as a result of intramembranous ossification.[VSAO]
2012-08-14
VSAO:0000023
VSAO
GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070
PSPUB:0000170
Intramembranous bone that forms deep in the organism.[TAO]
2012-08-14
TAO:0001645
TAO
TAO:wd
membrane bones
ZFA:0001636
Skeletal element that is composed of cartilage tissue and may be permanent or transient.
TAO still mixes tissue and element
AAO:0011130
CALOHA:TS-0118
EMAPA:32730
FMA:55107
VSAO:0000000
XAO:0004013
ZFA:0001501
cartilage organ
cartilaginous element
chondrogenic element
uberon
cartilage
UBERON:0007844
cartilage element
VSAO
VSAO
VSAO
Skeletal element that is composed of cartilage tissue and may be permanent or transient.
GO_REF:0000034
PSPUB:0000170
VSAO:0000000
TAO still mixes tissue and element
TAO
cartilage organ
FMA:55107
cartilaginous element
chondrogenic element
VSAO:0000000
cartilage
VSAO:0000000
Connective tissue, which consists of fibroblasts, the intercellular matrix of which contains a regular network of collagen and elastic fiber bundles. Examples: bone (tissue), cartilage (tissue), dense regular connective tissue.
the connective tissue hierarchy largely follows FMA with definitions from VSAO. Note that in FMA, loose-CT is irregular-CT. This means regular-CT is necessarily equivalent to dense-regular-CT (assuming a JEPD classification).
FMA:20103
uberon
UBERON:0007845
regular connective tissue
FMA
Connective tissue, which consists of fibroblasts, the intercellular matrix of which contains a regular network of collagen and elastic fiber bundles. Examples: bone (tissue), cartilage (tissue), dense regular connective tissue.
FMA:20103
Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts).
Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts).[VSAO]
Regular connective tissue, the intercellular matrix of which consists predominantly of collagen fiber bundles arranged in parallel arrays.[FMA]
FMA:64781
NCIT:C33453
UMLS:C0225333
VSAO:0000050
XAO:0004030
dense fibrous connective tissue
dense regular collagenous connective tissue
dense regular collagenous tissue
regular dense connective tissue
typus regularis (textus connectivus collagenosus compactus)
uberon
UBERON:0007846
dense regular connective tissue
FMA
ncithesaurus
Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts).
GO_REF:0000034
PSPUB:0000170
VSAO:0000050
Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts).[VSAO]
2012-08-14
VSAO:0000050
VSAO
GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070
PSPUB:0000170
Regular connective tissue, the intercellular matrix of which consists predominantly of collagen fiber bundles arranged in parallel arrays.[FMA]
2012-08-29
FMA:64781
FMA
UMLS:C0225333
ncithesaurus:Regular_Dense_Connective_Tissue
dense fibrous connective tissue
FMA:64781
dense regular collagenous connective tissue
FMA:64781
dense regular collagenous tissue
FMA:64781
typus regularis (textus connectivus collagenosus compactus)
FMA:64781
A bone that is part of a craniocervical region.
EMAPA:37245
MA:0000569
head or neck bone
uberon
cranial bone
UBERON:0007914
bone of craniocervical region
MA
MA
A bone that is part of a craniocervical region.
OBOL:automatic
EMAPA:37245
MA:th
head or neck bone
MA:0000569
A anatomical surface that is part of a cartilage element.
FMA:76668
cartilage surface
uberon
UBERON:0008115
surface of cartilage
A anatomical surface that is part of a cartilage element.
OBOL:automatic
cartilage surface
FMA:76668
Musculature system of the pharyngeal and head regions.
in MA this is restricted to skeletal muscles
EMAPA:37259
MA:0000571
TAO:0000328
ZFA:0000328
head or neck muscle
uberon
head muscles
head or neck muscle
UBERON:0008229
craniocervical region musculature
MA
MA
Musculature system of the pharyngeal and head regions.
ZFA:0000328
ZFA:curator
in MA this is restricted to skeletal muscles
MA
EMAPA:37259
MA:th
head or neck muscle
MA:0000571
head muscles
ZFA:0000328
head or neck muscle
MA:0000571
An endothelium that is part of a heart [Automatically generated definition].
this class includes any endothelia that are part of the heart. This might include the endocardial epithelia, as well as endothelia of vessels that are considered strictly part of the heart (e.g. outflow tract). As a grouping class, this may lack utility, and pending review this class may be obsoleted. For annotation consider a more specific class.
BTO:0004293
uberon
cardiac endothelium
UBERON:0008307
heart endothelium
An endothelium that is part of a heart [Automatically generated definition].
OBOL:automatic
cardiac endothelium
BTO:0004293
A transient embryonic complex that comprises the pharyngeal arches, bulges of tissues of mesoderm and neural crest derivation through which pass nerves and pharyngeal arch arteries. The arches are separated internally by pharyngeal pouches, evaginations of foregut endoderm, and externally by pharyngeal clefts, invaginations of surface ectoderm. The development of the system ends when the stucture it contributes to are forming, which may include (depending on species) the thymus, thyroid, parathyroids, maxilla, mandible, aortic arch, cardiac outflow tract, external and middle ear[GO,modified].
Currently defined in a vertebrate specific manner. The arch system has origins in basal deuterostomes, consider generalizing
EHDAA2:0000187
FMA:293041
NCIT:C34248
UMLS:C1519038
embryonic pharyngeal complex
pharyngeal apparatus
pharyngeal system
uberon
pharyngeal arch complex
pharyngeal arch region
pharyngeal arches and clefts
pharyngeal complex
UBERON:0008814
pharyngeal arch system
A transient embryonic complex that comprises the pharyngeal arches, bulges of tissues of mesoderm and neural crest derivation through which pass nerves and pharyngeal arch arteries. The arches are separated internally by pharyngeal pouches, evaginations of foregut endoderm, and externally by pharyngeal clefts, invaginations of surface ectoderm. The development of the system ends when the stucture it contributes to are forming, which may include (depending on species) the thymus, thyroid, parathyroids, maxilla, mandible, aortic arch, cardiac outflow tract, external and middle ear[GO,modified].
GO:0060037
GOC:dph
UMLS:C1519038
ncithesaurus:Pharyngeal_Apparatus
pharyngeal system
GO:0060037
pharyngeal arch region
EHDAA2:0000187
A head that is part of a embryo.
CALOHA:TS-0246
FBbt:00000155
FMA:293011
uberon
UBERON:0008816
embryonic head
A head that is part of a embryo.
OBOL:automatic
A brain that develops_from a neural tube.
a reasoner should automatically classify all the vertebrate ontology brain classes here
vertebrate brain
uberon
UBERON:0008823
neural tube derived brain
https://github.com/obophenotype/uberon/issues/338
ZFA
FMA
A brain that develops_from a neural tube.
OBOL:automatic
Any skeletal muscle organ in the hypodermis / superficial fascia
We follow MP and treat this as part of the hypodermis, although some sources may consider the hypodermis to be superficial to this
UBERON:0010934
EMAPA:18188
MA:0003140
hypodermal muscle layer
hypodermis muscle layer
superficial fascia muscular layer
panniculus carnosus
uberon
UBERON:0008876
hypodermis skeletal muscle layer
MP-def
Any skeletal muscle organ in the hypodermis / superficial fascia
ISBN:0123813611
MP:0011157
hypodermal muscle layer
MP:0011157
hypodermis muscle layer
MP:0011157
panniculus carnosus
MP:0011157
Subdivision of endoskeleton derived from pharyngeal arches
Anatomical cluster that is part of the cranium and consists of the jaws, hyoid and branchial arches.[TAO]
Anatomical cluster that is part of the cranium and consists of the jaws, hyoid, and branchial arches.[AAO]
The part of the skull derived from the embryonic pharyngeal arches. [Biology_Online][VHOG]
The skull of ancestral tetrapods has the three basic components that we have been considering: (1) chondrocranium, (2) splanchnocranium, and (3) dermatocranium (reference 1); Each part of the skull arises from a separate phylogenetic source. The most ancient part is the splanchnocranium (visceral cranium), which first arose to support pharyngeal slits in protochordates (reference 2).[well established][VHOG]
VSAO labels this term 'pharyngeal arch' (2012-06-01) - however, it clearly means pharyngeal arch skeleton.
many sources define this as the part of the endoskeletal that is from pharyngeal arches - this would make it part-disjoint from dermatocranium. However, there are many bones in AOs that have part-paths to both
AAO:0010157
TAO:0001216
VHOG:0000315
VSAO:0000149
XAO:0003176
ZFA:0001216
pharyngeal endoskeleton
viscerocranium
uberon
branchial arch skeleton
gill arch skeleton
pharyngeal arch
pharyngeal arch skeleton
pharyngeal skeleton
visceral cranium
visceral skeletal system
visceral skeleton
UBERON:0008895
splanchnocranium
http://upload.wikimedia.org/wikipedia/commons/7/77/Illu_facial_bones.jpg
redundant
Grays
Subdivision of endoskeleton derived from pharyngeal arches
ISBN:0073040584
Anatomical cluster that is part of the cranium and consists of the jaws, hyoid and branchial arches.[TAO]
2012-08-14
TAO:0001216
TAO
ZFIN:curator
Anatomical cluster that is part of the cranium and consists of the jaws, hyoid, and branchial arches.[AAO]
2012-06-20
AAO:0010157
AAO
AAO:EJS
The part of the skull derived from the embryonic pharyngeal arches. [Biology_Online][VHOG]
2012-09-17
VHOG:0000315
VHOG
The skull of ancestral tetrapods has the three basic components that we have been considering: (1) chondrocranium, (2) splanchnocranium, and (3) dermatocranium (reference 1); Each part of the skull arises from a separate phylogenetic source. The most ancient part is the splanchnocranium (visceral cranium), which first arose to support pharyngeal slits in protochordates (reference 2).[well established][VHOG]
2012-09-17
VHOG:0000315
VHOG
ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.242, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.235
VSAO labels this term 'pharyngeal arch' (2012-06-01) - however, it clearly means pharyngeal arch skeleton.
VSAO
pharyngeal endoskeleton
viscerocranium
VHOG:0000315
ZFA:0001216
pharyngeal arch
VSAO:0000149
pharyngeal arch skeleton
ZFA:0001216
pharyngeal skeleton
ZFA:0001216
visceral cranium
visceral skeletal system
visceral skeleton
UBERONREF:0000007
Skeletal element that forms superficially in the organism, usually in association with the ectoderm[VSAO].
Intramembranous bone that forms superficially in the organism.[TAO]
other AOs are not yet in sync with this classification
AAO:0010769
TAO:0001590
VSAO:0000130
XAO:0004015
ZFA:0001590
uberon
dermal bones
UBERON:0008907
dermal bone
wd
VSAO
VSAO
Skeletal element that forms superficially in the organism, usually in association with the ectoderm[VSAO].
GO_REF:0000034
VSAO:0000130
Intramembranous bone that forms superficially in the organism.[TAO]
2012-08-14
TAO:0001590
TAO
TAO:wd
dermal bones
ZFA:0001590
Bone element that is adjacent to the notochord.
We go with the latest VSAO in making this a subtype of bone, and add a logical definition based on the textual definition in VSAO. We also include the subtyping under 'replacement bone', for consistency with ZFA
Replacement bone that forms within the connective tissue surrounding the notochord.[TAO]
AAO:0010777
TAO:0001639
VSAO:0000307
ZFA:0001629
perichordal bones
uberon
perichordal bone
UBERON:0008909
perichordal bone
not in VSAO
ZFA
Bone element that is adjacent to the notochord.
GO_REF:0000034
VSAO:0000307
Replacement bone that forms within the connective tissue surrounding the notochord.[TAO]
2012-08-14
TAO:0001639
TAO
TAO:wd
perichordal bones
ZFA:0001629
perichordal bone
ZFA:0001629
System pertaining to blood vessels in the brain.
UBERON:0005284
BTO:0003840
EFO:0003491
EMAPA:35186
FMA:242007
FMA:61935
TAO:0000099
ZFA:0000099
brain vasculature
cerebrovascular system
intracerebral vasculature
uberon
UBERON:0008998
vasculature of brain
System pertaining to blood vessels in the brain.
BTO:0003840
cerebrovascular system
BTO:0003840
intracerebral vasculature
FMA:61935
A vein that is part of a craniocervical region.
EHDAA2:0004542
craniocervical vein
head and neck veins
vein of head and neck
uberon
UBERON:0009141
craniocervical region vein
A vein that is part of a craniocervical region.
OBOL:automatic
head and neck veins
EHDAA2:0004542
Sum total of mesenchyme in the embryo.
consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)
UBERON:0003313
EHDAA2:0001113
EHDAA:177
EMAPA:16097
uberon
UBERON:0009142
entire embryonic mesenchyme
EHDAA2
Sum total of mesenchyme in the embryo.
EMAPA:16549
RETIRED_EHDAA2:0001454
pharyngeal region
uberon
UBERON:0009145
pharyngeal region of foregut
EHDAA2
pharyngeal region
EMAPA:16549
An ectoderm that is part of a buccopharyngeal membrane.
EHDAA2:0000190
EMAPA:16260
uberon
UBERON:0009479
ectoderm of buccopharyngeal membrane
An ectoderm that is part of a buccopharyngeal membrane.
OBOL:automatic
An endoderm that is part of a buccopharyngeal membrane.
EHDAA2:0000191
EMAPA:16261
uberon
UBERON:0009480
endoderm of buccopharyngeal membrane
An endoderm that is part of a buccopharyngeal membrane.
OBOL:automatic
A portion of mesenchymal tissue associated with an individual pharyngeal arch.
this represents a part of the entire arch mesenchyme (UBERON:0010046), and is therefore a superclass of the individual arch mesenchyme classes. Alternate definition: primordial embryonic connective tissue associated with the branchial arches, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to facial and cranial nerve-associated structures.
EMAPA:32755
FMA:295694
branchial arch mesenchyme
pharyngeal arch mesenchyme
uberon
UBERON:0009494
pharyngeal arch mesenchymal region
EHDAA2
cjm
A portion of mesenchymal tissue associated with an individual pharyngeal arch.
this represents a part of the entire arch mesenchyme (UBERON:0010046), and is therefore a superclass of the individual arch mesenchyme classes. Alternate definition: primordial embryonic connective tissue associated with the branchial arches, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to facial and cranial nerve-associated structures.
MP:0011262
branchial arch mesenchyme
MP:0011262
pharyngeal arch mesenchyme
FMA:25054
region of trunk
trunk subdivision
uberon
UBERON:0009569
subdivision of trunk
region of trunk
FMA:25054
trunk subdivision
FMA:25054
EHDAA2:0001172
EMAPA:16977
VHOG:0000910
mantle layer lateral wall midbrain
midbrain lateral wall mantle layer
uberon
mantle layer lateral wall mesencephalon
UBERON:0009581
midbrain mantle layer
mantle layer lateral wall midbrain
VHOG:0000910
mantle layer lateral wall mesencephalon
VHOG:0000910
EMAPA:17580
VHOG:0000911
mantle layer lateral wall spinal cord
spinal cord lateral wall mantle layer
uberon
UBERON:0009583
spinal cord mantle layer
mantle layer lateral wall spinal cord
VHOG:0000911
Mesenchyme that is part of a 1st arch mandibular component.
UBERON:0010043
EHDAA2:0000034
EMAPA:16385
mesenchymal region of mandibular component of first pharyngeal arch
mesenchyme of mandibular component
uberon
mandibular component mesenchyme
mandibular mesenchyme
UBERON:0009584
1st arch mandibular mesenchyme
EMAPA
Mesenchyme that is part of a 1st arch mandibular component.
OBOL:automatic
mesenchymal region of mandibular component of first pharyngeal arch
mesenchyme of mandibular component
EMAPA:16385
A neural plate that develops_from a presumptive midbrain.
TAO:0007019
ZFA:0007019
uberon
UBERON:0009611
midbrain neural plate
ZFA
ZFA
A neural plate that develops_from a presumptive midbrain.
OBOL:automatic
A neural plate that develops_from a presumptive hindbrain.
TAO:0007022
ZFA:0007022
uberon
UBERON:0009614
hindbrain neural plate
ZFA
ZFA
A neural plate that develops_from a presumptive hindbrain.
OBOL:automatic
TODO - developmental relationships for lines
TAO:0007044
ZFA:0007044
MHB neural plate
midbrain-hindbrain boundary neural plate
uberon
UBERON:0009615
midbrain hindbrain boundary neural plate
ZFA
https://github.com/obophenotype/uberon/issues/438
Bgee:AN
MHB neural plate
midbrain-hindbrain boundary neural plate
ZFA:0007044
A presumptive structure that has the potential to develop into a midbrain.
TODO - unify naming conventions
BAMS:MES
EFO:0003432
EHDAA2:0000615
EMAPA:16140
TAO:0000148
ZFA:0000148
presumptive mesencephalon
uberon
early midbrain
future midbrain
mesencephalon
UBERON:0009616
presumptive midbrain
ZFA
ZFA
A presumptive structure that has the potential to develop into a midbrain.
OBOL:automatic
presumptive mesencephalon
ZFA:0000148
early midbrain
future midbrain
mesencephalon
EHDAA2:0000615
Bilateral mesenchymal mesoderm parallel and immediately adjacent to the neural tube/notochord; it generates a subset of extra-ocular, and other head, muscles.
A major contributor to neurocranium [PMID:16313393]
EHDAA2:0000736
EHDAA:364
EMAPA:16171
cephalic paraxial mesenchyme
cephalic paraxial mesoderm
cranial paraxial mesenchyme
cranial paraxial mesoderm
head paraxial mesenchyme
uberon
somitomere
somitomeric mesoderm
UBERON:0009617
head paraxial mesoderm
Bilateral mesenchymal mesoderm parallel and immediately adjacent to the neural tube/notochord; it generates a subset of extra-ocular, and other head, muscles.
cephalic paraxial mesenchyme
cephalic paraxial mesoderm
cranial paraxial mesenchyme
cranial paraxial mesoderm
head paraxial mesenchyme
EHDAA2:0000736
EHDAA2:0002094
trunk and cervical paraxial mesenchyme
uberon
trunk paraxial mesenchyme
UBERON:0009618
trunk paraxial mesoderm
trunk and cervical paraxial mesenchyme
EHDAA2:0002094
trunk paraxial mesenchyme
An anatomical cavity that surrounded_by a stomodeum.
lumen of stomatodaeum
lumen of stomodeum
stomatodeal cavity
uberon
UBERON:0009715
stomodeal lumen
An anatomical cavity that surrounded_by a stomodeum.
OBOL:automatic
EHDAA2:0004621
EMAPA:32754
FMA:293087
uberon
pharyngeal arch endoderm
UBERON:0009722
entire pharyngeal arch endoderm
pharyngeal arch endoderm
EHDAA2:0004621
The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing cardiac structures
decide whether to merge with cardiac mesoderm. In EHDAA2 this lasts CS12->unbounded, includes mesenchyme of individual components as parts
EHDAA2:0004162
EMAPA:36438
heart mesenchyme
uberon
UBERON:0009751
cardiac mesenchyme
The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing cardiac structures
MP:0011264
heart mesenchyme
EMAPA:36438
The many-lobed berry cluster of cells that is the terminous of a gland where the secretion is produced is acinar in form.
acinar
acinus
FMA:55588
uberon
acini
UBERON:0009842
glandular acinus
http://upload.wikimedia.org/wikipedia/commons/9/99/Gray1105.png
The many-lobed berry cluster of cells that is the terminous of a gland where the secretion is produced is acinar in form.
acinus
FMA:55588
acini
EFO:0003704
TAO:0005041
ZFA:0005041
ALPM
uberon
UBERON:0009881
anterior lateral plate mesoderm
ZFA
ALPM
ZFA:0005041
Mesenchyme that is part of a developing face.
EMAPA:35337
FMA:302884
face mesenchyme
mesenchyme of face
uberon
UBERON:0009891
facial mesenchyme
Mesenchyme that is part of a developing face.
OBOL:automatic
EHDAA2:0001315
EHDAA:1122
uberon
UBERON:0009920
optic neural crest
EHDAA2
A multicellular organism that existence_starts_with a post-embryonic stage.
MA:0002405
postnatal organism
TS28 mouse
post-hatching organism
post-natal organism
postnatal mouse
uberon
UBERON:0009953
post-embryonic organism
https://github.com/obophenotype/uberon/issues/667
A multicellular organism that existence_starts_with a post-embryonic stage.
OBOL:automatic
TS28 mouse
MA:0002405
post-hatching organism
post-natal organism
postnatal mouse
MA:0002405
An anatomical structure that has more than one cell as a part.
CARO:0010000
FBbt:00100313
multicellular structure
uberon
UBERON:0010000
multicellular anatomical structure
CARO
An anatomical structure that has more than one cell as a part.
CARO:0010000
multicellular structure
FBbt:00100313
Mesenchyme that is part of a pharyngeal arch 1.
EMAPA:16128
mesenchyme of 1st arch
uberon
UBERON:0010042
1st arch mesenchyme
Mesenchyme that is part of a pharyngeal arch 1.
OBOL:automatic
mesenchyme of 1st arch
EMAPA:16128
The sum total of mesenchymal tissue in the pharyngeal arch region. Pharyngeal mesenchyme is undifferentiated, loose connective tissue derived mostly from mesoderm, and also contains ectodermally derived neural crest cells.
EHDAA2:0001459
EMAPA:16550
XAO:0004524
associated mesenchyme of pharyngeal region
entire branchial arch associated mesenchyme
pharyngeal arch associated mesenchyme
uberon
UBERON:0010046
entire pharyngeal arch associated mesenchyme
EHDAA2
EHDAA2
cjm
The sum total of mesenchymal tissue in the pharyngeal arch region. Pharyngeal mesenchyme is undifferentiated, loose connective tissue derived mostly from mesoderm, and also contains ectodermally derived neural crest cells.
XAO:0004524
associated mesenchyme of pharyngeal region
EMAPA:16550
entire branchial arch associated mesenchyme
pharyngeal arch associated mesenchyme
EHDAA2:0001459
Gland of the epithelium lining the oral cavity. The most common are the salivary glands.
Note that Kardong classifies lacrimal glands here. EHDAA2 includes pituitary primordium, as this develops from oral mucosa
UBERON:0003293
EHDAA2:0001327
EHDAA:2181
EMAPA:16572
EMAPA:16723
VHOG:0000652
buccal gland
uberon
gland of oral opening
gland of oral region
mouth gland
oral cavity gland
oral region gland
UBERON:0010047
oral gland
Gland of the epithelium lining the oral cavity. The most common are the salivary glands.
ISBN:0073040584
Note that Kardong classifies lacrimal glands here. EHDAA2 includes pituitary primordium, as this develops from oral mucosa
EHDAA2
An epithelium consisting of cuboidal epithelial cells.
TODO - coordinate with CL, add cuboidal cell
in NCIT this is glandular
NCIT:C32415
UMLS:C0682577
uberon
UBERON:0010077
cuboidal epithelium
An epithelium consisting of cuboidal epithelial cells.
in NCIT this is glandular
NCIT
UMLS:C0682577
ncithesaurus:Cuboidal_Epithelium
Mesenchyme that has the potential to develop into a dermis.
check development
EHDAA2:0000598
uberon
UBERON:0010083
future dermis
EHDAA2
EHDAA2
XAO
Mesenchyme that has the potential to develop into a dermis.
OBOL:automatic
A developing anatomical structure that has the potential to develop into a myelencephalon.
EHDAA2:0000640
uberon
UBERON:0010096
future myelencephalon
A developing anatomical structure that has the potential to develop into a myelencephalon.
OBOL:automatic
Any portion of cardiac muscle tissue that is part of the conducting system of heart or the Purkinje fibers.
EHDAA2:0004528
FMA:83378
specialized conducting tissue of heart
specialized muscle tissue of heart
uberon
UBERON:0010131
conducting tissue of heart
Any portion of cardiac muscle tissue that is part of the conducting system of heart or the Purkinje fibers.
specialized conducting tissue of heart
FMA:83378
specialized muscle tissue of heart
FMA:83378
An anatomical cavity that surrounded_by a blood vessel.
FMA:312610
blood vessel lumen
uberon
UBERON:0010161
lumen of blood vessel
An anatomical cavity that surrounded_by a blood vessel.
OBOL:automatic
A roughly circular bulge in a surface.
requires review
AEO:0000205
EHDAA2:0003250
FMA:82506
uberon
UBERON:0010188
protuberance
FMA
A roughly circular bulge in a surface.
EHDAA2:0003250
An anatomical boundary that corresponds to some physical discontinuity.
CARO:0001004
uberon
UBERON:0010199
One might argue that all boundaries are actually fiat in the sense that there must be some fiat element at a fine enough scale of granularity. This ontology choses to ignore this issue as below the level of granularity relevant to anatomy. (DOS121102)
bona-fide anatomical boundary
CARO
An anatomical boundary that corresponds to some physical discontinuity.
CARO:0001004
Multi-tissue structure that is part of the heart tube and will become the cardiac atrium.
FMA:71005
TAO:0002228
ZFA:0001718
presumptive atrium heart tube
primordial atrium
primordial cardiac atrium
uberon
UBERON:0010227
future cardiac atrium
ZFA
Multi-tissue structure that is part of the heart tube and will become the cardiac atrium.
ZFA:0001718
presumptive atrium heart tube
ZFA:0001718
primordial atrium
FMA:71005
primordial cardiac atrium
FMA:71005
The core globe-shaped component of the camera-type eye.
See notes for camera-type eye
FMA:12513
MIAA:0000283
VHOG:0001616
bulbus oculi
eye globe
eyeball
uberon
eye
globe
UBERON:0010230
eyeball of camera-type eye
FMA
The core globe-shaped component of the camera-type eye.
UBERON:cjm
eye globe
VHOG:0001616
eyeball
FMA:12513
eye
globe
HP:0100886
MIAA:0000283
Mesenchyme that develops_from a neural crest and is part of a 1st arch mandibular mesenchyme.
EHDAA2:0000037
uberon
UBERON:0010252
1st arch mandibular mesenchyme from neural crest
inferred
Mesenchyme that develops_from a neural crest and is part of a 1st arch mandibular mesenchyme.
OBOL:automatic
Mesenchyme that develops_from a rhombencephalon neural crest.
EHDAA2:0004423
uberon
UBERON:0010258
mesenchyme from rhombencephalic neural crest
Mesenchyme that develops_from a rhombencephalon neural crest.
OBOL:automatic
Mesenchyme that develops_from a neural crest and is part of a 1st arch mesenchyme.
EMAPA:16129
mesenchyme derived from neural crest of mesenchyme of 1st arch
neural crest derived arch 1 mesenchyme
pharyngeal arch 1 mesenchyme from neural crest
uberon
branchial arch 1 mesenchyme from neural crest
UBERON:0010259
1st arch mesenchyme from neural crest
Mesenchyme that develops_from a neural crest and is part of a 1st arch mesenchyme.
OBOL:automatic
mesenchyme derived from neural crest of mesenchyme of 1st arch
EMAPA:16129
Portion of tissue that is dorsolateral to the floor plate and part of the midbrain.
DHBA:12322
EFO:0003567
EHDAA2:0004375
TAO:0000761
ZFA:0000761
basal plate midbrain
basal plate midbrain region
uberon
UBERON:0010285
midbrain basal plate
EHDAA2
EHDAA2
ZFA
Portion of tissue that is dorsolateral to the floor plate and part of the midbrain.
ZFA:0000761
basal plate midbrain
TAO:0000761
basal plate midbrain region
ZFA:0000761
Portion of neural tube that gives rise to the midbrain.
we follow ZFA in temporally dividing midbrain NT from presumptive midbrain, but in future this may be collapsed
TAO:0007039
ZFA:0007039
uberon
UBERON:0010286
midbrain neural tube
ZFA
Portion of neural tube that gives rise to the midbrain.
ZFA:0007039
.
uberon
UBERON:0010291
layer of sclera
cjm
.
An endothelium that is part of a sclera.
uberon
UBERON:0010294
scleral endothelium
Wikipedia
An endothelium that is part of a sclera.
OBOL:automatic
Mesenchyme surrounding the developing optic cup which develops into the sclera.
The mesenchyme surrounding the developing optic cup differentiates into the sclera, the dense fibrous coat of the eye.. http://www.ncbi.nlm.nih.gov/pubmed/16496288
uberon
UBERON:0010299
scleral mesenchyme
Mesenchyme surrounding the developing optic cup which develops into the sclera.
An epithelium that is part of a extraembryonic structure.
extra-embryonic epithelium
uberon
UBERON:0010303
extraembryonic epithelium
An epithelium that is part of a extraembryonic structure.
OBOL:automatic
Developing anatomical structure that develops into the eyeball and associated structures.
Multi-tissue structure that consists of the structures that develop into the retina and lens.[TAO]
TAO:0002201
ZFA:0001678
future eye
uberon
UBERON:0010312
immature eye
definitional
Developing anatomical structure that develops into the eyeball and associated structures.
ZFA:0001678
Multi-tissue structure that consists of the structures that develop into the retina and lens.[TAO]
2012-08-14
TAO:0002201
TAO
ZFIN:curator
An anatomical structure that develops from the neural crest.
Grouping term for query purposes
uberon
UBERON:0010313
neural crest-derived structure
An anatomical structure that develops from the neural crest.
An anatomical structure that has some part that develops from the neural crest.
Grouping term for query purposes
uberon
UBERON:0010314
structure with developmental contribution from neural crest
An anatomical structure that has some part that develops from the neural crest.
uberon
UBERON:0010316
germ layer / neural crest
A skeletal element that is part of a orbital region.
uberon
eye skeleton
ocular skeleton
skeletal element of orbital region
UBERON:0010321
skeletal element of eye region
A skeletal element that is part of a orbital region.
OBOL:automatic
Skeletal subdivision of the head including skull (cranium plus mandible), pharyngeal and/or hyoid apparatus.
we use 'cranial skeletal system', so that we can include the skull, which has joints/sutures as parts (recall, we follow FMA in distinguishing between the skeleton and skeletal system - only the latter includes joints)
that the cranial skeleton includes the pharyngeal arch skeleton. It is thus more inclusive that the cranium itself, and extends beyond the head in tetrapods. The AAO class called 'skull' belongs here, as it includes the whole splanchnocranium
Bony structure that encases the central nervous system and the primary sense organs of sight, olfaction, hearing, and equilibrium.[AAO]
Skeletal system which is part of the skull, including the splanchnocranium, chondrocranium, and dermatocranium.[TAO]
AAO:0000109
AAO:0000971
AAO:0010185
TAO:0000737
VSAO:0000049
XAO:0003075
ZFA:0000737
cranial skeleton
osteocranium
uberon
cranium
UBERON:0010323
cranial skeletal system
Skeletal subdivision of the head including skull (cranium plus mandible), pharyngeal and/or hyoid apparatus.
GO_REF:0000034
PSPUB:0000170
VSAO:0000049
Bony structure that encases the central nervous system and the primary sense organs of sight, olfaction, hearing, and equilibrium.[AAO]
2012-06-20
AAO:0000109
AAO
AAO:LAP
Skeletal system which is part of the skull, including the splanchnocranium, chondrocranium, and dermatocranium.[TAO]
2012-08-14
TAO:0000737
TAO
ZFIN:curator
cranium
ZFA:0000737
Mesenchyme that develops_from a neural crest and is part of a mandibular process mesenchyme.
EHDAA2:0004603
uberon
UBERON:0010336
mandibular process mesenchyme from neural crest
EHDAA2
Mesenchyme that develops_from a neural crest and is part of a mandibular process mesenchyme.
OBOL:automatic
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a mandibular process mesenchyme.
EHDAA2:0004604
uberon
UBERON:0010337
mandibular process mesenchyme from head mesenchyme
EHDAA2
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a mandibular process mesenchyme.
OBOL:automatic
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mandibular mesenchyme.
EHDAA2:0000036
uberon
UBERON:0010339
1st arch mandibular mesenchyme from head mesenchyme
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mandibular mesenchyme.
OBOL:automatic
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mesenchyme.
EMAPA:16130
mesenchyme derived from head mesoderm of mesenchyme of 1st arch
uberon
UBERON:0010341
1st arch mesenchyme from head mesenchyme
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mesenchyme.
OBOL:automatic
mesenchyme derived from head mesoderm of mesenchyme of 1st arch
EMAPA:16130
Mesenchyme that develops_from a neural crest and is part of a entire pharyngeal arch associated mesenchyme.
arch mesenchyme from neural crest
branchial arch mesenchyme from neural crest
neural crest derived arch mesenchyme
uberon
UBERON:0010359
Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme
pharyngeal arch mesenchyme from neural crest
Mesenchyme that develops_from a neural crest and is part of a entire pharyngeal arch associated mesenchyme.
OBOL:automatic
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a entire pharyngeal arch associated mesenchyme.
arch mesenchyme from head mesenchyme
branchial arch mesenchyme from head mesenchyme
head mesenchyme derived arch mesenchyme
uberon
UBERON:0010360
Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme
pharyngeal arch mesenchyme from head mesenchyme
Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a entire pharyngeal arch associated mesenchyme.
OBOL:automatic
Skeletal subdivision that undergoes indirect development and includes elements that develop as a replacement or substitution of other elements or tissues.
An endoskeleton is an internal support structure of an animal, composed of mineralized tissue. Endoskeleton develops within the skin or in the deeper body tissues. The vertebrate is basically an endoskeleton made up of two types of tissues (bone and cartilage). During early embryonic development the endoskeleton is composed of notochord and cartilage. The notochord in most vertebrates is replaced by vertebral column and cartilage is replaced by bone in most adults. In three phyla and one subclass of animals, endoskeletons of various complexity are found: Chordata, Echinodermata, Porifera, and Coleoidea. An endoskeleton may function purely for support (as in the case of sponges), but often serves as an attachment site for muscle and a mechanism for transmitting muscular forces. A true endoskeleton is derived from mesodermal tissue. Such a skeleton is present in echinoderms and chordates. The poriferan 'skeleton' consists of microscopic calcareous or siliceous spicules or a spongin network. The Coleoidae do not have a true endoskeleton in the evolutionary sense; here, a mollusk exoskeleton evolved into several sorts of internal structure, the 'cuttlebone' of cuttlefish being the best-known version. Yet they do have cartilaginous tissue in their body, even if it is not mineralized, especially in the head, where it forms a primitive cranium. The endoskeleton gives shape,support and protection to the body and provides a mean of locomotion.[Wikipedia:Endoskeleton]t
VSAO:0000037
XAO:0004026
replacement skeleton
uberon
UBERON:0010362
endoskeleton
VSAO
Skeletal subdivision that undergoes indirect development and includes elements that develop as a replacement or substitution of other elements or tissues.
GO_REF:0000034
PSPUB:0000170
VSAO:0000037
An endoskeleton is an internal support structure of an animal, composed of mineralized tissue. Endoskeleton develops within the skin or in the deeper body tissues. The vertebrate is basically an endoskeleton made up of two types of tissues (bone and cartilage). During early embryonic development the endoskeleton is composed of notochord and cartilage. The notochord in most vertebrates is replaced by vertebral column and cartilage is replaced by bone in most adults. In three phyla and one subclass of animals, endoskeletons of various complexity are found: Chordata, Echinodermata, Porifera, and Coleoidea. An endoskeleton may function purely for support (as in the case of sponges), but often serves as an attachment site for muscle and a mechanism for transmitting muscular forces. A true endoskeleton is derived from mesodermal tissue. Such a skeleton is present in echinoderms and chordates. The poriferan 'skeleton' consists of microscopic calcareous or siliceous spicules or a spongin network. The Coleoidae do not have a true endoskeleton in the evolutionary sense; here, a mollusk exoskeleton evolved into several sorts of internal structure, the 'cuttlebone' of cuttlefish being the best-known version. Yet they do have cartilaginous tissue in their body, even if it is not mineralized, especially in the head, where it forms a primitive cranium. The endoskeleton gives shape,support and protection to the body and provides a mean of locomotion.[Wikipedia:Endoskeleton]t
replacement skeleton
VSAO:curator
A skeletal element that has the potential to participate in endochondral ossification, and may participate in intramembranous ossification.
VSAO:0000139
XAO:0004017
ZFA:0005620
endochondral replacement element
uberon
UBERON:0010363
endochondral element
https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern
VSAO
A skeletal element that has the potential to participate in endochondral ossification, and may participate in intramembranous ossification.
GO_REF:0000034
PSPUB:0000170
VSAO:0000139
endochondral replacement element
VSAO:0000139
Skeletal subdivision that undergoes direct development and includes elements that either develop in association with the basement membrane of the ectoderm or are homologous with such elements; includes dermatocranium, components of the appendicular skeleton, teeth and tooth-like elements of the oropharynx, and integumentary elements.
exoskeleton
VSAO:0000035
XAO:0004025
uberon
dermal skeletal system
dermoskeleton
desmoskeleton
UBERON:0010364
This ontology covers metazoa, so we do not use exoskeleton as primary label, as in VSAO
dermal skeleton
VSAO
Skeletal subdivision that undergoes direct development and includes elements that either develop in association with the basement membrane of the ectoderm or are homologous with such elements; includes dermatocranium, components of the appendicular skeleton, teeth and tooth-like elements of the oropharynx, and integumentary elements.
GO_REF:0000034
PSPUB:0000170
VSAO:0000035
exoskeleton
VSAO:curator
dermal skeletal system
VSAO:curator
dermoskeleton
VSAO:curator
desmoskeleton
VSAO:curator
Epithelium composed of cells that develops from the ectoderm[FMA,modified].
FMA:69064
ectoderm-derived epithelium
uberon
UBERON:0010371
ecto-epithelium
Epithelium composed of cells that develops from the ectoderm[FMA,modified].
FMA:69064
The integrated unit (of the eye) that consists of the conjunctiva, the corneal surface, and the ocular mucosal adnexa including the lid margins and the meibomian gland openings, the lacrimal glands and the lacrimal drainage system, all which are critical to maintain ocular surface integrity and provide protection from external antigens and pathogenic microorganisms.
EMAPA:35336
MA:0002486
eye surface
eye surface region
ocular surface
uberon
UBERON:0010409
ocular surface region
The integrated unit (of the eye) that consists of the conjunctiva, the corneal surface, and the ocular mucosal adnexa including the lid margins and the meibomian gland openings, the lacrimal glands and the lacrimal drainage system, all which are critical to maintain ocular surface integrity and provide protection from external antigens and pathogenic microorganisms.
MP:0013754
eye surface
MA:0002486
The ciliary processes are formed by the inward folding of the various layers of the choroid, i.e. , the choroid proper and the lamina basalis, and are received between corresponding foldings of the suspensory ligament of the lens.
FMA:76551
ciliary processes
ciliary processes set
processus ciliares
set of ciliary processes
uberon
ciliary process
processus ciliares
UBERON:0010427
ciliary processes
http://upload.wikimedia.org/wikipedia/commons/b/b2/Gray875.png
The ciliary processes are formed by the inward folding of the various layers of the choroid, i.e. , the choroid proper and the lamina basalis, and are received between corresponding foldings of the suspensory ligament of the lens.
ciliary processes
FMA:76551
ciliary processes set
FMA:76551
processus ciliares
FMA:TA
set of ciliary processes
FMA:76551
ciliary process
processus ciliares
A bone that is shaped as a broad flat plate and composed of two thin layers of compact tissue enclosing between them a variable quantity of cancellous tissue, which is the location of red bone marrow.
In an adult mammal, most red blood cells are formed in flat bones
Flat bones are those bones which are found where the principal requirement is either extensive protection or the provision of broad surfaces for muscular attachment
FMA:7476
NCIT:C32616
UMLS:C0222649
galen:FlatBone
uberon
os planum
UBERON:0010428
Examples: cranium, the ilium, sternum, rib cage, the sacrum and the scapula; the occipital, parietal, frontal, nasal, lacrimal, vomer, scapula, os coxC&, sternum, and ribs
flat bone
FMA
A bone that is shaped as a broad flat plate and composed of two thin layers of compact tissue enclosing between them a variable quantity of cancellous tissue, which is the location of red bone marrow.
UMLS:C0222649
ncithesaurus:Flat_Bone
os planum
Skeletal element that forms as a replacement or substitution of another element or tissue.
VSAO:0000135
XAO:0004016
ZFA:0005624
uberon
UBERON:0010522
replacement element
VSAO
cjm
Skeletal element that forms as a replacement or substitution of another element or tissue.
GO_REF:0000034
PSPUB:0000170
VSAO:0000135
A vessel of the microcirculature, lying between the arterioles and venules; includes capillaries (blood and lymphatic), metarterioles and arteriovenous anastomoses.
MESH:A07.231.432
TAO:0005251
ZFA:0005251
uberon
microcirculatory vessels
UBERON:0010523
microcirculatory vessel
ZFA
A vessel of the microcirculature, lying between the arterioles and venules; includes capillaries (blood and lymphatic), metarterioles and arteriovenous anastomoses.
MESH:A07.231.432
ZFA:0005251
microcirculatory vessels
TAO:0005251
Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints.
Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO]
FMA:23879
VSAO:0000042
skeletal subdivision
uberon
subdivision of skeleton (in vivo)
UBERON:0010912
subdivision of skeleton
cjm
UBERONREF:0000003
VSAO
Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints.
UBERONREF:0000003
Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO]
2012-08-14
VSAO:0000042
incorrect
VSAO
VSAO:curator
skeletal subdivision
VSAO:0000042
subdivision of skeleton (in vivo)
FMA:23879
Any muscle organ that is part of either the head or the neck.
NCIT:C32716
UMLS:C0448281
muscle of head or neck
uberon
muscle of head and neck
UBERON:0010959
craniocervical muscle
prolog
Any muscle organ that is part of either the head or the neck.
UMLS:C0448281
ncithesaurus:Head_and_Neck_Muscle
A cartilage element that is part of a splanchnocranium.
EFO:0003689
TAO:0001460
ZFA:0001460
pharyngeal arch cartilages
splanchnocranium cartilage
uberon
UBERON:0011004
pharyngeal arch cartilage
ZFA
ZFA
A cartilage element that is part of a splanchnocranium.
OBOL:automatic
pharyngeal arch cartilages
ZFA:0001460
splanchnocranium cartilage
ZFA:0001460
Joint in which the articulating bones or cartilages are connected by ligaments or fibrocartilage without an intervening synovial cavity. Examples: sagittal suture, inferior tibiofibular syndesmosis, costochondral joint, pubic symphysis.
FMA:7491
solid joint
uberon
UBERON:0011134
nonsynovial joint
FMA
Joint in which the articulating bones or cartilages are connected by ligaments or fibrocartilage without an intervening synovial cavity. Examples: sagittal suture, inferior tibiofibular syndesmosis, costochondral joint, pubic symphysis.
FMA:7491
solid joint
FMA:7491
Subdivision of the skeletal system which consists of the axial skeleton plus associated joints.
FMA:7483
uberon
UBERON:0011137
axial skeletal system
http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton
FMA
Subdivision of the skeletal system which consists of the axial skeleton plus associated joints.
Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints.
axial skeletal system
FMA:302077
post-cranial axial skeletal system
uberon
UBERON:0011138
postcranial axial skeletal system
http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton
FMA
cjm
Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints.
axial skeletal system
Subdivision of skull that consists of the facial bones.
EHDAA2:0002206
EHDAA:8361
EMAPA:18022
FMA:53673
MA:0000318
facial skeleton
uberon
facial bone
ossa facialia
ossa faciei
viscerocranium
UBERON:0011156
facial skeleton
http://upload.wikimedia.org/wikipedia/commons/7/77/Illu_facial_bones.jpg
FMA
FMA
Subdivision of skull that consists of the facial bones.
MP:0005274
facial skeleton
FMA:53673
facial bone
MA:0000318
ossa facialia
ossa faciei
viscerocranium
MA:0000318
The skull can be divided into two: the neurocranium and the facial skeleton
FMA:54964
skull subdivision
subdivision of skull
uberon
UBERON:0011158
primary subdivision of skull
FMA
The skull can be divided into two: the neurocranium and the facial skeleton
skull subdivision
FMA:54964
subdivision of skull
FMA:54964
uberon
UBERON:0011159
primary subdivision of cranial skeletal system
FMA
A bone that is part of a neurocranium [Automatically generated definition].
EMAPA:35238
MA:0001478
chondrocranium bone
uberon
UBERON:0011164
neurocranium bone
A bone that is part of a neurocranium [Automatically generated definition].
OBOL:automatic
chondrocranium bone
MA:0001478
A multi cell part structure that is part of a central nervous system.
FMA:83143
cell part cluster of neuraxis
neuraxis layer
uberon
UBERON:0011215
central nervous system cell part cluster
A multi cell part structure that is part of a central nervous system.
OBOL:automatic
cell part cluster of neuraxis
FMA:83143
neuraxis layer
FMA:83143
A subdivision of an anatomical system.
FBbt:00007330
FMA:67509
uberon
UBERON:0011216
organ system subdivision
FBbt
A subdivision of an anatomical system.
Muscles within the eye (bulbus oculi).[AAO]
AAO:0010038
EMAPA:18808
FMA:49150
intrinsic muscle of eyeball
intrinsic ocular muscle
uberon
UBERON:0011222
intra-ocular muscle
EMAPA
Muscles within the eye (bulbus oculi).[AAO]
2012-06-20
AAO:0010038
AAO
AAO:EJS
intrinsic ocular muscle
EMAPA:18808
Synovial sac which surrounds parts of one or more tendons. Examples: synovial tendon sheath of manual digit 2, radial bursa.
synovium
BTO:0001823
FMA:40878
uberon
UBERON:0011233
Alternate def: A synovial sheath is a layer of a tendon sheath containing tendons in the hand and foot. They lie internal to the fibrous tendon sheaths. An example is the common synovial sheath for the flexor tendons. [Wikipedia:Synovial_sheath]
synovial membrane of synovial tendon sheath
Synovial sac which surrounds parts of one or more tendons. Examples: synovial tendon sheath of manual digit 2, radial bursa.
FMA:45087
synovium
BTO:0001823
FMA:40877
uberon
UBERON:0011234
fibrous membrane of synovial tendon sheath
The part of the trunk that is in the dorsum[cjm].
In humans, the subdivision of trunk which is demarcated from the trunk proper by the external surface of the posterolateral part of the rib cage, the anterior surface of the thoracic vertebral column and the posterior axillary lines, the external surface of the posterior abdominal wall; together with the trunk proper, it constitutes the trunk[FMA]
EMAPA:35162
FMA:25056
MA:0000020
back of trunk
dorsal part of trunk
dorsum of trunk
trunk back
uberon
UBERON:0011270
dorsal trunk
FMA
FMA
The part of the trunk that is in the dorsum[cjm].
UBERONREF:0000006
back of trunk
FMA:25056
dorsum of trunk
FMA:25056
trunk back
FMA:25056
compare with 'stratum basale of epidermis'. This class is the source for many adult structures - see WP2062. See also: 'enveloping layer of ectoderm'
EHDAA2:0001845
uberon
basal cell layer of skin
outer epithelium of body
UBERON:0011272
embryonic skin basal layer
EHDAA2
EHDAA2
EHDAA2
outer epithelium of body
Wikipathways:WP2062
A blood vasculature that is part of a head.
Blood vessel part of cranial vasculature.[TAO]
TAO:0005297
ZFA:0005297
cranial blood vessel
set of blood vessels of head
uberon
cranial blood vessels
UBERON:0011362
cranial blood vasculature
A blood vasculature that is part of a head.
OBOL:automatic
Blood vessel part of cranial vasculature.[TAO]
2012-08-14
TAO:0005297
TAO
ZFIN:curator
cranial blood vessel
ZFA:0005297
cranial blood vessels
TAO:0005297
Anatomical structure that is an aggregation of similar cells from which cartilages and bones form, and from which chondrogenesis and osteogenesis are initiated during repair and/or regeneration. (Hall and Miyake 1995).
consider obsoleting, coordinate with VSAO
VSAO:0000006
XAO:0004021
uberon
UBERON:0011585
cell condensation
VSAO
Anatomical structure that is an aggregation of similar cells from which cartilages and bones form, and from which chondrogenesis and osteogenesis are initiated during repair and/or regeneration. (Hall and Miyake 1995).
GO_REF:0000034
PSPUB:0000170
VSAO:0000006
A subdivision of the head that corresponds to the jaw skeleton, containing both soft tissue, skeleton and teeth (when present). The jaw region is divided into upper and lower regions.
EMAPA:32905
NCIT:C114916
uberon
UBERON:0011595
jaw region
http://eol.org/collections/11578
EMAPA
FMA-abduced
ZFA-abduced
A subdivision of the head that corresponds to the jaw skeleton, containing both soft tissue, skeleton and teeth (when present). The jaw region is divided into upper and lower regions.
EHDAA2:0001020
lower jaw future lip
uberon
UBERON:0011596
future lower lip
EHDAA2
lower jaw future lip
EHDAA2:0001020
An epithelium that develops_from a ectoderm and is part of a oral epithelium.
EHDAA2:0004137
uberon
UBERON:0011642
oral epithelium from ectoderm
EHDAA2
EHDAA2
An epithelium that develops_from a ectoderm and is part of a oral epithelium.
OBOL:automatic
A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column.
Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem
axial subdivision of organism
uberon
body segment
main body segment
UBERON:0011676
subdivision of organism along main body axis
A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column.
A cardiovascular system that is part of a conceptus.
EHDAA2:0000216
FMA:305965
NCIT:C34148
conceptus cardiovascular system
uberon
embryonic circulatory system
fetal circulatory system
UBERON:0011695
embryonic cardiovascular system
A cardiovascular system that is part of a conceptus.
OBOL:automatic
An anatomical space that is part of a bone of lower jaw.
AAO:0000273
uberon
UBERON:0011772
lower jaw opening
An anatomical space that is part of a bone of lower jaw.
OBOL:automatic
Ectodermal placode that does not develop into a component of the nervous system.
uberon
UBERON:0011814
non-neurogenic ectodermal placode
cjm
Ectodermal placode that does not develop into a component of the nervous system.
An anatomical junction that divides and overlaps with and atrium and a ventricle in the heart.
EHDAA2:0004149
FMA:85125
uberon
AV region
AV segment
atrial ventricular junction
atrioventricular junction
atrioventricular segment
UBERON:0011820
atrioventricular region
An anatomical junction that divides and overlaps with and atrium and a ventricle in the heart.
AV region
AV segment
atrial ventricular junction
GO:0003294
atrioventricular junction
FMA:85125
GO:0003294
atrioventricular segment
Connective tissue, which consists of a population of connective tissue cells, the intercellular matrix of which contains an irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, mucoid tissue, connective tissue of peritoneum, connective tissue of fibrous pericardium.
FMA:20107
uberon
UBERON:0011821
irregular connective tissue
FMA
Connective tissue, which consists of a population of connective tissue cells, the intercellular matrix of which contains an irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, mucoid tissue, connective tissue of peritoneum, connective tissue of fibrous pericardium.
FMA:20107
Irregular connective tissue is an irregular connective tissue, the intercellular matrix of which contains a dense irregular network of collagen and elastic fiber bundles. Examples: connective tissue of peritoneum, connective tissue of fibrous pericardium.
Tissue characterized by a thick, random arrangement of collagen and elastin fibers with very few cells. The majority of the cells are fibroblasts, but mast cells and macrophages may also be seen. It is found in the dermis, periosteum, perichondrium, capsules of organs and sheaths of nerves and muscles[NCIT]
FMA:20109
NCIT:C32882
UMLS:C0738366
irregular dense connective tissue
typus irregularis (textus connectivus collagenosus compactus)
uberon
UBERON:0011822
dense irregular connective tissue
FMA
Irregular connective tissue is an irregular connective tissue, the intercellular matrix of which contains a dense irregular network of collagen and elastic fiber bundles. Examples: connective tissue of peritoneum, connective tissue of fibrous pericardium.
FMA:20109
Tissue characterized by a thick, random arrangement of collagen and elastin fibers with very few cells. The majority of the cells are fibroblasts, but mast cells and macrophages may also be seen. It is found in the dermis, periosteum, perichondrium, capsules of organs and sheaths of nerves and muscles[NCIT]
2012-08-29
ncithesaurus:Irregular_Dense_Connective_Tissue
NCIT
UMLS:C0738366
ncithesaurus:Irregular_Dense_Connective_Tissue
typus irregularis (textus connectivus collagenosus compactus)
FMA:20109
Dense connective tissue is mainly composed of collagen type I. Crowded between the collagen fibers are rows of fibroblasts, fiber-forming cells, that manufacture the fibers. Dense connective tissue forms strong, rope-like structures such as tendons and ligaments. Tendons attach skeletal muscles to bones; ligaments connect bones to bones at joints. Ligaments are more stretchy and contain more elastic fibers than tendons. Dense connective tissue also make up the lower layers of the skin (dermis), where it is arranged in sheets
our OWL definition states that this is differentiated from other connective tissue types by virtue of the fact that the collage fiber component predominates, as opposed to cells and fluid.
Connective tissue in which the fibrous component predominates. The cells, ground substance, and tissue fluid represent a minor component[NCIT]
AAO:0000121
NCIT:C32450
UMLS:C1511770
uberon
UBERON:0011823
dense connective tissue
Dense connective tissue is mainly composed of collagen type I. Crowded between the collagen fibers are rows of fibroblasts, fiber-forming cells, that manufacture the fibers. Dense connective tissue forms strong, rope-like structures such as tendons and ligaments. Tendons attach skeletal muscles to bones; ligaments connect bones to bones at joints. Ligaments are more stretchy and contain more elastic fibers than tendons. Dense connective tissue also make up the lower layers of the skin (dermis), where it is arranged in sheets
Connective tissue in which the fibrous component predominates. The cells, ground substance, and tissue fluid represent a minor component[NCIT]
2012-08-29
ncithesaurus:Dense_Connective_Tissue
NCIT
UMLS:C1511770
ncithesaurus:Dense_Connective_Tissue
FMA:75634
uberon
UBERON:0011824
fibrous connective tissue
FMA
Irregular connective tissue, the intercellular matrix of which contains a sparse irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, neuroglial tissue, mucoid tissue.
FMA:19783
NCIT:C33007
UMLS:C1253917
textus connectivus collagenosus laxus
textus connectivus laxus
uberon
UBERON:0011825
loose connective tissue
FMA
Irregular connective tissue, the intercellular matrix of which contains a sparse irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, neuroglial tissue, mucoid tissue.
FMA:19783
UMLS:C1253917
ncithesaurus:Loose_Connective_Tissue
textus connectivus collagenosus laxus
FMA:19783
FMA:TA
textus connectivus laxus
FMA:19783
FMA:TA
An acinus that is part of a exocrine gland.
exocrine gland acinus
uberon
UBERON:0011858
acinus of exocrine gland
An acinus that is part of a exocrine gland.
OBOL:automatic
the FMA class specifically refers to ureter
FMA:63212
MESH:D024022
NCIT:C32339
NIF_Subcellular:sao7547390221
uberon
UBERON:0011860
collection of collagen fibrils
ZFA
the FMA class specifically refers to ureter
FMA
The connective tissue bundles in the extracellular matrix of bone tissue that are composed of collagen, and play a role in tissue strength and elasticity
uberon
UBERON:0011863
bone collagen fibril
The connective tissue bundles in the extracellular matrix of bone tissue that are composed of collagen, and play a role in tissue strength and elasticity
MP:0011642
The connective tissue bundles in the extracellular matrix of tendon tissue that are composed of collagen, and play a role in tissue strength and elasticity
uberon
UBERON:0011864
tendon collagen fibril
The connective tissue bundles in the extracellular matrix of tendon tissue that are composed of collagen, and play a role in tissue strength and elasticity
MP:0011643
Front (ventral) portion of the vascular, pigmentary, or middle coat of the eye, including the ciliary body and the iris.
EMAPA:37417
Haller tunica vascula
anterior part of uveal tract
anterior uveal tract
anterior vascular layer of the eyeball
anterior vascular tunic of the eye
tunica vasculosa bulbosa
ventral uveal tract
uberon
ciliary body and iris
vasculosa oculi
UBERON:0011892
anterior uvea
ZFA
MP
lexical
Front (ventral) portion of the vascular, pigmentary, or middle coat of the eye, including the ciliary body and the iris.
MP:0005194
EMAPA:37417
MA:th
Haller tunica vascula
MP:0005194
tunica vasculosa bulbosa
MP:0005194
vasculosa oculi
MP:0005194
Epimysium is a layer of connective tissue which ensheaths the entire muscle. It is composed of dense irregular connective tissue. It is continuous with fascia and other connective tissue wrappings of muscle including the endomysium, and perimysium. It is also continuous with tendons where it becomes thicker and collagenous.
The Epimysium also protects muscles from friction against other muscles and bones
FMA:9726
NCIT:C32527
UMLS:C0504096
fascia of muscle organ
uberon
epimysia
UBERON:0011899
epimysium
FMA
FMA
Epimysium is a layer of connective tissue which ensheaths the entire muscle. It is composed of dense irregular connective tissue. It is continuous with fascia and other connective tissue wrappings of muscle including the endomysium, and perimysium. It is also continuous with tendons where it becomes thicker and collagenous.
UMLS:C0504096
ncithesaurus:Epimysium
fascia of muscle organ
FMA:9726
epimysia
The aggregate of the coelemic cavity lumen plus the membranes that line the lumen.
EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining.
coelomic
EHDAA2:0004731
enterocoelom
haemocoelom
schizocoelom
uberon
coelem
coelomic cavity
UBERON:0011997
coelom
EHDAA2
The aggregate of the coelemic cavity lumen plus the membranes that line the lumen.
UBERON:cjm
enterocoelom
NCBITaxon:33511
coelomic cavity
EHDAA2:0004731
The cavity within a myotome
The central cavity within the mesoderm is the paired primary or embryonic coelom. Parts of the embryonic coelom often become enclosed in the mesoderm, forming a myocoel within the epimere, a nephrocoel within the mesomere, and simple coelom (body cavity) within the lateral plate mesoderm.[well established][VHOG]
EMAPA:31134
VHOG:0001283
uberon
UBERON:0012054
myocoele
The cavity within a myotome
The central cavity within the mesoderm is the paired primary or embryonic coelom. Parts of the embryonic coelom often become enclosed in the mesoderm, forming a myocoel within the epimere, a nephrocoel within the mesomere, and simple coelom (body cavity) within the lateral plate mesoderm.[well established][VHOG]
2012-09-17
VHOG:0001283
VHOG
ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.166 and Figure 5.6
Bone that forms as a replacement of another structural tissue.
Bone that forms as a replacement of another structural tissue.[TAO]
This class was introduced to be consistent with the ZFA hierarchy. The corresponding TAO term was obsoleted, and never introduced into VSAO. Note that VSAO does have replacement element.
AAO:0010768
TAO:0001637
ZFA:0001628
replacement bones
uberon
UBERON:0012075
replacement bone
ZFA
ZFA
Bone that forms as a replacement of another structural tissue.
ZFA:0001628
Bone that forms as a replacement of another structural tissue.[TAO]
2012-08-14
TAO:0001637
TAO
TAO:wd
This class was introduced to be consistent with the ZFA hierarchy. The corresponding TAO term was obsoleted, and never introduced into VSAO. Note that VSAO does have replacement element.
ZFA
replacement bones
ZFA:0001628
Anatomical system that consists of the integumental system plus all mucosae and submucosae.
uberon
dermatological system
UBERON:0012125
dermatological-muscosal system
Anatomical system that consists of the integumental system plus all mucosae and submucosae.
dermatological system
OBI:MC
A zone of skin that is part of a craniocervical region.
EMAPA:37276
MA:0000574
NCIT:C12294
UMLS:C1522650
uberon
UBERON:0012180
head or neck skin
A zone of skin that is part of a craniocervical region.
OBOL:automatic
EMAPA:37276
MA:th
UMLS:C1522650
ncithesaurus:Skin_of_the_Scalp_and_Neck
Epithelium that derives from the mesoderm. [Automatically generated definition].
FMA:86452
mesoderm-derived epithelium
mesoepithelium
uberon
UBERON:0012275
meso-epithelium
Epithelium that derives from the mesoderm. [Automatically generated definition].
OBOL:automatic
One of five swellings formed during the development of the face
FMA:293103
uberon
embryonic facial process
facial primordium
primordium of face
UBERON:0012314
embryonic facial prominence
One of five swellings formed during the development of the face
An artery of the neck
EMAPA:37075
NCIT:C52850
UMLS:C1707349
uberon
UBERON:0012320
cervical artery
An artery of the neck
EMAPA:37075
MA:th
UMLS:C1707349
ncithesaurus:Cervical_Artery
The deep cervical artery (Profunda cervicalis) is an artery of the neck.
FMA:10659
uberon
profunda cervicalis
UBERON:0012321
deep cervical artery
FMA
The deep cervical artery (Profunda cervicalis) is an artery of the neck.
profunda cervicalis
A bone element that is part of a jaw region.
Do not manually classify under here - bones are automatically classified
EMAPA:35453
MA:0003130
jaw bone
uberon
UBERON:0012360
bone of jaw
A bone element that is part of a jaw region.
OBOL:automatic
A layer of tissue between the muscularis and serosa.
FMA:45636
NCIT:C94494
UMLS:C0225334
uberon
UBERON:0012375
Contains nerves, blood vessels, lymphatics and lymph nodes
subserosa
A layer of tissue between the muscularis and serosa.
UMLS:C0225334
ncithesaurus:Subserosa
EMAPA:37567
MA:0001802
uberon
UBERON:0012416
respiratory system arterial smooth muscle
EMAPA:37567
MA:th
A smooth muscle tissue that is part of a respiratory system venous blood vessel.
EMAPA:37586
MA:0001812
uberon
UBERON:0012418
respiratory system venous smooth muscle
A smooth muscle tissue that is part of a respiratory system venous blood vessel.
OBOL:automatic
EMAPA:37586
MA:th
The sclera and cornea form the fibrous tunic of the bulb of the eye; the sclera is opaque, and constitutes the posterior five-sixths of the tunic; the cornea is transparent, and forms the anterior sixth.
tunica fibrosa
FMA:58102
fibrous layer of eyeball
uberon
corneosclera
fibrous tunic
UBERON:0012430
tunica fibrosa of eyeball
FMA
The sclera and cornea form the fibrous tunic of the bulb of the eye; the sclera is opaque, and constitutes the posterior five-sixths of the tunic; the cornea is transparent, and forms the anterior sixth.
fibrous layer of eyeball
FMA:58102
corneosclera
fibrous tunic
EHDAA2:0000472
EMAPA:16054
VHOG:0000767
uberon
extraembryonic cavities
UBERON:0012466
extraembryonic cavity
extraembryonic cavities
EHDAA2:0000472
A vein that drains a lip.
labial vein of face
lip vein
vena labialis
uberon
labial vein
UBERON:0013136
vein of lip
FMA
A vein that drains a lip.
OBOL:automatic
lip vein
OBOL:automatic
vena labialis
Any vein within the general circulation that transports blood back to the right atrium of the heart.
FMA:66644
NCIT:C33719
UMLS:C0447117
systemic venous tree organ part
uberon
UBERON:0013140
systemic vein
Any vein within the general circulation that transports blood back to the right atrium of the heart.
ncithesaurus:Systemic_Vein
UMLS:C0447117
ncithesaurus:Systemic_Vein
systemic venous tree organ part
FMA:66644
The secretory unit of a serous gland. The acinar portion is composed of serous secreting cells.
FMA:86279
acinus of serous gland
uberon
UBERON:0013232
serous acinus
The secretory unit of a serous gland. The acinar portion is composed of serous secreting cells.
Anatomical cavity that is the lumen of the skull and contains the brain.
EMAPA:37497
FMA:9644
MA:0003061
NCIT:C77638
UMLS:C0230041
cavitas cranii
uberon
intracranial cavity
intracranial space
UBERON:0013411
cranial cavity
http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg
Wikipedia
Anatomical cavity that is the lumen of the skull and contains the brain.
UBERON:cjm
EMAPA:37497
MA:th
UMLS:C0230041
ncithesaurus:Cranial_Cavity
cavitas cranii
FMA:9644
FMA:TA
intracranial cavity
intracranial space
The space that surrounds an organism.
external to organism
outside of body
uberon
UBERON:0013514
space surrounding organism
The space that surrounds an organism.
uberon
UBERON:0013522
subdivision of tube
Anatomical space that is an opening in a bone of the skull.
FMA:53165
foramen of skull
cranial conduit
cranial foramen
uberon
foramina of the skull
UBERON:0013685
foramen of skull
Anatomical space that is an opening in a bone of the skull.
TAO:curator
foramen of skull
cranial conduit
FMA:53165
foramina of the skull
2
2
An anatomical space which is the lumen of some anatomical conduit and connects two or more spaces together[FMA,modified].
FMA:9338
foramen space
uberon
UBERON:0013686
anatomical conduit space
FMA
An anatomical space which is the lumen of some anatomical conduit and connects two or more spaces together[FMA,modified].
FMA:9338
Vascular endothelium found in blood vessels of the blood-brain-barrier.
BTO:0001852
BTO:0003248
CALOHA:TS-0092
uberon
cerebromicrovascular endothelium
UBERON:0013694
brain endothelium
Vascular endothelium found in blood vessels of the blood-brain-barrier.
CALOHA:TS-0092
cerebromicrovascular endothelium
CALOHA:TS-0092
Musculature of the head and neck, spine, and ribs.
EHDAA2:0000159
EMAPA:18166
uberon
UBERON:0013700
axial musculature
Musculature of the head and neck, spine, and ribs.
HP:0003327
A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages.
uberon
UBERON:0013701
main body axis
A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages.
The region of the organism associated with the visceral organs.
Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424].
AEO:0000103
BTO:0001489
EMAPA:36031
FMA:231424
uberon
body
whole body
UBERON:0013702
body proper
AEO
The region of the organism associated with the visceral organs.
AEO:0000103
Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424].
FMA:231424
body
AEO:0000103
whole body
BTO:0001489
A tubular passage that extends from the primitive pit into the head process during the early stages of embryonic development in mammals. It perforates the splanchnopleure layer so that the yolk sac and the amnion are connected temporarily.
FMA:293127
NCIT:C34230
UMLS:C1518428
uberon
chordal canal
UBERON:0013704
notochordal canal
A tubular passage that extends from the primitive pit into the head process during the early stages of embryonic development in mammals. It perforates the splanchnopleure layer so that the yolk sac and the amnion are connected temporarily.
UMLS:C1518428
ncithesaurus:Notochordal_Canal
Fluid contained within the notochordal canal
notochord fluid
portion of notochordal fluid
uberon
UBERON:0013727
Distinct feature of coelocanths
notochordal fluid
Fluid contained within the notochordal canal
A organ component layer that is part of a integumental system.
layer of skin
skin layer
uberon
UBERON:0013754
integumentary system layer
A organ component layer that is part of a integumental system.
OBOL:automatic
A blood that is part of a artery.
FMA:83066
arterial blood
blood in artery
portion of arterial blood
uberon
UBERON:0013755
arterial blood
A blood that is part of a artery.
OBOL:automatic
arterial blood
FMA:83066
blood in artery
FMA:83066
portion of arterial blood
FMA:83066
A blood that is part of a vein.
FMA:83067
blood in vein
portion of venous blood
venous blood
uberon
UBERON:0013756
venous blood
A blood that is part of a vein.
OBOL:automatic
blood in vein
FMA:83067
portion of venous blood
FMA:83067
venous blood
FMA:83067
A blood that is part of a capillary.
FMA:263901
NCIT:C32212
blood in capillary
portion of blood in capillary
portion of capillary blood
uberon
UBERON:0013757
capillary blood
A blood that is part of a capillary.
OBOL:automatic
portion of blood in capillary
FMA:263901
Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements.
EMAPA:37843
digestive organ
digestive system organ
uberon
UBERON:0013765
digestive system element
Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements.
EMAPA:37843
MA:th
Mesenchyme that develops_from the neural crest[Automatically generated definition].
EMAPA:32735
FMA:293883
mesenchyme from neural crest
neural crest derived mesenchyme
neural crest mesenchyme
uberon
UBERON:0014387
mesenchyme derived from neural crest
Mesenchyme that develops_from the neural crest[Automatically generated definition].
OBOL:automatic
Subdivision of skeletal system that consists of all skeletal elements in the thoracic region of the trunk. In most vertebrates this is the rib cage and sternum.
EHDAA2:0002013
FMA:77169
skeleton of thorax
thoracic part of axial skeleton
thoracic skeleton
uberon
UBERON:0014477
thoracic skeleton
Subdivision of skeletal system that consists of all skeletal elements in the thoracic region of the trunk. In most vertebrates this is the rib cage and sternum.
thoracic skeleton
EHDAA2:0002013
A neuromere that is part of the presumptive midbrain
mesomere
midbrain segment
segment of midbrain
EHDAA2:0004352
FMA:61997
mesomere of nervous system
neuromere of mesomere group
uberon
future mesencephalon
mesomere group
UBERON:0014776
midbrain neuromere
A neuromere that is part of the presumptive midbrain
mesomere group
EHDAA2:0004352
A neuromere that is part of the presumptive spinal cord
TAO:0001332
ZFA:0001332
spinal cord metameric segment
spinal neuromeres
uberon
spinal cord segment
UBERON:0014777
spinal neuromere
A neuromere that is part of the presumptive spinal cord
spinal neuromeres
TAO:0001332
spinal cord segment
TAO:0001332
A muscle organ that consists of skeletal muscle tissue ensheathed in epimysium, that develops from myotome and that is innervated by some somatic motor neuron. Skeletal muscles are typically attached (via a tendon) to a bone but there are exceptions (e.g. intrinsic tongue muscles).
skeletal muscle
AAO:0011099
BTO:0001103
CALOHA:TS-0933
EFO:0000888
EHDAA:5035
EHDAA:5043
EHDAA:5978
EHDAA:5984
EMAPA:35988
EV:0100377
GAID:141
MA:0003148
MAT:0000302
MESH:D018482
MIAA:0000302
OpenCyc:Mx4rv2kf-5wpEbGdrcN5Y29ycA
TAO:0005277
VHOG:0000319
XAO:0000174
ZFA:0005277
uberon
UBERON:0014892
skeletal muscle organ
A muscle organ that consists of skeletal muscle tissue ensheathed in epimysium, that develops from myotome and that is innervated by some somatic motor neuron. Skeletal muscles are typically attached (via a tendon) to a bone but there are exceptions (e.g. intrinsic tongue muscles).
GOC:dos
A portion of tissue that will develop into vasculature.
EFO:0003708
TAO:0005076
ZFA:0005076
uberon
UBERON:0014903
primordial vasculature
A portion of tissue that will develop into vasculature.
ZFA:0005076
ZFA:curator
consider merging into myocardial compact layer
FMA:83105
perimysial connective tissue of subepicardium
subepicardial connective tissue
uberon
UBERON:0015128
subepicardial layer of epicardium
FMA
perimysial connective tissue of subepicardium
FMA:83105
subepicardial connective tissue
FMA:83105
Visceral intrapericardial fat contiguous with the myocardial surface.
FMA:9871
epicardial adipose tissue
pericardial adipose tissue
uberon
UBERON:0015129
epicardial fat
Visceral intrapericardial fat contiguous with the myocardial surface.
A gland that is typically found in or near the orbital region, in or around either the medial or lateral canthi, and is typically associated with secretions onto the eyeball or associated ducts. Includes the Harderian, nictitans and lacrimal glands.
the only orbital gland found in anuran amphibians is either the Harderian or the lacrimal; if it is a lacrimal, then a progressive lateral migration of the lacrimal glands must occur through the amniotes[PMID:7559104]
the only orbital gland found in anuran amphibians is the Harderian[PMID:8843648]
ocular gland
uberon
orbital gland
UBERON:0015152
gland of ocular region
inferred
A gland that is typically found in or near the orbital region, in or around either the medial or lateral canthi, and is typically associated with secretions onto the eyeball or associated ducts. Includes the Harderian, nictitans and lacrimal glands.
An eye consisting of multiple light-sensing organs
uberon
UBERON:0015165
multi-unit eye
An eye consisting of multiple light-sensing organs
present on tentacular crown
present on mantle edge in arcacean Bivalvia
The eyes (optic cushions) on the oral surface of Asteroida (Echinodermata), close to the base of the terminal tentacles, are also composed of a number of simple ocelli - as many as 80-200 in certain species
A region of somite adjacent to presomitic mesoderm.
TAO:0001462
XAO:0004074
ZFA:0001462
uberon
inter-somited border
intersomitic boundary
intersomitic fissure
intersomitic junction
segmental border
somite boundary
UBERON:0015178
somite border
A region of somite adjacent to presomitic mesoderm.
intersomitic junction
XAO:0004074
somite boundary
ZFA:0001462
Epithelium located in the intersomitic region.
XAO:0004077
intersomitic epithelium
intersomitic membrane
uberon
UBERON:0015179
somite boundary epithelium
Epithelium located in the intersomitic region.
XAO:0004077
XAO:EJS
intersomitic epithelium
XAO:0004077
intersomitic membrane
XAO:0004077
Any structure that is placed on one side of the left-right axis of a bilaterian.
This class is primarily to implement taxon constraints. It may be removed in the future.
uberon
UBERON:0015212
lateral structure
Any structure that is placed on one side of the left-right axis of a bilaterian.
A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile.
heart
SPD:0000130
cardiac pump
heart or heart like organ
circulatory vessel
uberon
cardiac structure
UBERON:0015228
circulatory organ
A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile.
A basement membrane of epithelium that is part of a respiratory system.
EMAPA:37570
MA:0001815
uberon
UBERON:0015329
respiratory system basement membrane
MA
A basement membrane of epithelium that is part of a respiratory system.
OBOL:automatic
EMAPA:37570
MA:th
EMAPA:37597
MA:0002449
heart/pericardium
uberon
UBERON:0015410
heart plus pericardium
MA
EMAPA:37597
MA:th
heart/pericardium
MA:0002449
A smooth muscle tissue that is part of a hypodermis.
FMA:77862
muscle layer in fatty layer of subcutaneous tissue
stratum musculosum panniculi adiposi telae subcutaneae
uberon
UBERON:0015783
smooth muscle layer in fatty layer of subcutaneous tissue
A smooth muscle tissue that is part of a hypodermis.
OBOL:automatic
muscle layer in fatty layer of subcutaneous tissue
FMA:77862
stratum musculosum panniculi adiposi telae subcutaneae
FMA:77862
FMA:TA
A epithelium that is part of a camera-type eye.
EMAPA:35957
MA:0003162
uberon
UBERON:0015808
eye epithelium
A epithelium that is part of a camera-type eye.
OBOL:automatic
A epithelium that is part of a foregut.
EMAPA:32922
MA:0003204
uberon
UBERON:0015833
foregut epithelium
A epithelium that is part of a foregut.
OBOL:automatic
The external part of the developing pharynx that is made of ectoderm. During vertebrate development, pockets form in pharyngeal ectoderm between the pharyngeal arches.
UBERON:2001379
TAO:0001379
ZFA:0001379
uberon
UBERON:0016545
pharyngeal ectoderm
The external part of the developing pharynx that is made of ectoderm. During vertebrate development, pockets form in pharyngeal ectoderm between the pharyngeal arches.
A layer of of the central nervous system that is part of gray matter.
grey matter layer
FMA:83142
CNS gray matter layer
CNS grey matter layer
gray matter layer of neuraxis
grey matter layer of neuraxis
uberon
UBERON:0016548
central nervous system gray matter layer
A layer of of the central nervous system that is part of gray matter.
gray matter layer of neuraxis
FMA:83142
FMA:68861
rexed lamina
uberon
UBERON:0016570
lamina of gray matter of spinal cord
rexed lamina
FMA:68861
Primordium that develops into the central nervous system
UBERON:3000469
future CNS
presumptive central nervous system
uberon
UBERON:0016879
future central nervous system
Primordium that develops into the central nervous system
Primordium that develops into the nervous system
UBERON:3000477
AAO:0000477
presumptive nervous system
uberon
UBERON:0016880
future nervous system
Primordium that develops into the nervous system
presumptive nervous system
AAO:0000477
The part of the conceptus that may be lost before birth or will be discarded at birth, or when the embryo becomes an independent organism.
AEO:0000195
EHDAA2:0000003
EMAPA:16042
extra-embryonic component
extraembryonic component
uberon
UBERON:0016887
entire extraembryonic component
AEO
AEO
The part of the conceptus that may be lost before birth or will be discarded at birth, or when the embryo becomes an independent organism.
AEO:0000195
AEO:JB
extraembryonic component
AEO:0000195
An embryonic anatomical entity that will turn into one or more other anatomical entities, perhaps with other anatomical entities, later in development.
AEO:0000132
uberon
UBERON:0016888
transitional anatomical structure
AEO
An embryonic anatomical entity that will turn into one or more other anatomical entities, perhaps with other anatomical entities, later in development.
AEO:0000132
AEO:JB
A mesenchyme-derived anatomical entity undergoing a transtion to become another structure.
AEO:0001016
uberon
UBERON:0017650
developing mesenchymal structure
A mesenchyme-derived anatomical entity undergoing a transtion to become another structure.
AEO:0001016
AEO:JB
A zone of skin that is part of a lower lip.
FMA:24767
lower lip skin
uberon
UBERON:0018150
skin of lower lip
A zone of skin that is part of a lower lip.
OBOL:automatic
lower lip skin
FMA:24767
A boundary delimiting a rhombomere.
rhombomere junction
uberon
UBERON:0018239
rhombomere boundary
A boundary delimiting a rhombomere.
GO:0021654
Added for consistency with MA EMAPA and EHDAA2. See https://github.com/obophenotype/mouse-anatomy-ontology/issues/104
EHDAA2:0001842
EMAPA:35578
MA:0000165
uberon
UBERON:0018254
skeletal musculature
MA
Any portion of submucosa that lines the digestive tract.
uberon
UBERON:0018257
submucosa of digestive tract
Any portion of submucosa that lines the digestive tract.
Any organ component layer that consists of muscle tissue.
NCITA class may refer to smooth muscle only
FMA:45634
NCIT:C75444
uberon
UBERON:0018260
layer of muscle tissue
Any organ component layer that consists of muscle tissue.
NCITA class may refer to smooth muscle only
NCIT
FMA:83450
ventricular cardiac muscle tissue
ventricular heart muscle
uberon
ventricular muscle
UBERON:0018649
cardiac muscle tissue of ventricle
ventricular cardiac muscle tissue
ventricular heart muscle
ventricular muscle
An interconnected tubular multi-tissue structure that contains fluid that is actively transported around the heart.
FMA:73747
ZFA:0005811
cardiac vasculature
uberon
UBERON:0018674
heart vasculature
An interconnected tubular multi-tissue structure that contains fluid that is actively transported around the heart.
ZFA:0005811
ZFA:CVS
cardiac vasculature
FMA:73747
BTO:0002439
genital mucosa
uberon
UBERON:0019042
reproductive system mucosa
genital mucosa
BTO:0002439
Adipose tissue which is located throughout skeletal muscle and is responsible for the marbling seen in certain cuts of beef. In humans, excess accumulation of intramuscular fat is associated with insulin resistance and type 2 diabetes.
BTO:0004043
uberon
intramuscular fat
UBERON:0019143
intramuscular adipose tissue
Adipose tissue which is located throughout skeletal muscle and is responsible for the marbling seen in certain cuts of beef. In humans, excess accumulation of intramuscular fat is associated with insulin resistance and type 2 diabetes.
BTO:0004043
intramuscular fat
BTO:0004043
Any region of epithelium that is part of a skin region.
BTO:0004382
uberon
UBERON:0019204
skin epithelium
Any region of epithelium that is part of a skin region.
The part of the eye that consists of both the retina and the optic choroid
chorioretina
choroid and retina
retinachoroid
retinachoroidal region
uberon
UBERON:0019207
chorioretinal region
The part of the eye that consists of both the retina and the optic choroid
UBERON:drseb
DHBA:10654
FMA:268630
gray matter of the hindbrain
uberon
UBERON:0019263
gray matter of hindbrain
gray matter of the hindbrain
DHBA:HGM
DHBA:10649
FMA:83913
uberon
UBERON:0019267
gray matter of midbrain
EMAPA:35952
MA:0003174
uberon
UBERON:0019304
sensory organ epithelium
An exocrine gland that is part of a integumental system.
integumental exocrine gland
integumental system exocrine gland
uberon
UBERON:0019319
exocrine gland of integumental system
An exocrine gland that is part of a integumental system.
GOC:dos
integumental exocrine gland
integumental system exocrine gland
FMA:58315
uberon
surface of region of wall of eyeball
UBERON:0022288
surface of eyeball
surface of region of wall of eyeball
FMA:58315
A portion of organism substance that is secreted by a reproductive gland.
uberon
genital fluid
genital secretion
reproductive system fluid
reproductive system fluid/secretion
reproductive system secretion
UBERON:0022293
reproductive gland secretion
A portion of organism substance that is secreted by a reproductive gland.
UBERON:cjm
Single layer of a laminar structure, identified by different density, arrangement or size of cells and processes arranged in flattened layers or lamina[CUMBO].
this is currently used to group some cellular layers that may not strictly conform to the CARO definition of cell-part layer. Consider genericisizing and introducing subtypes for cellular layer, fibrous layer and cell soma layer
lamina
layer
NLX:149357
uberon
UBERON:0022303
nervous system cell part layer
Single layer of a laminar structure, identified by different density, arrangement or size of cells and processes arranged in flattened layers or lamina[CUMBO].
NLX:149357
lamina
CUMBO:CUMBO
layer
CUMBO:CUMBO
Serous membrane layer that is adjacent to and lines an organ.
FMA:15860
visceral wall of serous membrane
uberon
UBERON:0022350
visceral serous membrane
Serous membrane layer that is adjacent to and lines an organ.
visceral wall of serous membrane
FMA:15860
Serous membrane layer that lines to a body cavity.
cavity lining
FMA:15859
MA:0002448
parietal wall of serous membrane
uberon
UBERON:0022351
parietal serous membrane
Serous membrane layer that lines to a body cavity.
cavity lining
MA:0002448
parietal wall of serous membrane
FMA:15859
An embryonic or larval epithelium that is committed to form part of the nervous system.
neurepithelium
AEO:0001008
BTO:0000314
EHDAA2_RETIRED:0004654
FMA:64807
embryonic neuroepithelium
neuroepithelium
uberon
UBERON:0034705
developing neuroepithelium
An embryonic or larval epithelium that is committed to form part of the nervous system.
AEO:0001008
AEO:JB
neurepithelium
BTO:0000314
embryonic neuroepithelium
neuroepithelium
AEO:0001008
An epithelium that is undergoing proliferation to provide large numbers of neuronal cells.
AEO:0001009
uberon
UBERON:0034706
proliferating neuroepithelium
AEO
An epithelium that is undergoing proliferation to provide large numbers of neuronal cells.
AEO:0001009
A neuroepithelium some of whose cells are undergoing terminal differentiation to become neuronal cells.
AEO:0001010
uberon
UBERON:0034707
differentiating neuroepithelium
AEO
A neuroepithelium some of whose cells are undergoing terminal differentiation to become neuronal cells.
AEO:0001010
DHBA:12694
EMAPA:32916
marginal zone of hindbrain
uberon
MZH
UBERON:0034709
hindbrain marginal layer
marginal zone of hindbrain
DHBA:12694
MZH
DHBA:12694
EHDAA2:0001267
EMAPA:17585
spinal cord lateral wall ventricular layer
uberon
UBERON:0034710
spinal cord ventricular layer
EHDAA2
spinal cord lateral wall ventricular layer
EHDAA2:0001267
the area of axial mesoderm that develops into the prechordal plate
prechordal mesenchyme
uberon
UBERON:0034878
prechordal mesoderm
the area of axial mesoderm that develops into the prechordal plate
MGI:anna
lumen of gland
uberon
UBERON:0034905
gland lumen
An multicellular anatomical structure that has subparts of multiple organs as a part.
CARO:0020001
uberon
anatomical cluster
UBERON:0034921
multi organ part structure
CARO
An multicellular anatomical structure that has subparts of multiple organs as a part.
CARO:0020001
anatomical cluster
CARO:0020001
A cluster of cells, largely surrounded by a morphological boundary.
CARO:0020002
FMA:62807
uberon
UBERON:0034922
cell cluster
CARO
A cluster of cells, largely surrounded by a morphological boundary.
CARO:0020002
A collection of anatomical structures that are alike in terms of their morphology or developmental origin.
resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected
uberon
UBERON:0034925
anatomical collection
A collection of anatomical structures that are alike in terms of their morphology or developmental origin.
Any organ component layer that consists of smooth muscle tissue.
uberon
UBERON:0034933
layer of smooth muscle tissue
Any organ component layer that consists of smooth muscle tissue.
FMA:55268
organ sector
organ zonal region
organ zone
uberon
organ region with floating fiat boundary
UBERON:0034944
zone of organ
organ sector
FMA:55268
organ zone
FMA:55268
organ region with floating fiat boundary
FMA:55268
NCIT:C25787
uberon
duct epithelium
ductal epithelium
UBERON:0034969
epithelial layer of duct
Mesenchyme that is part of a developing jaw [Automatically generated definition].
EMAPA:32907
EMAPA:35454
uberon
UBERON:0034995
jaw mesenchyme
Mesenchyme that is part of a developing jaw [Automatically generated definition].
OBOL:automatic
EMAPA:32904
MA:0003220
uberon
UBERON:0035037
jaw epithelium
Any material entity that is located in the digestive tract. This includes undigested food and liquid as well as unexcreted waste products. It also includes other entities such as ingested stones used to aid digestion. Any microbial cells or cell populations are also included.
Note that we treat any material entity that is ingested as an anatomical structure by defintion, although this may be expanding the CARO usage somewhat
digestive tract contents
uberon
ingested material entity
UBERON:0035118
material entity in digestive tract
Any material entity that is located in the digestive tract. This includes undigested food and liquid as well as unexcreted waste products. It also includes other entities such as ingested stones used to aid digestion. Any microbial cells or cell populations are also included.
digestive tract contents
Anatomical surface, which is the external surface of the whole body. Examples: There is only one body surface.
FMA:61695
NCIT:C29667
surface of body
uberon
UBERON:0035159
entire surface of organism
Anatomical surface, which is the external surface of the whole body. Examples: There is only one body surface.
FMA:61695
surface of body
FMA:61695
FMA:51797
ciliary vein
uberon
UBERON:0035546
uveal vein
ciliary vein
FMA:51797
The part of the circulatory system that lies within the subcutaneous tissue layers close to the surface of the skin.
FMA:225275
superficial part of circulatory system
superficial vasculature
dermis vasculature
hypodermis vasculature
uberon
skin vasculature
subcutaneous vasculature
vasculature of skin
UBERON:0035549
vasculature of integument
The part of the circulatory system that lies within the subcutaneous tissue layers close to the surface of the skin.
vasculature of skin
FMA:225275
Any of the veins carrying deoxygenated blood from the subcutaneous tissue layers.
FMA:76719
NCIT:C33666
uberon
superfical vein
superficial veins
superficial vessels
UBERON:0035550
superficial vein
Any of the veins carrying deoxygenated blood from the subcutaneous tissue layers.
ncithesaurus:Superficial_Vein
superfical vein
superficial veins
superficial vessels
The part of the circulatory system that lies deep beneath the subcutaneous tissue layers away from the surface of the skin.
deep part of circulatory system
uberon
UBERON:0035551
deep vasculature
The part of the circulatory system that lies deep beneath the subcutaneous tissue layers away from the surface of the skin.
A blood vessel carrying deoxygenated blood far beneath the skin usually accompanying an artery.
FMA:76718
NCIT:C32444
uberon
deep veins
deep vessels
UBERON:0035552
deep vein
A blood vessel carrying deoxygenated blood far beneath the skin usually accompanying an artery.
ncithesaurus:Deep_Vein
deep veins
deep vessels
The parts of the orbital region that are outside of the the eyeball, including the lacrimal apparatus, the extraocular muscles and the eyelids, eyelashes, eyebrows and the conjunctiva
FMA:76554
NCIT:C32574
adnexa oculi
uberon
accessory parts of orbital region
accessory visual structures
accessory visual structures set
adnexal parts of orbital region
appendage of eye
appendages of the eye
eye adnexa
set of accessory visual structures
structurae oculi accessoriae
UBERON:0035639
ocular adnexa
The parts of the orbital region that are outside of the the eyeball, including the lacrimal apparatus, the extraocular muscles and the eyelids, eyelashes, eyebrows and the conjunctiva
HPO:pr
UBERON:cjm
adnexa oculi
accessory visual structures
accessory visual structures
FMA:76554
accessory visual structures set
FMA:76554
appendage of eye
appendages of the eye
set of accessory visual structures
FMA:76554
structurae oculi accessoriae
EHDAA2:0004181
FMA:9464
cardiac chamber cavity
heart cavity
heart lumen
uberon
UBERON:0035763
cavity of cardiac chamber
FMA
cardiac chamber cavity
FMA:9464
heart cavity
FMA:9464
heart lumen
EHDAA2:0004181
The primordial mouth region of the developing head.
FMA:293105
primitive mouth
primordial mouth
uberon
UBERON:0035804
future mouth
The primordial mouth region of the developing head.
MP:0003119
primitive mouth
FMA:293105
FMA:12241
uberon
UBERON:0035809
serous cavity
The sum of epicardial and paracardial fat deposits.
ZFA:0005765
uberon
UBERON:0035814
pericardial fat
The sum of epicardial and paracardial fat deposits.
Fat deposits in the mediastinum outside the parietal pericardium .
intrathoracic fat
uberon
UBERON:0035815
paracardial fat
Fat deposits in the mediastinum outside the parietal pericardium .
intrathoracic fat
Any fat deposit surrounding a visceral organ.
uberon
UBERON:0035818
visceral fat
Any fat deposit surrounding a visceral organ.
UBERON:cjm
BTO:0004378
EMAPA:37987
FMA:67473
blood vessel wall
uberon
vascular wall
UBERON:0035965
wall of blood vessel
EMAPA:37987
MA:th
blood vessel wall
FMA:67473
vascular wall
BTO:0004378
An region of the mesoderm that includes anterior lateral mesoderm of the first heart field plus contiguous pharyngeal mesoderm that gives rise to second-heart-field-derived regions of the heart and branchiomeric muscles.
uberon
UBERON:0036146
cardiopharyngeal field
An region of the mesoderm that includes anterior lateral mesoderm of the first heart field plus contiguous pharyngeal mesoderm that gives rise to second-heart-field-derived regions of the heart and branchiomeric muscles.
BGEE:ann
Material anatomical entity that forms the outermost boundary of an anatomical structure.
AAO:0010270
AEO:0000154
ZFA:0005594
uberon
UBERON:0036215
anatomical surface region
Material anatomical entity that forms the outermost boundary of an anatomical structure.
A bodily fluid that is located in the coelom.
he coelomic fluid serves several functions; it acts as a hydroskeleton, it allows free movement and growth of internal organs, it serves for transport of gases, nutrients and waste products between different parts of the body, it allows storage of sperm and eggs during maturation and it acts as a reservoir for waste [Wikipedia:Coelom#Coelomic_fluid]
BTO:0001708
uberon
UBERON:0036217
coelomic fluid
A bodily fluid that is located in the coelom.
Any gland that is part os the respiratory system.
uberon
UBERON:0036225
respiratory system gland
Any gland that is part os the respiratory system.
UBERON:cjm
A notochord that has persisted beyond the embryonic stage.
uberon
UBERON:0036242
post-embryonic notochord
A notochord that has persisted beyond the embryonic stage.
UBERON:cjm
A transudate found in the serous sac.
serous fluid
FMA:20932
serous sac fluid
uberon
UBERON:0036244
secretion of serous membrane
A transudate found in the serous sac.
FMA:20932
serous fluid
FMA:20932
FMA:53133
cranial orifice
skull orifice
uberon
UBERON:0036253
orifice of skull
cranial orifice
FMA:53133
skull orifice
FMA:53133
A mucosa that is part of a lip region [Automatically generated definition].
NCIT:C12226
labial mucosa
uberon
UBERON:0036294
mucosa of lip
A mucosa that is part of a lip region [Automatically generated definition].
OBOL:automatic
labial mucosa
UBERON:cjm
uberon
UBERON:0036302
vasculature of central nervous system plus retina
FMA:259905
uberon
UBERON:0036303
vasculature of central nervous system
FMA:231590
uberon
UBERON:0036553
wall of synovial tendon sheath
FMA
FMA
FMA:58098
eyeball wall
uberon
UBERON:0036925
wall of eyeball
FMA
FMA
eyeball wall
FMA:58098
wall of organ which has as its parts the endocardium, myocardium , epicardium, and the cardiac septum, surrounded by the pericardial sac proper and is continuous with the walls of the systemic and pulmonary arterial and venous trees.
FMA:7274
cardiac wall
uberon
UBERON:0037144
wall of heart
FMA
FMA
FMA
FMA
wall of organ which has as its parts the endocardium, myocardium , epicardium, and the cardiac septum, surrounded by the pericardial sac proper and is continuous with the walls of the systemic and pulmonary arterial and venous trees.
FMA:7274
cardiac wall
FMA:7274
A zone of skin that is part of the face.
eriks
2012-02-05T05:23:01Z
EMAPA:36657
FMA:24758
NCIT:C33561
UMLS:C0222084
face skin
uberon
facial skin
UBERON:1000021
skin of face
A zone of skin that is part of the face.
UBERON:EJS
UMLS:C0222084
ncithesaurus:Skin_of_the_Face
face skin
EMAPA:36657
FMA:24758
An anatomical junction between two parts of the digestive tract.
2021-02-05T11:19:31Z
uberon
UBERON:1100000
digestive tract junction
An anatomical junction between two parts of the digestive tract.
ORCID:0000-0002-7073-9172
Cartilage which is part of the axial skeleton.
This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon
teleost_anatomy_curators
ZFA:0001457
uberon/phenoscape-anatomy
postcranial axial cartilage
Cartilage which is part of the axial skeleton.
ZFIN:curator
Structures of the dermis, epidermis, glands and pigment cells recognizable on the external surfaces of the integument.
This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon
amphibian_anatomy_curators
uberon/phenoscape-anatomy
Not clear how this differs from parent class. See https://github.com/obophenotype/uberon/issues/1305
external integument structure
Structures of the dermis, epidermis, glands and pigment cells recognizable on the external surfaces of the integument.
AAO:EJS
Dermal, epidermal, glandular and pigment structures of the external head integument.
This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon
amphibian_anatomy_curators
uberon/phenoscape-anatomy
head external integument structure
Dermal, epidermal, glandular and pigment structures of the external head integument.
AAO:EJS
Dermal, epidermal, glandular and pigment structures of the body integument.
This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon
amphibian_anatomy_curators
uberon/phenoscape-anatomy
body external integument structure
Dermal, epidermal, glandular and pigment structures of the body integument.
AAO:EJS
Blood vessels in respiratory skin.
Modified from the original AAO source
amphibian_anatomy_curators
uberon/phenoscape-anatomy
vasculature of respiratory integument
Blood vessels in respiratory skin.
AAO:EJS
An anatomical surface that is part of a bone
bone surface
surface of bone
A region of cuticle and its underlying epidermis.
FBbt:00007284
uberon
UBERON:6007284
insect region of integument
A region of cuticle and its underlying epidermis.
FBC:DOS
FBbt:00007289
uberon
UBERON:6007289
insect tagmatic subdivision of integument
The cranio-antennal muscle that is attached to the dorsal tentorial arm and the proximal margin of the scapus.
anterior tentorio-scapal muscle
lagonzalezmo
lagonzalezmo
lagonzalezmo
The cranio-antennal muscle that is attached to the dorsal tentorial arm and the proximal margin of the scapus.
lagonzalezmo
2021-04-03
anterior tentorio-scapal muscle
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
"Origin: Anterior or dorsal tentorial arms"
"Insertion: Anterior (ventral) basal margin of the scape"
The cranio-antennal muscle that is continuous with the dorsal or anterior tentorial arm and the proximo-dorsal margin of the scapus.
posterior tentorio-scapal muscle
lagonzalezmo
jgiron
jgiron
The cranio-antennal muscle that is continuous with the dorsal or anterior tentorial arm and the proximo-dorsal margin of the scapus.
lagonzalezmo
2021-04-03
posterior tentorio-scapal muscle
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
"Origin: Anterior or dorsal tentorial arms"
"Insertion: Posterior (dorsal) basal margin of the scape"
The cranio-antennal muscle that extends between the dorsal or anterior tentorial arm and the proximo-lateral margin of the scapus.
lateral tentorio-scapal muscle
lagonzalezmo
jgiron
jgiron
The cranio-antennal muscle that extends between the dorsal or anterior tentorial arm and the proximo-lateral margin of the scapus.
lagonzalezmo
2021-04-03
lateral tentorio-scapal muscle
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
"Origin: Anterior or dorsal tentorial arms"
"Insertion: Lateral basal margin of the scape"
The cranio-antennal muscle that is continuous with the dorsal or anterior tentorial arm and the proximal margin of the scapus.
medial tentorio-scapal muscle
lagonzalezmo
lagonzalezmo
lagonzalezmo
The cranio-antennal muscle that is continuous with the dorsal or anterior tentorial arm and the proximal margin of the scapus.
lagonzalezmo
2021-04-03
medial tentorio-scapal muscle
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
"Origin: Anterior or dorsal tentorial arms"
"Insertion: Mesal basal margin of the scape"
The cranio-antennal muscle that is continuous with the frons and the pedicellus.
fronto-pedicellar muscle
lagonzalezmo
lagonzalezmo
lagonzalezmo
The cranio-antennal muscle that is continuous with the frons and the pedicellus.
lagonzalezmo
2021-04-03
fronto-pedicellar muscle
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
"Origin: Frons"
"Insertion: Lateral edge of the pedicel"
The cranio-antennal muscle that is continuous with the dorsal or dorsolateral regions of the scapus and the lateral or dorsolateral regions of the pedicellus.
lateral scapo-pedicellar muscle
lagonzalezmo
lagonzalezmo
lagonzalezmo
The cranio-antennal muscle that is continuous with the dorsal or dorsolateral regions of the scapus and the lateral or dorsolateral regions of the pedicellus.
lagonzalezmo
2021-04-03
lateral scapo-pedicellar muscle
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
"Origin: Dorsal or dorsolateral wall of the scape"
"Insertion: Lateral or dorsolateral wall of the pedicel"
The cranio-antennal muscle that is continuous with the scapus and the pedicellus.
medial scapo-pedicellar muscle
lagonzalezmo
lagonzalezmo
lagonzalezmo
The cranio-antennal muscle that is continuous with the scapus and the pedicellus.
lagonzalezmo
2021-04-03
medial scapo-pedicellar muscle
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
"Origin: Mesal or dorsomesal wall of the scape"
"Insertion: Mesal, anteriomesal or anterior edge of the pedicel"
The cranio-labral muscle that is continuous with the frons and the labrum.
frontolabral muscle
lagonzalezmo
lagonzalezmo
The cranio-labral muscle that is continuous with the frons and the labrum.
lagonzalezmo
2021-04-03
frontolabral muscle
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
"Origin: Mesally on the frons or on the antennal base"
"Insertion: Mesally on the outer basal wall of the labrum"
The cranio-labral muscle that is continuous with the frontoclypeal ridge and the labrum.
epistoepipharyngeal muscle
lagonzalezmo
lagonzalezmo
The cranio-labral muscle that is continuous with the frontoclypeal ridge and the labrum.
lagonzalezmo
2021-04-03
epistoepipharyngeal muscle
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
"Origin: Epistomal sulcus"
"Insertion: Basal labral wall"
The cranio-labral muscle that is continuous with the frons and the tormae.
frontoepypharyngeal muscle
lagonzalezmo
lagonzalezmo
lagonzalezmo
The cranio-labral muscle that is continuous with the frons and the tormae.
lagonzalezmo
2021-04-03
frontoepypharyngeal muscle
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
"Origin: Mesally on the frons or on the antennal base,
usually on the same level as musculus
frontolabralis"
"Insertion: Basal labral wall or tormae"
The apodeme at either side of the proximal margin of the labrum.
tormae
lagonzalezmo
jgiron
The apodeme at either side of the proximal margin of the labrum.
jgiron
2021-04-22
tormae
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Tormae: lateral apodemes of labral base"
The cranio-labral muscle that extends betwen the sides of the labrum.
transversal labral muscle
lagonzalezmo
jgiron
jgiron
The cranio-labral muscle that extends betwen the sides of the labrum.
lagonzalezmo
2021-04-03
transversal labral muscle
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
"Origin: Ventral labral wall"
"Insertion: Ventral labral wall of the other side"
The cranio-mandibular muscle that is continuous with the head capsule and the insect mandible.
internal cranio-mandibular muscle
lagonzalezmo
The cranio-mandibular muscle that is continuous with the head capsule and the insect mandible.
lagonzalezmo
2021-04-03
internal cranio-mandibular muscle
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
"Origin: Ventral, posterior, lateral and/or dorsal parts of
the head capsule and/or posterior and
anterior tentorial arms"
"Insertion: Tendon that inserts at the median edge of the
mandible"
The cranio-mandibular muscle that extends between the gena and the lateral margin of the insect mandible.
posteroexternal cranio-mandibular muscle
lagonzalezmo
lagonzalezmo
lagonzalezmo
The cranio-mandibular muscle that extends between the gena and the lateral margin of the insect mandible.
lagonzalezmo
2021-04-03
posteroexternal cranio-mandibular muscle
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
"Origin: Gena and postgena"
"Insertion: Tendon that inserts at the lateral edge of the mandible"
The cranio-mandibular muscle that is continuous with the gena and the insect mandible.
anteroexternal cranio-mandibular muscle
lagonzalezmo
lagonzalezmo
The cranio-mandibular muscle that is continuous with the gena and the insect mandible.
lagonzalezmo
2021-04-03
anteroexternal cranio-mandibular muscle
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
"Origin: Gena, below the compound eye"
"Insertion: With a tendon on the mandible, posterior to the anterior articulation complex"
The sclerite of the hypopharynx.
fulturae
hypopharyngeal arms
oral arms
suspensorium
jgiron
lagonzalezmo
The sclerite of the hypopharynx.
jgiron
2021-04-22
fulturae
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
hypopharyngeal arms
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
oral arms
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
suspensorium
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Suspensorium (=fulturae, hypopharyngeal arms, oral arms): sclerotized strengthening elements of proximal hypopharynx."
The cranio-mandibular muscle that is continuous with the suspensorium and the insect mandible.
hypopharyngeomandibular muscle
lagonzalezmo
lagonzalezmo
The cranio-mandibular muscle that is continuous with the suspensorium and the insect mandible.
lagonzalezmo
2021-04-03
hypopharyngeomandibular muscle
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
"Origin: Small sclerite close to the loral arm
(Thermobia), scleroticed arm that elongates
the loral arm (Neoptera)"
"Insertion: Inner side of the lateral wall of the mandible"
The cranio-mandibular muscle that is continuous with the dorsal tentorial arm and the proximal margin of the insect mandible.
superolateral tentorio-mandibular muscle
lagonzalezmo
lagonzalezmo
jgiron
The cranio-mandibular muscle that is continuous with the dorsal tentorial arm and the proximal margin of the insect mandible.
lagonzalezmo
2021-04-03
superolateral tentorio-mandibular muscle
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
"Origin: Anterior and dorsal tentorial arm"
"Insertion: Outer basal edge of the mandibular body, between processus paratentorialis and posterior articulation"
The cranio-mandibular muscle that extends between the anterior tentorial arm and the proximal-ventral margin of the insect mandible.
inferolateral tentorio-mandibular muscle
lagonzalezmo
lagonzalezmo
jgiron
The cranio-mandibular muscle that extends between the anterior tentorial arm and the proximal-ventral margin of the insect mandible.
lagonzalezmo
2021-04-03
inferolateral tentorio-mandibular muscle
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
"Origin: Anterior tentorial arm"
"Insertion: Ventral basal margin of the mandible"
The cranio-mandibular muscle that is continuous with the anterior tentorial arm and the insect mandible.
superomedial tentorio-mandibular muscle
lagonzalezmo
lagonzalezmo
The cranio-mandibular muscle that is continuous with the anterior tentorial arm and the insect mandible.
lagonzalezmo
2021-04-03
superomedial tentorio-mandibular muscle
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
"Origin: Anterior and dorsal tentorial arm below musculus
tentoriomandibularis externus dorsalis"
"Insertion: Upper inner end of the mandible, just below the
posterior mandibular condyle"
The cranio-mandibular muscle that extends between the anterior tentorial arm and the dorso-medial region of the insect mandible.
inferomedial tentorio-mandibular muscle
lagonzalezmo
lagonzalezmo
jgiron
The cranio-mandibular muscle that extends between the anterior tentorial arm and the dorso-medial region of the insect mandible.
lagonzalezmo
2021-04-03
inferomedial tentorio-mandibular muscle
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
"Origin: Anterior tentorial arm, below musculus tentoriomandibularis lateralis superior"
"Insertion: Mediodorsal wall of the mandibular cavity"
The skeletal muscle continuous with the head capsule and the insect maxilla.
insect cranio-maxillar muscle
lagonzalezmo
lagonzalezmo
lagonzalezmo
The skeletal muscle continuous with the head capsule and the insect maxilla.
lagonzalezmo
2021-04-04
The cranio-maxillar muscle that is continuous with the gena and the cardo.
cranio-cardinal muscle
lagonzalezmo
lagonzalezmo
lagonzalezmo
The cranio-maxillar muscle that is continuous with the gena and the cardo.
lagonzalezmo
2021-04-03
cranio-cardinal muscle
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
"Origin: Postgena and gena"
"Insertion: Basal cardinal process"
The cranio-maxillar muscle that is continuous with the gena and the lacinia.
cranio-lacinial muscle
lagonzalezmo
lagonzalezmo
lagonzalezmo
The cranio-maxillar muscle that is continuous with the gena and the lacinia.
lagonzalezmo
2021-04-03
cranio-lacinial muscle
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
"Origin: Posterior part of the gena"
"Insertion: Basal edge of lacinia"
The cranio-maxillar muscle that is continuous with the tentorium and the cardo.
tentorio-cardinal muscle
lagonzalezmo
lagonzalezmo
lagonzalezmo
The cranio-maxillar muscle that is continuous with the tentorium and the cardo.
lagonzalezmo
2021-04-03
tentorio-cardinal muscle
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
"Origin: Tentorium"
"Insertion: Distal part of the cardo, close to the carostipital
sulcus"
The cranio-maxillar muscle that is continuous with the tentorium and the stipital ridge.
anterior tentorio-stipital muscle
lagonzalezmo
lagonzalezmo
lagonzalezmo
The cranio-maxillar muscle that is continuous with the tentorium and the stipital ridge.
lagonzalezmo
2021-04-03
anterior tentorio-stipital muscle
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
"Origin: Tentorium"
"Insertion: Stipital ridge"
The ridge that is part of the stipes.
stipital ridge
lagonzalezmo
lagonzalezmo
The ridge that is part of the stipes.
jgiron
2021-04-22
stipital ridge
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
The cranio-maxillar muscle that is continuous with the tentorium and the stipes.
posterior tentorio-stipital muscle
lagonzalezmo
lagonzalezmo
lagonzalezmo
The cranio-maxillar muscle that is continuous with the tentorium and the stipes.
lagonzalezmo
2021-04-03
posterior tentorio-stipital muscle
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
"Origin: Tentorium"
"Insertion: Basally on the stipes, close to the stipitocardinal
suture"
The cranio-maxillar muscle that is continuous with the stipes and the lacinia.
stipito-lacinial muscle
lagonzalezmo
lagonzalezmo
lagonzalezmo
The cranio-maxillar muscle that is continuous with the stipes and the lacinia.
lagonzalezmo
2021-04-03
stipito-lacinial muscle
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
"Origin: Lateral wall of the stipes, basal to the maxillary
palpus"
"Insertion: Basal edge of lacinia, in some cases common
tendon with 0mx4"
The cranio-maxillar muscle that is continuous with the stipes and the galea.
stipito-galeal muscle
lagonzalezmo
lagonzalezmo
lagonzalezmo
The cranio-maxillar muscle that is continuous with the stipes and the galea.
lagonzalezmo
2021-04-03
stipito-galeal muscle
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
"Origin: Lateral wall of the stipes, basal to the maxillary
palpus"
"Insertion: Basal edge of galea"
The cranio-maxillar muscle that is continuous with the stipes and the maxillary palpus.
stipito-palpal muscle
lagonzalezmo
lagonzalezmo
lagonzalezmo
The cranio-maxillar muscle that is continuous with the stipes and the maxillary palpus.
lagonzalezmo
2021-04-03
stipito-palpal muscle
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
The mere that is part of the maxillary palpus.
maxillary palpomere
jgiron
jgiron
The mere that is part of the maxillary palpus.
jgiron
2021-04-21
The maxillary palpomere that is attached to the distal margin of the palpiger and to the proximal margin of the maxillary palpomere II.
maxillary palpomere I
jgiron
jgiron
lagonzalezmo
The maxillary palpomere that is attached to the distal margin of the palpiger and to the proximal margin of the maxillary palpomere II.
jgiron
2021-04-21
maxillary palpomere I
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
The maxillary palpomere that is attached to the distal margin of the maxillary palpomere I and to the proximal margin of the maxillary palpomere III.
maxillary palpomere II
jgiron
lagonzalezmo
jgiron
jgiron
The maxillary palpomere that is attached to the distal margin of the maxillary palpomere I and to the proximal margin of the maxillary palpomere III.
jgiron
2021-04-21
maxillary palpomere II
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
The maxillary palpomere that is attached to the distal margin of the maxillary palpomere II and to the proximal margin of the maxillary palpomere IV.
maxillary palpomere III
jgiron
lagonzalezmo
jgiron
jgiron
The maxillary palpomere that is attached to the distal margin of the maxillary palpomere II and to the proximal margin of the maxillary palpomere IV.
jgiron
2021-04-21
maxillary palpomere III
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
The maxillary palpomere that is attached to the distal margin of the maxillary palpomere III and to the proximal margin of the maxillary palpomere V.
maxillary palpomere IV
lagonzalezmo
maxillary palpomere IV
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
The maxillary palpomere that is attached to the distal margin of the maxillary palpomere IV.
maxillary palpomere V
lagonzalezmo
lagonzalezmo
maxillary palpomere V
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
The cranio-maxillar muscle that is continuous with the first maxillar palpomere and the second maxillar palpomere.
first maxillar palpopalpal muscle
lagonzalezmo
lagonzalezmo
lagonzalezmo
The cranio-maxillar muscle that is continuous with the first maxillar palpomere and the second maxillar palpomere.
lagonzalezmo
2021-04-03
first maxillar palpopalpal muscle
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
"Origin: Basal edge of palpomere 1"
"Insertion: Basal edge of palpomere 2"
The cranio-maxillar muscle that is continuous with the second maxillar palpomere and the third maxillar palpomere.
second maxillar palpopalpal muscle
lagonzalezmo
lagonzalezmo
lagonzalezmo
The cranio-maxillar muscle that is continuous with the second maxillar palpomere and the third maxillar palpomere.
lagonzalezmo
2021-04-03
second maxillar palpopalpal muscle
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
"Origin: Mesal edge of palpomere 2"
"Insertion: Mesal edge of palpomere 3"
The cranio-maxillar muscle that is continuous with the third maxillar palpomere and the fourth maxillar palpomere.
third maxillar palpopalpal muscle
lagonzalezmo
lagonzalezmo
lagonzalezmo
The cranio-maxillar muscle that is continuous with the third maxillar palpomere and the fourth maxillar palpomere.
lagonzalezmo
2021-04-03
third maxillar palpopalpal muscle
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
"Origin: Basal edge of palpomere 3"
"Insertion: Basal edge of palpomere 4"
The cranio-maxillar muscle that is continuous with the fourth maxillar palpomere and the fifth maxillar palpomere.
fourth maxillar palpopalpal muscle
lagonzalezmo
lagonzalezmo
lagonzalezmo
The cranio-maxillar muscle that is continuous with the fourth maxillar palpomere and the fifth maxillar palpomere.
lagonzalezmo
2021-04-03
fourth maxillar palpopalpal muscle
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
"Origin: Mesal edge of palpomere 4"
"Insertion: Mesal edge of palpomere 5"
The cranio-labial muscle that is continuous with the postoccipital phragma and the glossa.
postoccipitoglossal muscle
lagonzalezmo
lagonzalezmo
lagonzalezmo
The cranio-labial muscle that is continuous with the postoccipital phragma and the glossa.
lagonzalezmo
2021-04-03
postoccipitoglossal muscle
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
"Origin: Postoccipital phragma"
"Insertion: glossa"
The internal apodeme that is continuous with the cuticle of the notum and is attached to a dorsal longitudinal muscle.
phragma
lagonzalezmo
imiko
lagonzalezmo
imiko
The internal apodeme that is continuous with the cuticle of the notum and is attached to a dorsal longitudinal muscle.
lagonzalezmo
2021-04-03
phragma
Beutel RG, Friedrich F, Yang X-K, Ge S-Q (2014) Insect Morphology and Phylogeny Insect morphology and phylogeny: a textbook for students of entomology. De Gruyter.
https://doi.org/10.1515/9783110264043
"Phragma: large, ridge-shaped internal apodeme."
"Phragma (=antecosta): dorsal thoracic transverse ridge, attachment site of dorsal longitudinal indirect flight muscles." (p. 121)
The phragma that is continuous with the postocciput.
postoccipital phragma
jgiron
The phragma that is continuous with the postocciput.
jgiron
2021-04-09
postoccipital phragma
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
The cranio-labial muscle that is continuous with the postoccipital phragma and the prementum.
postoccipitopremental muscle
lagonzalezmo
lagonzalezmo
lagonzalezmo
The cranio-labial muscle that is continuous with the postoccipital phragma and the prementum.
lagonzalezmo
2021-04-03
postoccipitopremental muscle
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
"Origin: Postoccipital phragma, laterad to musculus
postoccipitoparaglossalis"
"Insertion: Posteriolateral angle of the prementum"
The cranio-labial muscle that is continuous with the posterior tentorial arm and the prementum.
tentorio-premental muscle
lagonzalezmo
lagonzalezmo
lagonzalezmo
The cranio-labial muscle that is continuous with the posterior tentorial arm and the prementum.
lagonzalezmo
2021-04-03
tentorio-premental muscle
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
"Origin: Posterior tentorial arms, cranium"
"Insertion: Laterobasal edge of prementum"
The cranio-labial muscle that is continuous with the posterior tentorial arm and the paraglossa.
tentorio-paraglossal muscle
lagonzalezmo
lagonzalezmo
lagonzalezmo
The cranio-labial muscle that is continuous with the posterior tentorial arm and the paraglossa.
lagonzalezmo
2021-04-03
tentorio-paraglossal muscle
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
"Origin: Posterior tentorial arms, postoccipital ridge or
cranium"
"Insertion: Paraglossa, close to the labial palp"
The cranio-labial muscle that is continuous with the submentum and the prementum.
submentopremental muscle
lagonzalezmo
lagonzalezmo
lagonzalezmo
The cranio-labial muscle that is continuous with the submentum and the prementum.
lagonzalezmo
2021-04-03
submentopremental muscle
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
"Origin: Mediobasal part of submentum or gula"
"Insertion: Mediobasal edge of prementum, close to the gales"
The cranio-labial muscle that is continuous with the submentum and the mentum.
submentomental muscle
lagonzalezmo
lagonzalezmo
lagonzalezmo
The cranio-labial muscle that is continuous with the submentum and the mentum.
lagonzalezmo
2021-04-03
submentomental muscle
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
"Origin: submentum"
"Insertion: mentum"
The cranio-labial muscle that is continuous with the prementum and the paraglossa.
premento-paraglossal muscle
lagonzalezmo
lagonzalezmo
lagonzalezmo
The cranio-labial muscle that is continuous with the prementum and the paraglossa.
lagonzalezmo
2021-04-03
premento-paraglossal muscle
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
"Origin: Mesal on the basal edge of the prementum"
"Insertion: Dorsobasal edge of paraglossa"
The cranio-labial muscle that is continuous with the prementum and the glossa.
premento-glossal muscle
lagonzalezmo
lagonzalezmo
lagonzalezmo
The cranio-labial muscle that is continuous with the prementum and the glossa.
lagonzalezmo
2021-04-03
premento-glossal muscle
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
"Origin: Mesally on the prementum"
"Insertion: Mediobasal edge of glossa"
The cranio-labial muscle that is continuous with the prementum and the labial palpus.
premento-palpal muscle
lagonzalezmo
lagonzalezmo
lagonzalezmo
The cranio-labial muscle that is continuous with the prementum and the labial palpus.
lagonzalezmo
2021-04-03
premento-palpal muscle
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
"Origin: prementum"
"Insertion: labial palpus"
The skeletal muscle continuous with the head capsule and the hypopharynx.
cranio-hypopharyngeal muscle
lagonzalezmo
lagonzalezmo
The skeletal muscle continuous with the head capsule and the hypopharynx.
lagonzalezmo
2021-04-04
The cranio-antennal muscle that is continuous with the frons and the suspensorium.
fronto-oral muscle
lagonzalezmo
lagonzalezmo
lagonzalezmo
The cranio-antennal muscle that is continuous with the frons and the suspensorium.
lagonzalezmo
2021-04-03
fronto-oral muscle
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
"Origin: Frons"
"Insertion: Oral arms of the suspensorial sclerites"
The cranio-antennal muscle that is continuous with the anterior tentorial arm and the suspensorium.
tentorio-oral muscle
lagonzalezmo
lagonzalezmo
lagonzalezmo
The cranio-antennal muscle that is continuous with the anterior tentorial arm and the suspensorium.
lagonzalezmo
2021-04-03
tentorio-oral muscle
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
"Origin: Anterior tentorial arm, epistomal sulcus or
frons close to epistomal sulcus"
"Insertion: Oral arms of the suspensorial sclerites, well
seperated from above"
The skeletal muscle continuous with the head capsule and the tentorium.
insect cranio-tentorial muscle
lagonzalezmo
lagonzalezmo
lagonzalezmo
The skeletal muscle continuous with the head capsule and the tentorium.
lagonzalezmo
2021-04-04
The cranio-antennal muscle that is continuous with the tentorial bridge and the frons.
tentorio-frontal muscle
lagonzalezmo
lagonzalezmo
lagonzalezmo
The cranio-antennal muscle that is continuous with the tentorial bridge and the frons.
lagonzalezmo
2021-04-03
tentorio-frontal muscle
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
"Origin: Laterad on the anterior corpotentorium"
"Insertion: Frons"
The cranio-antennal muscle that is continuous with the tentorial bridge and the tentorium.
tentorio-tentorial muscle
lagonzalezmo
lagonzalezmo
The cranio-antennal muscle that is continuous with the tentorial bridge and the tentorium.
lagonzalezmo
2021-04-03
tentorio-tentorial muscle
Wipfler B, Machida R, Mueller B, Beutel RG (2011). On the head morphology of Grylloblattodea (Insecta) and the systematic position of the order, with a new nomenclature for the head muscles of Dicondylia. Systematic Entomology, 36(2), 241-266.
https://doi.org/10.1111/j.1365-3113.2010.00556.x
"Origin: Ventrolaterad on the anterior corpotentorium"
"Insertion: Mesad on the posterior tentorium"
The skeletal muscle tissue that is part of the insect leg.
insect leg muscle
lagonzalezmo
jgiron
The skeletal muscle tissue that is part of the insect leg.
jgiron
2021-04-21
The skeletal muscle tissue that is part of the insect thorax.
insect thoracic muscle
lagonzalezmo
jgiron
The skeletal muscle tissue that is part of the insect thorax.
jgiron
2021-04-21
The thoracic muscle that is not fan-shaped and runs along the dorsal region, parallel to the anterior-posterior axis.
dorsal longitudinal thoracic muscle
lagonzalezmo
imiko
imiko
imiko
The thoracic muscle that is not fan-shaped and runs along the dorsal region, parallel to the anterior-posterior axis.
jgiron
2021-04-09
dorsal longitudinal thoracic muscle
Friedrich, F., & Beutel, R. G. (2008). The thorax of Zorotypus (Hexapoda, Zoraptera) and a new nomenclature for the musculature of Neoptera.
Arthropod Structure & Development, 37(1), 29-54.
https://doi.org/10.1016/j.asd.2007.04.003
The insect thoracic muscle that runs parallel to the dorsal-ventral axis.
dorso-ventral thoracic muscle
lagonzalezmo
jgiron
The insect thoracic muscle that runs parallel to the dorsal-ventral axis.
jgiron
2021-04-22
dorso-ventral thoracic muscle
Friedrich, F., & Beutel, R. G. (2008). The thorax of Zorotypus (Hexapoda, Zoraptera) and a new nomenclature for the musculature of Neoptera.
Arthropod Structure & Development, 37(1), 29-54.
https://doi.org/10.1016/j.asd.2007.04.003
The thoracic muscle that extends between the notum (or tergum) and the pleura.
tergo-pleural muscle
imiko
jgiron
jgiron
The thoracic muscle that extends between the notum (or tergum) and the pleura.
jgiron
2021-04-09
tergo-pleural muscle
Friedrich, F., & Beutel, R. G. (2008). The thorax of Zorotypus (Hexapoda, Zoraptera) and a new nomenclature for the musculature of Neoptera.
Arthropod Structure & Development, 37(1), 29-54.
https://doi.org/10.1016/j.asd.2007.04.003
The thoracic muscle that extends between the sternum and the pleura.
sterno-pleural muscle
lagonzalezmo
jgiron
jgiron
The thoracic muscle that extends between the sternum and the pleura.
jgiron
2021-04-09
sterno-pleural muscle
Friedrich, F., & Beutel, R. G. (2008). The thorax of Zorotypus (Hexapoda, Zoraptera) and a new nomenclature for the musculature of Neoptera.
Arthropod Structure & Development, 37(1), 29-54.
https://doi.org/10.1016/j.asd.2007.04.003
The thoracic muscle that is not fan-shaped and runs along the ventral region, parallel to the anterior-posterior axis.
ventral-longitudinal muscle
lagonzalezmo
imiko
imiko
imiko
The thoracic muscle that is not fan-shaped and runs along the ventral region, parallel to the anterior-posterior axis.
jgiron
2021-04-09
ventral-longitudinal muscle
Friedrich, F., & Beutel, R. G. (2008). The thorax of Zorotypus (Hexapoda, Zoraptera) and a new nomenclature for the musculature of Neoptera.
Arthropod Structure & Development, 37(1), 29-54.
https://doi.org/10.1016/j.asd.2007.04.003
The dorsal longitudinal muscle continuous with the prophragma and the postocciput.
prophragma-occipital muscle
lagonzalezmo
lagonzalezmo
The dorsal longitudinal muscle continuous with the prophragma and the postocciput.
lagonzalezmo
2021-04-06
prophragma-occipital muscle
Friedrich, F., & Beutel, R. G. (2008). The thorax of Zorotypus (Hexapoda, Zoraptera) and a new nomenclature for the musculature of Neoptera.
Arthropod Structure & Development, 37(1), 29-54.
https://doi.org/10.1016/j.asd.2007.04.003
"origin: prophragma"
"insertion: postocciput"
The dorsal longitudinal muscle continuous with the pronotum and the postocciput.
pronoto-occipital muscle
lagonzalezmo
lagonzalezmo
The dorsal longitudinal muscle continuous with the pronotum and the postocciput.
lagonzalezmo
2021-04-06
pronoto-occipital muscle
Friedrich, F., & Beutel, R. G. (2008). The thorax of Zorotypus (Hexapoda, Zoraptera) and a new nomenclature for the musculature of Neoptera.
Arthropod Structure & Development, 37(1), 29-54.
https://doi.org/10.1016/j.asd.2007.04.003
"origin: pronotum"
"insertion: postocciput"
The dorsal longitudinal muscle continuous with the prophragma and the cervical sclerite.
prophragma-cervical muscle
lagonzalezmo
lagonzalezmo
The dorsal longitudinal muscle continuous with the prophragma and the cervical sclerite.
lagonzalezmo
2021-04-06
prophragma-cervical muscle
Friedrich, F., & Beutel, R. G. (2008). The thorax of Zorotypus (Hexapoda, Zoraptera) and a new nomenclature for the musculature of Neoptera.
Arthropod Structure & Development, 37(1), 29-54.
https://doi.org/10.1016/j.asd.2007.04.003
"origin: prophragma"
"insertion: cervical sclerite"
The dorsal longitudinal muscle continuous with the cervical sclerite and the postocciput.
dorsal cervico-occipital muscle
lagonzalezmo
lagonzalezmo
The dorsal longitudinal muscle continuous with the cervical sclerite and the postocciput.
lagonzalezmo
2021-04-04
dorsal cervico-occipital muscle
Friedrich, F., & Beutel, R. G. (2008). The thorax of Zorotypus (Hexapoda, Zoraptera) and a new nomenclature for the musculature of Neoptera.
Arthropod Structure & Development, 37(1), 29-54.
https://doi.org/10.1016/j.asd.2007.04.003
"origin: cervical sclerite"
"insertion: postocciput"
The dorsal longitudinal muscle continuous with the pronotum and the prophragma.
pronoto-phragmal muscle
lagonzalezmo
lagonzalezmo
lagonzalezmo
The dorsal longitudinal muscle continuous with the pronotum and the prophragma.
lagonzalezmo
2021-04-04
pronoto-phragmal muscle
Friedrich, F., & Beutel, R. G. (2008). The thorax of Zorotypus (Hexapoda, Zoraptera) and a new nomenclature for the musculature of Neoptera.
Arthropod Structure & Development, 37(1), 29-54.
https://doi.org/10.1016/j.asd.2007.04.003
"origin: pronotum"
"insertion: prophragma"
The phragma of the mesonotum that attaches to muscles attached to the pronotum.
prophragma
lagonzalezmo
imiko
imiko
The phragma of the mesonotum that attaches to muscles attached to the pronotum.
jgiron
2021-04-09
The dorsoventral thoracic muscle of the prothorax that is attached to the anterior margin of a cervical sclerite and the dorso-lateral region of the postocciput.
anterior cervico-occipital muscle
lagonzalezmo
lagonzalezmo
jgiron
jgiron
The dorsoventral thoracic muscle of the prothorax that is attached to the anterior margin of a cervical sclerite and the dorso-lateral region of the postocciput.
jgiron
2021-04-22
anterior cervico-occipital muscle
Friedrich, F., & Beutel, R. G. (2008). The thorax of Zorotypus (Hexapoda, Zoraptera) and a new nomenclature for the musculature of Neoptera.
Arthropod Structure & Development, 37(1), 29-54.
https://doi.org/10.1016/j.asd.2007.04.003
"The dorsoventral muscle that arises from dorsolateral postocciput and inserts on anterior tip of first lateral cervical sclerite."
The dorsoventral thoracic muscle that extends between the antero-lateral region of the pronotum and the medial region of the propleuron.
anterior pronoto-cervical muscle
lagonzalezmo
jgiron
jgiron
The dorsoventral thoracic muscle that extends between the antero-lateral region of the pronotum and the medial region of the propleuron.
jgiron
2021-04-22
anterior pronoto-cervical muscle
Friedrich, F., & Beutel, R. G. (2008). The thorax of Zorotypus (Hexapoda, Zoraptera) and a new nomenclature for the musculature of Neoptera.
Arthropod Structure & Development, 37(1), 29-54.
https://doi.org/10.1016/j.asd.2007.04.003
"The dorsoventral muscle that arises from anterolateral pronotum and inserts on atypically on middle region of anterior propleural sclerite."
The dorsoventral thoracic muscle that extends between the tentorium and the prophragma.
prophragma-tentorial muscle
lagonzalezmo
jgiron
jgiron
The dorsoventral thoracic muscle that extends between the tentorium and the prophragma.
jgiron
2021-04-22
prophragma-tentorial muscle
Friedrich, F., & Beutel, R. G. (2008). The thorax of Zorotypus (Hexapoda, Zoraptera) and a new nomenclature for the musculature of Neoptera.
Arthropod Structure & Development, 37(1), 29-54.
https://doi.org/10.1016/j.asd.2007.04.003
The dorsoventral thoracic muscle that extends between the profurca and the lateral region of the prophragma.
profurca-prophragmal muscle
lagonzalezmo
jgiron
jgiron
The dorsoventral thoracic muscle that extends between the profurca and the lateral region of the prophragma.
jgiron
2021-04-22
profurca-prophragmal muscle
Friedrich, F., & Beutel, R. G. (2008). The thorax of Zorotypus (Hexapoda, Zoraptera) and a new nomenclature for the musculature of Neoptera.
Arthropod Structure & Development, 37(1), 29-54.
https://doi.org/10.1016/j.asd.2007.04.003
"The dorsoventral muscle that arises from posterior face of proximal profurcal arm and inserts on lateral prophragma."
The dorsoventral thoracic muscle that extends between the posterior region (occipital region) of the head capsule and the profurca.
profurca-occipital muscle
lagonzalezmo
jgiron
jgiron
The dorsoventral thoracic muscle that extends between the posterior region (occipital region) of the head capsule and the profurca.
jgiron
2021-04-22
profurca-occipital muscle
Friedrich, F., & Beutel, R. G. (2008). The thorax of Zorotypus (Hexapoda, Zoraptera) and a new nomenclature for the musculature of Neoptera.
Arthropod Structure & Development, 37(1), 29-54.
https://doi.org/10.1016/j.asd.2007.04.003
The dorsal longitudinal thoracic muscle that extends between the medial region of the prophragma and the medial region of the mesophragma.
prophragma-mesophragmal muscle
lagonzalezmo
jgiron
jgiron
The dorsal longitudinal thoracic muscle that extends between the medial region of the prophragma and the medial region of the mesophragma.
jgiron
2021-04-22
prophragma-mesophragmal muscle
Friedrich, F., & Beutel, R. G. (2008). The thorax of Zorotypus (Hexapoda, Zoraptera) and a new nomenclature for the musculature of Neoptera.
Arthropod Structure & Development, 37(1), 29-54.
https://doi.org/10.1016/j.asd.2007.04.003
"The dorsal longitudinal muscle that arises from median prophragma and inserts on median mesophragma."
The dorsoventral thoracic muscle that extends between the profurca and the mesonotum.
profurca-mesonotal muscle
lagonzalezmo
jgiron
jgiron
The dorsoventral thoracic muscle that extends between the profurca and the mesonotum.
jgiron
2021-04-22
profurca-mesonotal muscle
Friedrich, F., & Beutel, R. G. (2008). The thorax of Zorotypus (Hexapoda, Zoraptera) and a new nomenclature for the musculature of Neoptera.
Arthropod Structure & Development, 37(1), 29-54.
https://doi.org/10.1016/j.asd.2007.04.003
The skeletal muscle tissue that is part of the insect abdomen.
insect abdominal muscle
lagonzalezmo
jgiron
The skeletal muscle tissue that is part of the insect abdomen.
jgiron
2021-04-22
The insect abdominal muscle that runs along the lateral region, parallel to the dorsal-ventral axis.
lateral abdominal muscle
lagonzalezmo
jgiron
jgiron
The insect abdominal muscle that runs along the lateral region, parallel to the dorsal-ventral axis.
jgiron
2021-04-22
lateral abdominal muscle
Klug, R., & Bradler, S. (2006). The pregenital abdominal musculature in phasmids and its implications for the basal phylogeny of Phasmatodea (Insecta: Polyneoptera).
Organisms Diversity & Evolution, 6(3), 171-184.
https://doi.org/10.1016/j.ode.2005.08.004
The insect abdominal muscle that runs along the ventral region, parallel to the anterior-posterior axis.
ventral longitudinal abdominal muscle
lagonzalezmo
jgiron
jgiron
The insect abdominal muscle that runs along the ventral region, parallel to the anterior-posterior axis.
jgiron
2021-04-22
ventral longitudinal abdominal muscle
Klug, R., & Bradler, S. (2006). The pregenital abdominal musculature in phasmids and its implications for the basal phylogeny of Phasmatodea (Insecta: Polyneoptera).
Organisms Diversity & Evolution, 6(3), 171-184.
https://doi.org/10.1016/j.ode.2005.08.004
The insect abdominal muscle that runs along the dorsal region, parallel to the anterior-posterior axis.
dorsal longitudinal abdominal muscle
jgiron
jgiron
jgiron
The insect abdominal muscle that runs along the dorsal region, parallel to the anterior-posterior axis.
jgiron
2021-04-22
dorsal longitudinal abdominal muscle
Klug, R., & Bradler, S. (2006). The pregenital abdominal musculature in phasmids and its implications for the basal phylogeny of Phasmatodea (Insecta: Polyneoptera).
Organisms Diversity & Evolution, 6(3), 171-184.
https://doi.org/10.1016/j.ode.2005.08.004
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
joined with
coalesced
fused with
quality
fused
A structural quality inhering in a bearer by virtue of the bearer's being merged with another entity.
merged with
PATO:0000642
fused to
A structural quality inhering in a bearer by virtue of the bearer's being merged with another entity.
PATOC:GVG
2
2
1
2
true
MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z
infer input from direct reg
GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z),
e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'
enabling an MF enables its parts
true
GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'
involved in BP
This rule is dubious: added as a quick fix for expected inference in GO-CAM. The problem is most acute for transmembrane proteins, such as receptors or cell adhesion molecules, which have some subfunctions inside the cell (e.g. kinase activity) and some subfunctions outside (e.g. ligand binding). Correct annotation of where these functions occurs leads to incorrect inference about the location of the whole protein. This should probably be weakened to "... -> overlaps"
If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.
inferring direct reg edge from input to regulatory subfunction
inferring direct neg reg edge from input to regulatory subfunction
inferring direct positive reg edge from input to regulatory subfunction
effector input is compound function input
Input of effector is input of its parent MF
if effector directly regulates X, its parent MF directly regulates X
if effector directly positively regulates X, its parent MF directly positively regulates X
if effector directly negatively regulates X, its parent MF directly negatively regulates X
'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).
'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).