]> definition editor note 1 IAO:0000116 editor_note editor_note uberon curator notes 1 IAO:0000232 curator_notes curator_notes uberon imported from dubious_for_taxon 1 1 RO:0002174 S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T. dubious_for_taxon dubious_for_taxon this relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take time to resolve. Example: metencephalon in teleost uberon present_in_taxon 1 1 RO:0002175 S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S applicable for taxon present_in_taxon present_in_taxon uberon external_definition 1 An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000001 external_definition external_definition uberon axiom_lost_from_external_ontology 1 A textual description of an axiom loss in this ontology compared to an external ontology. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000002 axiom_lost_from_external_ontology axiom_lost_from_external_ontology uberon homology_notes 1 Notes on the homology status of this class. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000003 homology_notes homology_notes uberon external_comment 1 An alternate comment for a class taken unmodified from an external source. Note that obo format only allows a single comment for a class, and does not provide a structured means of adding provenance info. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000005 external_comment external_comment uberon implements_design_pattern 1 UBPROP:0000006 implements_design_pattern implements_design_pattern uberon has_relational_adjective 1 UBPROP:0000007 Used to connect a class to an adjectival form of its label. For example, a class with label 'intestine' may have a relational adjective 'intestinal'. has_relational_adjective has_relational_adjective uberon taxon_notes 1 Notes on the how instances of this class vary across species. UBPROP:0000008 taxon_notes taxon_notes uberon function_notes 1 Notes on the evolved function of instances of this class. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000009 function_notes function_notes uberon structure_notes 1 Notes on the structure, composition or histology of instances of this class. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000010 structure_notes structure_notes uberon development_notes 1 Notes on the ontogenic development of instances of this class. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000011 development_notes development_notes uberon external_ontology_notes 1 Notes on how similar or equivalent classes are represented in other ontologies. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000012 external_ontology_notes external_ontology_notes uberon terminology_notes 1 Notes on how lexical conventions regarding this class, in particular any issues that may arise due to homonyny or synonymy. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000013 terminology_notes terminology_notes uberon is count of 1 UBPROP:0000100 is_count_of is_count_of uberon preceding element is 1 A property used in conjunction with repeated_element_number to indicate an axis and directionality along that axis. If P preceding_element_is R, and P is_count_of S, and X P N, and X' P N+1, then it follows that every X R some X', and the class expression [S and R some X' and inv(R) some X] is empty (i.e. X is followed by X', with no intermediates) UBPROP:0000101 preceding_element_is preceding_element_is uberon pharyngeal arch number 1 UBPROP:0000103 gill arch N = PA N-2. the term branchial_arch is ambiguous. pharyngeal_arch_number pharyngeal_arch_number uberon x pharyngeal_arch_number N if and only if (i) x is a pharyngeal arch, and (ii) x is ancestrally pharyngeal arch number N in a series of pharyngeal arches repeated along a antero-posterior axis, with arch_number 1 being the mandibular arch. phalanx number 1 Most land mammals including humans have a 2-3-3-3-3 formula in both the hands (or paws) and feet. Primitive reptiles typically had the formula 2-3-4-4-5, and this pattern, with some modification, remained in many later reptiles and in the mammal-like reptiles. The phalangeal formula in the flippers of cetaceans (marine mammals) is 2-12-8-1 UBPROP:0000105 phalanx_number phalanx_number uberon x phalanx_number N if and only if (i) x is a phalanx, and (ii) x is phalanx number N in a series of phalanges repeated along an prixomo-distal axis, with phalanx_number 1 being the proximalmost phalanx. Note that in humans, the distalmost phalanx has phlanax_number 3, except in ray_number 1, where the distalmost has phalanx_number 2 fma_set_term 1 FMA has terms like 'set of X'. In general we do not include set-of terms in uberon, but provide a mapping between the singular form and the FMA set term UBPROP:0000202 fma_set_term fma_set_term uberon CUMBO developmental_classification A class that represents an early developmental structure, like a blastocyst. This part of the ontology is undergoing review to remove inappropriate grouping classes. EFO slim derived from the union of EHDAA2 and EMAPA - still to be checked functional_classification Subset consisting of classes creating for grouping purposes A grouping class that depends on an assumption of homology between subclasses classes that have some inconsistency with FMA somewhat fuzzy grouping for analysis purposes, currently composed of something like: liver, heart, skeletal, kidney, bladder, brain, skin, mouth, esophagus, stomach, small intestine, large intestines, trachea nose, lungs, brain, spinal cord, peripheral nerves, kidneys, ureters, bladder, urethra, gonads abstract class brought in to group ontology classes but not informative organs, excluding individual muscles and skeletal elements Phenotype slim Uberon slim - subset that excludes obscure terms and deep compositional terms abstract upper-level terms not directly useful for analysis core classes typically found across vertebrates. one purpose is to create a rough set of terms that could be used to start a new vertebrate AO contributor 1 dc-contributor dc-contributor uberon subset_property has_alternative_id has_broad_synonym database_cross_reference has_exact_synonym has_narrow_synonym has_obo_namespace has_related_synonym in_subset shorthand depicted_by 1 foaf-depicted_by foaf-depicted_by uberon part of BFO:0000050 part_of part_of uberon has part BFO:0000051 has_part has_part uberon preceded_by BFO:0000062 X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X) is preceded by preceded_by preceded_by takes place after uberon precedes BFO:0000063 precedes precedes uberon anterior_to 2009-07-31T02:15:46Z BSPO:0000096 anterior_to anterior_to cjm uberon 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 distal_to BSPO:0000097 distal_to distal_to uberon 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). dorsal_to BSPO:0000098 dorsal_to dorsal_to uberon 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). posterior_to BSPO:0000099 caudal_to posterior_to posterior_to uberon 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. proximal_to BSPO:0000100 proximal_to proximal_to uberon x proximal_to y iff x is closer to the point of attachment with the body than y. ventral_to BSPO:0000102 uberon 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 bisects an organism from back (e.g. spinal column) to front (e.g. belly). deep_to BSPO:0000107 Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines. deep_to deep_to uberon superficial_to BSPO:0000108 Near the outer surface of the organism. Thus, skin is superficial to the muscle layer. superficial_to superficial_to uberon in_left_side_of BSPO:0000120 X in_left_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the left portion. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern in_left_side_of in_left_side_of uberon in_right_side_of BSPO:0000121 X in_right_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the right portion. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern in_right_side_of in_right_side_of uberon in_posterior_side_of BSPO:0000122 X posterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the posterior portion. in_posterior_side_of in_posterior_side_of uberon in_anterior_side_of BSPO:0000123 X anterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the anterior portion. in_anterior_side_of in_anterior_side_of uberon in_proximal_side_of BSPO:0000124 X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion. in_proximal_side_of in_proximal_side_of uberon in_distal_side_of BSPO:0000125 X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion. in_distal_side_of in_distal_side_of uberon in_lateral_side_of BSPO:0000126 X in_lateral_side_of Y <=> if X is in_left_side_of Y or X is in_right_side_of Y. X is often, but not always a paired structure https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern in_lateral_side_of in_lateral_side_of uberon proximalmost_part_of BSPO:0001106 X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y proximalmost_part_of proximalmost_part_of uberon distalmost_part_of BSPO:0001108 X distalmost_part_of Y <=> X is part_of Y and X is adjacent_to the distal boundary of Y distalmost_part_of distalmost_part_of uberon location_of RO:0001015 location_of location_of uberon located_in RO:0001025 located_in located_in uberon has boundary RO:0002002 has_boundary has_boundary uberon innervated_by FMA:85999 RO:0002005 dbprop:nerve http://code.google.com/p/obo-relations/issues/detail?id=6 innervated_by innervated_by nerve supply uberon 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. RO:0002007 bounding_layer_of bounding_layer_of uberon simultaneous_with RO:0002082 Relation between occurrents, shares start and end boundaries. coincides_with is_equal_to simultaneous_with simultaneous_with uberon 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]. RO:0002087 X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) directly preceded by immediately_preceded_by immediately_preceded_by is directly preceded by is immediately preceded by starts_at_end_of uberon innervates RO:0002134 http://code.google.com/p/obo-relations/issues/detail?id=6 innervates innervates uberon continuous_with RO:0002150 continuous_with continuous_with uberon homologous_to RO:0002158 homologous_to homologous_to uberon connected to Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship. Connection does not imply overlaps. RO:0002170 connected_to connected_to uberon 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. RO:0002176 connects connects 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) uberon attaches_to_part_of RO:0002177 attaches_to_part_of attaches_to_part_of uberon supplies FMA:86003 RO:0002178 arterial supply of relation between an artery and the structure is supplies with blood. source: FMA supplies supplies uberon drains RO:0002179 drains drains drains blood from drains from source: Wikipedia uberon develops_from RO:0002202 develops_from develops_from uberon develops_into RO:0002203 develops_into develops_into uberon surrounded_by RO:0002219 surrounded_by surrounded_by uberon x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y adjacent_to RO:0002220 adjacent_to adjacent_to uberon x adjacent_to y iff: x and y share a boundary surrounds RO:0002221 inverse of surrounded_by surrounds surrounds uberon starts RO:0002223 Relation between occurrents, shares a start boundary with. starts starts uberon starts with RO:0002224 starts_with starts_with uberon ends RO:0002229 Relation between occurrents, shares an end boundary with. ends ends finishes uberon ends with RO:0002230 ends_with ends_with uberon has developmental contribution from RO:0002254 has_developmental_contribution_from has_developmental_contribution_from uberon developmentally_induced_by RO:0002256 developmentally_induced_by developmentally_induced_by sources for developmentally_induced_by relationships in Uberon: Developmental Biology, Gilbert, 8th edition, figure 6.5(F) 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. uberon developmentally preceded by RO:0002258 developmentally_preceded_by developmentally_preceded_by uberon developmentally_replaces RO:0002285 developmentally_replaces developmentally_replaces uberon has member RO:0002351 has_member has_member uberon attaches_to FMA:85990 RO:0002371 attaches_to attaches_to uberon branching_part_of FMA:85994 RO:0002380 branching_part_of branching_part_of uberon we need to check if FMA branch_of implies part_of. the relation we intend to use here should - for example, see vestibulocochlear nerve has potential to developmentally contribute to RO:0002385 has_potential_to_developmentally_contribute_to has_potential_to_developmentally_contribute_to uberon x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y has potential to develop into RO:0002387 has_potential_to_develop_into has_potential_to_develop_into uberon x has the potential to develop into y iff x develops into y or if x is capable of developing into y contributes to morphology of RO:0002433 contributes_to_morphology_of contributes_to_morphology_of uberon composed primarily of RO:0002473 UBREL:0000002 composed_primarily_of composed_primarily_of uberon x composed_primarily_of y iff: more than half of the mass of x is made from parts of y existence starts during BFO:0000068 RO:0002488 Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s. begins_to_exist_during existence_starts_during existence_starts_during uberon existence starts with RO:0002489 Relation between continuant and occurrent, such that c comes into existence at the start of p. existence_starts_with existence_starts_with uberon existence ends during BFO:0000069 RO:0002492 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. ceases_to_exist_during existence_ends_during existence_ends_during uberon existence ends with RO:0002493 Relation between continuant and occurrent, such that c ceases to exist at the end of p. existence_ends_with existence_ends_with uberon transformation of RO:0002494 transformation_of transformation_of transforms from uberon immediate transformation of RO:0002495 direct_transformation_of immediate_transformation_of immediate_transformation_of immediately transforms from uberon existence starts during or after RO:0002496 existence_starts_during_or_after existence_starts_during_or_after uberon existence ends during or before RO:0002497 existence_ends_during_or_before existence_ends_during_or_before uberon has material contribution from RO:0002507 has_material_contribution_from has_material_contribution_from uberon has skeleton A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision. RO:0002551 has sekeletal support has supporting framework has_skeleton has_skeleton uberon has_branching_part RO:0002569 has_branching_part has_branching_part uberon luminal space of RO:0002572 luminal_space_of luminal_space_of uberon skeleton of RO:0002576 skeleton_of skeleton_of uberon produces RO:0003000 produces produces uberon produced_by RO:0003001 produced_by produced_by uberon anteriorly connected to anteriorly_connected_to uberon 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. channel for carries channel_for uberon channels_from channels_from uberon channels_into channels_into uberon conduit for conduit_for uberon x is a conduit for y iff y passes through the lumen of x. distally connected to distally_connected_to uberon x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y. evolved_from Status: experimental evolved_from uberon existence starts and ends during existence_starts_and_ends_during uberon extends_fibers_into extends_fibers_into uberon in_central_side_of X in_central_side Y <=> if Y is subdivided into left and right portions around some median divisor, all parts of X are closer to the median divisor than the outermost lateral sides. https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern in_central_side_of uberon posteriorly connected to posteriorly_connected_to uberon 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. protects protects uberon proximally connected to proximally_connected_to uberon x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y. 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 uberon transitively distally connected to . transitively_distally_connected_to uberon transitively proximally connected to . transitively_proximally_connected_to uberon nose BTO:0000840 CALOHA:TS-2037 EHDAA2:0001274 EHDAA:1502 EMAPA:16542 EV:0100037 EV:0100370 FMA:46472 GAID:77 MA:0000281 MAT:0000139 MESH:D009666 MIAA:0000139 OpenCyc:Mx4rvViCbJwpEbGdrcN5Y29ycA Organ that is the specialized structure of the face that contains olfactory neurons. The peripheral olfactory organ is paired[ZFA:0000047]. TAO:0000047 The olfactory organ of vertebrates, consisting of nares, olfactory epithelia and the structures and skeletal framework of the nasal cavity. UBERON:0000004 UMLS:C0028429 ZFA:0000047 a protuberance in vertebrates that houses the nostrils, or nares, which admit and expel air for respiration in conjunction with the mouth. Behind the nose are the olfactory mucosa and the sinuses. Behind the nasal cavity, air next passes through the pharynx, shared with the digestive system, and then into the rest of the respiratory system. In humans, the nose is located centrally on the face; on most other mammals, it is on the upper tip of the snout[WP]. GO: The nose is the specialized structure of the face that serves as the organ of the sense of smell and as part of the respiratory system. Includes the nasi externus (external nose) and cavitas nasi (nasal cavity)[Wikipedia:Nose]. galen:Nose nasal sac nasus nose olfactory apparatus peripheral olfactory organ proboscis the organ that is specialized for smell and is part of the respiratory system the structure of the nose varies across vertebrates. In tetrapods the nose is part of the respiratory system.[PMID:25312359] uberon islet of Langerhans A primitive exocrine pancreas can be found in holocephalan cartilaginous fish; a pancreatic duct directly ending in the gut lumen is connected to a glandular structure made of exocrine cells and associated with cell islets, which comprises three different hormone-producing cell types: insulin, somatostatin and glucagon (Yui and Fujita, 1986) AAO:0010406 Anatomical structure which consists of glands developed from pancreatic ducts in the larvae and secrete insulin.[AAO] BTO:0000991 CALOHA:TS-0741 EFO:0000856 EMAPA:32927 EV:0100130 FMA:16016 GAID:324 MA:0000127 MAT:0000076 MESH:D007515 MIAA:0000076 Mammals, birds, reptiles and amphibians have a pancreas with similar histology and mode of development, while in some fish, the islet cells are segregated as Brockmann bodies.[well established][VHOG] UBERON:0000006 UMLS:C0022131 VHOG:0000646 XAO:0000159 island of Langerhans island of pancreas islets of langerhans pancreatic insula pancreatic islet the clusters of hormone-producing cells that are scattered throughout the pancreas uberon peripheral nervous system (...) 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] 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. AAO:0000429 BAMS:PNS BILA:0000081 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 Nervous structures including ganglia outside of the central nervous system. Kimmel et al, 1995.[TAO] PNS Part of nervous system in which nerves extend throughout the body outside of the brain and spinal cord.[AAO] TAO:0000142 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) UBERON:0000010 UMLS:C0206417 UMLS:C1305921 VHOG:0000399 XAO:0000178 ZFA:0000142 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=247 lateral part of the basal amygdalar nucleus lateral part of the basolateral nucleus nucleus amygdalae basalis, pars lateralis nucleus amygdaloideus basalis, pars lateralis magnocellularis nucleus basalis lateralis amygdalae pars peripherica pars peripherica; systema nervosum periphericum systema nervosum periphericum uberon zone of skin (...) 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] Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis. EHDAA2:0001844 EHDAA:6530 EMAPA:17525 EV:0100152 FMA:86166 GAID:933 MA:0000151 MAT:0000284 MESH:D012867 MIAA:0000284 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 OpenCyc:Mx4rvVjX3ZwpEbGdrcN5Y29ycA UBERON:0000014 VHOG:0000860 portion of skin region of skin skin skin region skin zone uberon 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 anatomical boundary A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures. AEO:0000192 CARO:0000010 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. FMA:50705 UBERON:0000015 uberon endocrine pancreas BTO:0000650 CALOHA:TS-1302 EFO:0002542 EMAPA:35305 EV:0100129 FMA:16018 In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG] MA:0001582 TAO:0001260 The part of the pancreas that acts as an endocrine gland, consisting of the islets of Langerhans, which secrete insulin and other hormones. [TFD][VHOG] The part of the pancreas that is part of the endocrine system and is made up of islet cells, which produce insulin, glucagon and somatostatin. The zebrafish endocrine pancreas is composed of small groups of islet cells that are distributed throughout the exocrine pancreas. The islet cells produce insulin, glucagon and somatostatin.[TAO] UBERON:0000016 VHOG:0000049 ZFA:0001260 create a separate class for distributed pancreas, eg cyclostomes? endocrine and exocrine pancreas are not co-associated in hagfishes or lampreys endocrine pancreas endocrine part of pancreas islets of Langerhans part of pancreas pars endocrina pancreatis uberon exocrine pancreas AAO:0010407 BTO:0000434 CALOHA:TS-1241 EMAPA:35328 EV:0100093 FMA:16017 In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG] MA:0002415 TAO:0001249 The exocrine pancreas is composed of acinar epithelial cells and ductal epithelium that manufacture the proteolytic enzymes and bicarbonate required for digestion.[TAO] The part of the pancreas that acts as an exocrine gland, consisting of the pancreatic acini, which produce pancreatic juice and secrete it into the intestine to aid in protein digestion. [TFD][VHOG] The part of the pancreas that is part of the exocrine system and which produces and store zymogens of digestive enzymes, such as chymotrypsinogen and trypsinogen in the acinar cells [GO]. UBERON:0000017 UMLS:C0553695 VHOG:0000048 XAO:0000137 ZFA:0001249 exocrine component of pancreas exocrine pancreas exocrine part of pancreas pars exocrina pancreatis uberon camera-type eye A cavitated compound organ that transduces light waves into neural signals.[TAO] AAO:0010340 An organ of sight that includes the camera-type eyeball and supporting structures such as the lacrimal apparatus, the conjunctiva, the eyelid. BTO:0004688 EHDAA2:0000484 EHDAA:936 EMAPA:16198 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:54448 MA:0000261 OpenCyc:Mx8Ngx4rwKSh9pwpEbGdrcN5Y29ycB4rvVil5pwpEbGdrcN5Y29ycB4rvViTvpwpEbGdrcN5Y29ycA TAO:0000107 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] UBERON:0000019 UMLS:C0015392 UMLS:C1280202 VHOG:0000275 XAO:0000179 ZFA:0000107 camera-type eye plus associated structures eye eyes orbital part of face orbital region regio orbitalis uberon vertebrate eye sense organ AEO:0000094 An organ that is capable of transducing sensory stimulus to the nervous system. BSA:0000121 BTO:0000202 CALOHA:TS-2043 EHDAA2:0001824 EHDAA:500 EMAPA:16192 EMAPA:35955 FBbt:00005155 GAID:63 HAO:0000930 MA:0000017 MESH:D012679 Sinnesorgan UBERON:0000020 UMLS:C0935626 VHOG:0001407 WBbt:0006929 organ of sense organ system organ of sensory organ system organ of sensory system sense organ system organ sensillum sensor sensory organ sensory organ system organ sensory system organ uberon tube Any hollow cylindrical anatomical structure containing a lumen through which substances are transported. UBERON:0000025 anatomical tube duct galen:Tube 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 uberon appendage AEO:0000193 An appendage is an external body part, or natural prolongation, that protrudes from an organism's body, such as a vertebrate's limbs[BILA][BILA:0000018]. BILA:0000018 BTO:0001492 CARO:0010003 EFO:0000799 EHDAA2:0003193 EV:0100155 FBbt:00007000 HAO:0000144 MAT:0000023 MESH:D005121 MIAA:0000023 Major subdivision of an organism that protrudes from the body[DOS, CARO]. OpenCyc:Mx4rvViC-JwpEbGdrcN5Y29ycA Organ or organ part that is attached to the body of an organism. For example a limb[GO, modified][GO:0048736]. UBERON:0000026 UMLS:C0598782 VSAO:0000075 XAO:0000218 appendages appendicular extremitaet extremity limbs/digits/tail this is currently a subtype of organism subdivision - which would exclude feathers uberon head AAO:0010335 AEO:0000106 BILA:0000115 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 OpenCyc:Mx4rEOLm4rgPEdmAAAACs6hRjg OpenCyc:Mx4rvVi6YJwpEbGdrcN5Y29ycA 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] SPD:0000016 TAO:0001114 TGMA:0000002 The head is the anterior-most division of the body [GO]. UBERON:0000033 UMLS:C0018670 VHOG:0001644 Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG] WBbt:0005739 XAO:0003024 ZFA:0001114 adult head cephalic area galen:Head head (volume) uberon serous membrane A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO] FMA:9581 GAID:19 MESH:D012704 TAO:0005425 UBERON:0000042 UMLS:C0036760 ZFA:0005425 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. multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer. serosa tunica serosa uberon wall of serous sac tendon AEO:0000091 BTO:0001356 CALOHA:TS-1021 Dense regular connective tissue that connects muscle to bone.[VSAO] Dense regular connective tissue that connects muscle to bone[VSAO]. EHDAA2:0003091 EMAPA:35854 EV:0100149 FMA:9721 GAID:276 MA:0000115 MESH:D013710 OpenCyc:Mx4rvVjefJwpEbGdrcN5Y29ycA 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] UBERON:0000043 UMLS:C0039508 VHOG:0001286 VSAO:0000073 XAO:0000173 ZFA:0005647 galen:Tendon 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 sinew tendo uberon ganglion A biological tissue mass, most commonly a mass of nerve cell bodies. A ganglion is a cluster of neurons. It is part of a nervous system. It may include glial cells. The neurons are arranged in a specific constellation: neuronal somata are concentrated at the surface, thus forming a cell cortex, and neurites are concentrated in the centre of the ganglion to form the neuropil. A ganglion is a distinct unit but several ganglia may be anterio-posteriorly joined by connectives or transversally by commissures AAO:0010426 AEO:0000135 BAMS:G BTO:0000497 CALOHA:TS-0397 Cranial sensory placodes are focused areas of the head ectoderm of vertebrates that contribute to the development of the cranial sense organs and their associated ganglia. Placodes have long been considered a key character of vertebrates, and their evolution is proposed to have been essential for the evolution of an active predatory lifestyle by early vertebrates.[well established][VHOG] EFO:0000899 EHDAA2:0003135 EHDAA:2897 EHDAA:4662 EHDAA:5621 EHDAA:918 EMAPA:32846 EV:0100372 FBbt:00005137 FMA:5884 MA:0002406 MAT:0000207 MAT:0000343 MESH:D005724 MIAA:0000207 MIAA:0000343 Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system.[AAO] Structures containing a collection of nerve cell bodies. (Source: BioGlossary, www.Biology-Text.com)[TAO] Subdivision of nervous system which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord. Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion (adapted from Foundational Model of Anatomy)[NIFSTD:nlx_anat_100302]. TAO:0000190 TGMA:0001016 TODO - check vert vs invert. Other species: Any of a number of aggregations of neurons, glial cells and their processes, surrounded by a glial cell and connective tissue sheath (plural: ganglia). // Subdivision of neural tree (organ) which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord); together with a nucleus and its associated nerve, it constitutes a neural tree (organ). Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion. // a cluster of nerve cells and associated glial cells (nuclear location) // Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system. UBERON:0000045 UMLS:C0017067 VHOG:0000156 WBbt:0005189 XAO:0000209 ZFA:0000190 ganglia ganglionic neural ganglion uberon simple eye An eye with one concave chamber. Note that 'simple' does not imply a reduced level of complexity or acuity. TGMA:0000729 UBERON:0000047 uberon macula GAID:777 MESH:D008267 Patches of thickened, pseudostratified epithelium of the inner ear, consisting of regular arrays of sensory hair cells interspersed with supporting cells. Each patch has its own charcteristic shape and polarity pattern. (See Anatomical Atlas entry for sensory patches of the ear by T. Whitfield.)[TAO] TAO:0000386 Thickened areas of the saccule or utricle where the termination of the vestibular nerve occurs[MESH,modified]. UBERON:0000054 ZFA:0000386 acoustic macula acoustic maculae macula maculae macular sensory macula sensory patch this refers to the inner ear structure, not the macula of the retina. We follow ZFA in including a grouping class for the macula of utricle and sacule uberon vessel A tubular structure that contains, conveys body fluid, such as blood or lymph. UBERON:0000055 uberon ureter AAO:0010254 Anatomical structure consisting of long narrow duct which carries urine from the kidney to the urinary bladder.[AAO] BTO:0001409 CALOHA:TS-1084 EFO:0000930 EHDAA2:0002139 EHDAA:9341 EMAPA:17950 EV:0100097 FMA:9704 GAID:438 MA:0000378 MAT:0000120 MESH:D014513 MIAA:0000120 Muscular duct that propels urine from the kidneys to the urinary bladder, or related organs. OpenCyc:Mx4rvhmm6JwpEbGdrcN5Y29ycA The duct of amniotes that carries urine from a metanephric kidney to the urinary bladder. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG] UBERON:0000056 UMLS:C0041951 VHOG:0000605 XAO:0000144 galen:Ureter in humans, consists of adventitial, muscular and mucoa layers metanephric duct uberon ureteral ureteric urethra BTO:0001426 CALOHA:TS-1132 EFO:0000931 EMAPA:30901 EV:0100099 FMA:19667 GAID:390 In human males, the urethra travels through the penis, and carries semen as well as urine. In females, the urethra is shorter and emerges above the vaginal opening. MA:0000379 MAT:0000121 MESH:D014521 MIAA:0000121 OpenCyc:Mx4rvVjkypwpEbGdrcN5Y29ycA UBERON:0000057 UMLS:C0041967 VHOG:0001264 XAO:0000153 galen:Urethra the fibromuscular tubular canal through which urine is discharged from the bladder to the exterior via the external urinary meatus; in males, the urethra is joined by the ejaculatory ducts and serves as a passageway for semen during ejaculation, as well as a canal for urine during voiding; in females, the urethra is shorter and emerges above the vaginal opening uberon urethral duct A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171]. A tubular structure that transports secreted or excreted substances. AAO:0011123 FBbt:00100314 FMA:30320 Most ducts, but not all, are exocrine gland ducts. Some ontologies classify structures such as the oviduct here. TAO:0005171 UBERON:0000058 UMLS:C0687028 XAO:0004000 ZFA:0005171 anatomical duct ducts exocrine duct exocrine gland duct galen:Duct uberon large intestine A subdivision of the digestive tract that connects the small intestine to the cloaca or anus. Lacks or has few villi[Kardong]. AAO:0010396 BTO:0000706 CALOHA:TS-1306 EFO:0000840 EMAPA:19252 EV:0100077 FMA:7201 GAID:306 Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG] MA:0000333 MESH:A03.492.411.495 MIAA:0000046 OpenCyc:Mx4rvVkF5pwpEbGdrcN5Y29ycA UBERON:0000059 UMLS:C0021851 VHOG:0000054 XAO:0000131 galen:LargeIntestine intestinum crassum uberon anatomical wall EMAPA:25036 FMA:82482 Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers. UBERON:0000060 UBERON:0009915 galen:Wall in FMA, serosa is a wall organ wall uberon wall wall of organ anatomical structure AAO:0010825 AEO:0000003 BILA:0000003 CARO:0000003 EHDAA2:0003003 EMAPA:0 FBbt:00007001 FMA:67135 GAID:781 HAO:0000003 MA:0003000 MESH:D000825 Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. TAO:0000037 TGMA:0001823 UBERON:0000061 VHOG:0001759 WBbt:0000100 XAO:0003000 ZFA:0000037 biological structure connected biological structure uberon organ Anatomical structure that performs a specific function or group of functions [WP]. 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 CARO:0020004 EFO:0000634 EMAPA:35949 ENVO:01000162 FMA:67498 MA:0003001 OpenCyc:Mx4rv5XMb5wpEbGdrcN5Y29ycA OpenCyc:Mx4rwP3iWpwpEbGdrcN5Y29ycA 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. UBERON:0000062 UMLS:C0178784 WBbt:0003760 anatomical unit body organ element uberon 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. 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 FMA:86140 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. UBERON:0000063 organ region with fixed fiat boundary organ segment segment of organ uberon organ part A multicellular structure that is a part of an organ. AAO:0011124 EFO:0000635 FMA:82472 UBERON:0000064 cardinal organ part currently defined in a very broad sense, may be replaced by more specific classes in the future regional part of organ uberon respiratory tract Anatomical structure that is part of the respiratory system. In mammals consists of upper and lower tracts EHDAA2:0001606 EHDAA:1568 EHDAA:2219 EMAPA:16737 FMA:265130 OpenCyc:Mx4rvvM--pwpEbGdrcN5Y29ycA UBERON:0000065 VHOG:0000393 uberon fully formed stage BTO:0001043 BilaDO:0000004 EFO:0001272 FBdv:00005369 The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage. UBERON:0000066 WBls:0000041 XtroDO:0000084 adult stage fully formed animal stage juvenile-adult stage uberon embryo stage part A stage that is part of the embryo stage. UBERON:0000067 embryonic stage part uberon embryo 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 UBERON:0000068 WBls:0000003 WBls:0000092 WBls:0000102 XAO:1000012 embryogenesis embryonic stage uberon death stage End of the life of an organism. UBERON:0000071 XAO:0000437 XtroDO:0000085 death ncit:Death is an outcome uberon proximo-distal subdivision of respiratory tract An section of a respiratory tract. EMAPA:16737 FMA:45660 MA:0000434 MA:0000434 has subclasses upper and lower, so it corresponds to a segment of the tract, rather than the tract as a whole UBERON:0000072 respiratory tract subdivision of respiratory tract uberon regional part of nervous system 2009-06-18T09:00:04Z Any part or collection of parts of the central or peripheral nervous system. Parts may span both CNS and PNS. Melissa Haendel UBERON:0000073 UMLS:C1518256 part of nervous system uberon renal glomerulus 2009-06-18T09:26:37Z A capillary tuft which forms a close network with the visceral epithelium (podocytes) and the mesangium to form the filtration barrier and is surrounded by Bowman's capsule in nephrons of the vertebrate kidney[GO]. BTO:0000530 CALOHA:TS-0862 EFO:0003667 EMAPA:28329 EV:0100386 FMA:15624 MA:0001657 MESH:D007678 Melissa Haendel TAO:0001288 UBERON:0000074 UMLS:C0022663 ZFA - The multi-tissue structure where the glomerular basement membrane supported by mesonephric podocytes filters blood from the glomerular capillaries. GUDMAP: 'Together, the Bowman's capsule and the glomerulus comprise the definitive renal corpuscle.' - here the glomerulus is part of the capsule? ZFA:0001288 glomerular capillary tuft glomerular tuft glomerulus glomerulus renis malphigian glomerulus renal corpuscle renal glomeruli uberon subdivision of skeletal system Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism. FMA:85544 UBERON:0000075 UBERON:0010322 UMLS:C1519343 galen:ComplexSkeletalStructure skeletal system part skeletal system subdivision uberon external ectoderm (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 The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm. UBERON:0000076 UMLS:C1515087 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) surface (external) ectoderm surface ectoderm uberon mixed endoderm/mesoderm-derived structure 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:0000077 uberon male reproductive system BTO:0000082 By far, sexual reproduction is the more common pattern among living vertebrate forms and its widespread occurrence suggests that it is the plesiomorphic, or primitive, reproductive mode among the vertebrates.[well established][VHOG] CALOHA:TS-1310 EFO:0000970 EHDAA2:0001054 EHDAA:8136 EMAPA:17968 EV:0100101 FBbt:00004927 FMA:45664 GAID:386 HAO:0000505 MA:0000396 MESH:D005837 OpenCyc:Mx4rvViCepwpEbGdrcN5Y29ycA TGMA:0000634 The organs associated with producing offspring in the gender that produces spermatozoa. UBERON:0000079 UMLS:C0017422 UMLS:C1963704 VHOG:0000725 WBbt:0008423 XAO:0000155 genitalia of male organism male genital organ male genital system male genital tract male genitalia male genitals male organism genitalia male organism reproductive system male reproductive tract reproductive system of male organism systema genitale masculinum uberon mesonephros A kidney formed of nephric tubules arising in the middle region of the nephric ridge; a transient embryonic stage that replaces the pronephros, but is itself replaced by the adult metanephros [in mammals; in fishes and amphibians it is the adult kidney]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG] AAO:0010384 As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates. (...) In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG] BTO:0001542 By contrast to the pronephros, the histological features of the mammalian mesonephros, with its primitive glomeruli, suggest that it probably functions as a primitive kidney, and is involved in the production of much of the amniotic fluid. Within the two mesonephroi, one located on either side of the dorsal mesentery of the hindgut, a substantial number (in the region of about 40 or more) of cranio-caudally segmented mesonephric tubules are formed. It has, however, been suggested that only the most rostrally located 4-6 pairs of mesonephric tubules drain into the mesonephric portion of the nephric duct. This is now seen to extend along the length of the mesonephroi, being located towards their lateral sides. The mesonephros is also retained over a considerably longer period than the pronephros, but gradually undergoes regression in a cranio-caudal direction. While the rostral part displays clear evidence of regression its more caudal part appears to display evidence of functional activity. Within the medial part of the mesonephros, vesicles are formed, although no glomeruli are formed there in this species. It is, however, difficult to believe that the relatively enormous mesonephroi do not have an excretory role in the mouse, only serving as a base for gonadal differentiation. In the human embryo, the medial part of the mesonephric tubules enlarges, become invaginated by capillaries, and form glomeruli. These then take on an excretory role. In the mouse, the mesonephric ducts appear to be patent throughout their length[GUDMAP, modified] CALOHA:TS-0624 EFO:0000928 EHDAA2:0001130 EHDAA:1581 EHDAA:5903 EMAPA:16744 EMAPA:27644 FMA:72171 GAID:1308 In mammals, the mesonephros is the second of the three embryonic kidneys to be established and exists only transiently. In fish and amphibians, the mesonephros will form the mature kidney MESH:D001755 Organ that is the definitive adult kidney. It replaces the earlier pronephros, which degenerates as the mesonephros becomes functional in feeding stage tadpoles.[AAO] TAO:0000529 The second stage of the kidney. It serves as the main excretory organ of aquatic vertebrates and as a temporary embryonic kidney in higher vertebrates. It is composed of the mesonephric duct (also called the Wolffian duct), mesonephric tubules, and associated capillary tufts. A single tubule and its associated capillary tuft is called a mesonephric excretory unit; these units are similar in structure and function to nephrons of the adult kidney. The mesonephros is derived from intermediate mesoderm in the vertebrate embryo. UBERON:0000080 UMLS:C0025492 VHOG:0000038 Wolffian body XAO:0000141 ZFA:0000529 amphibian adult kidney corpus Wolffi mesonephric mesonephric kidney mesonephroi middle kidney opisthonephros opisto nephros opistonephros uberon metanephros A kidney formed of nephric tubules arising in the posterior region of the nephric ridge and drained by a ureter; replaces the embryonic pronephros and mesonephros [in mammals]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG] BTO:0001543 During the fifth week of gestation, the mesonephric duct develops an outpouching, the ureteric bud, near its attachment to the cloaca. This bud, also called the metanephrogenic diverticulum, grows posteriorly and towards the head of the embryo. The elongated stalk of the ureteric bud, the metanephric duct, later forms the ureter. As the cranial end of the bud extends into the intermediate mesoderm, it undergoes a series of branchings to form the collecting duct system of the kidney. It also forms the major and minor calyces and the renal pelvis EHDAA2:0001137 EHDAA:3089 EHDAA:5911 EMAPA:17207 EMAPA:17373 FMA:72172 In mammals, the metanephros is the excretory organ of the fetus, which develops into the mature kidney and is formed from the rear portion of the nephrogenic cord. The metanephros is an endocrine and metabolic organ that filters the blood and excretes the end products of body metabolism in the form of urine[GO] TODO check developmental relationships The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes.[well established][VHOG] UBERON:0000081 UMLS:C0231049 VHOG:0000039 definite kidney definitive kidney hind kidney metanephric metanephric kidney metanephron uberon mesonephric tubule A mesonephric tubule is an epithelial tube that is part of the mesonephros[GO]. Genital ridge that is next to the mesonephros[WP]. AAO:0010389 Any of the renal tubules composing the mesonephros. In mammals they function as excretory structures during the early embryonic development but are later incorporated into the reproductive system. [TFD][VHOG] As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates.[well established][VHOG] EHDAA2:0001134 EMAPA:27588 EMAPA:27659 TODO check UBERON:0000083 VHOG:0000500 XAO:0000148 renal tubules tubuli mesonephrici uberon ureteric bud An epithelial swelling on the Wolffian duct that elongates to invade the adjacent metanephric mesenchyme[MP] BTO:0001646 EHDAA2:0002140 EHDAA:3091 EHDAA:5917 EMAPA:17209 EMAPA:17376 Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts. [Embryology, See_Dudek_RW_and_Fix_JD, Third_Edition_(2004)_Philadelphia:_Lippincott_William_and_Wilkins, p.137][VHOG] Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts[VHOG:0000541]. The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG] UBERON:0000084 UMLS:C1284058 VHOG:0000541 diverticulum diverticulum metanephricum gemma ureterica metanephric bud metanephric diverticulum uberon ureteric ampulla ureteric diverticulum morula A spherical embryonic mass of blastomeres formed before the blastula and resulting from cleavage of the fertilized ovum. BTO:0001508 EHDAA2 has embryo starting later EHDAA2:0000005 FMA:292334 GAID:1295 MESH:A16.254.270.550 UBERON:0000085 UMLS:C0026573 morula (2-16 cells) uberon zona pellucida A glycoprotein membrane surrounding the plasma membrane of an oocyte. It is a vital constitutive part of the latter, external but not extraneous to it. The zona pellucida first appears in multilaminar primary oocytes. BTO:0003135 EHDAA2:0002220 EHDAA:31 EHDAA:62 EMAPA:16035 FMA:18674 GAID:410 MA:0001715 MESH:D015044 Outside the plasma membrane, three envelopes surround the ovum. The first, the primary egg envelope, lies between the plasma membrane and the surrounding cells of the ovary. The most consistent component of this primary layer is the vitelline membrane, a transparent jacket of fibrous protein. In mammals, the homologous structure is called the zona pellucida.[well established][VHOG] TAO:0001111 UBERON:0000086 UMLS:C0043519 VHOG:0000720 ZFA:0001111 oolemma pellucid zone striated membrane uberon vitelline envelope vitelline membrane zona pellucida - vitelline membrane zona radiata zona striata inner cell mass A group of cells found in the mammalian blastocyst that give rise to the embryo. [Biology_Online][VHOG] A mass of cells that develop into the body of the embryo and some extraembryonic tissues A small sphere of cells known as the inner cell mass lies within the trophoblast (of all eutherian mammals).[well established][VHOG] EFO:0000547 EHDAA2:0000830 EHDAA:40 EMAPA:16041 FMA:86557 ICM This structure forms in the earliest steps of development, before implantation into the endometrium of the uterus has occurred.The ICM lies within the blastocyst cavity and is entirely surrounded by the single layer of cells called trophoblast. [Wikipedia:Inner_cell_mass] UBERON:0000087 UMLS:C1283994 VHOG:0000742 early embryoblast embryoblast embryoblastus; massa cellularis interna; pluriblastus senior pluriblast uberon trophoblast Aggregate of cells forming the outer layer of a blastocyst, which provide nutrients to the embryo and develop into a large part of the placenta. They are formed during the first stage of pregnancy and are the first cells to differentiate from the fertilized egg. [Wikipedia:Trophoblast] BTO:0001079 CALOHA:TS-1070 EV:0100120 FMA:83029 GAID:1152 MESH:A11.936 The postimplantation derivatives of the trophectoderm, which make up most of the fetal part of the placenta UBERON:0000088 UMLS:C0041178 massa cellularis externa the mesectodermal cell layer arising from the trophectoderm that erodes the uterine mucosa and contributes to the formation of the placenta the mesectodermal cell layer arising from the trophectoderm that erodes the uterine mucosa and contributes to the formation of the placenta[MP] trophoblast layer trophoblastic trophoblastus trophoderm uberon bilaminar disc A flattened, almost circular bilaminar plate of cells formed when the inner cell mass (aka embryoblast) forms two epithelial layers, each of a distinct lineage, separated by an extracellular basement membrane: the external (dorsal) layer is called the epiblast and the internal (ventral) layer is called the hypoblast (aka primitive endoderm); together, they compose the bilaminar embryonic disc. FMA:293863 UBERON:0000091 UMLS:C1283997 bilaminar disk bilaminary embryonic disc bilaminary germ disc embryonic disc embryonic shield germinal disc germinal disk uberon post-embryonic stage BilaDO:0000003 In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997) OGES:000010 OGES:000014 OGES:000024 UBERON:0000092 WBls:0000022 WBls:0000093 WBls:0000103 post-hatching stage postembryonic postembryonic stage stage succeeding embryo, including mature structure uberon membrane organ 2009-07-30T05:19:13Z FMA:7145 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] UBERON:0000094 cjm membrane membrane of organ uberon life cycle 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 UBERON:0000104 entire life cycle entire lifespan life lifespan ncithesaurus:Life uberon life cycle stage A spatiotemporal region encompassing some part of the life cycle of an organism. BILS:0000105 EFO:0000399 FBdv:00007012 FMA:24120 HsapDv:0000000 MmusDv:0000000 OlatDv:0000010 PdumDv:0000090 UBERON:0000105 WBls:0000002 XAO:1000000 ZFS:0000000 ZFS:0100000 developmental stage ncithesaurus:Developmental_Stage stage the WBls class 'all stages' belongs here as it is the superclass of other WBls stages this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here uberon we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage zygote stage 1-cell 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] BILS:0000106 BilaDO:0000005 EFO:0001322 EHDAA:27 EMAPA:16033 FBdv:00005288 PdumDv:0000100 UBERON:0000106 VHOG:0000745 XAO:1000001 ZFS:0000001 fertilized egg stage fertilized egg stage one cell stage one-cell stage uberon zygote zygotum cleavage stage BILS:0000107 BilaDO:0000006 EFO:0001290 FBdv:00000054 MESH:A16.254.270 MmusDv:0000004 OGES:000015 OGES:000020 PdumDv:0000200 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. UBERON:0000107 XAO:1000004 ZFS:0000046 uberon 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. BILS:0000108 BilaDO:0000007 EFO:0001282 HsapDv:0000006 MmusDv:0000007 OGES:000003 OGES:000016 OGES:000021 OpenCyc:Mx4rEetFnKP2EdqAAAACs4vPlg UBERON:0000108 WBls:0000005 XAO:1000003 ZFS:0000045 consider adding a preceding stage 'morula stage' as part of cleavage uberon gastrula stage 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 UBERON:0000109 WBls:0000010 XAO:1000005 ZFS:0000047 blastocystis trilaminaris stage trilaminar blastocyst stage trilaminar blastoderm stage trilaminar disk stage trilaminar germ stage trilaminar stage uberon neurula stage BILS:0000110 BilaDO:0000009 HsapDv:0000012 MmusDv:0000017 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. UBERON:0000110 XAO:1000006 uberon organogenesis stage 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:0000111 segmentation stage uberon sexually immature stage BILS:0000112 BTO:0002168 EFO:0001300 EV:0300051 In mammals this would include infant (nourishment from lactation) and juvenile (prepubertal no longer dependent on mother) MmusDv:0000043 OGES:000009 The stage of being a sexually immature adult animal[XAO:1000010]. UBERON:0000112 XAO:1000010 XtroDO:0000083 ZFS:0000051 immature stage juvenile stage subadult stage uberon lung connective tissue EMAPA:35521 FMA:27533 MA:0001782 UBERON:0000114 connective tissue of lung lung interstitial tissue lung interstitium pulmonary connective tissue pulmonary interstitial tissue pulmonary interstitium the connective tissue located between the respiratory (airway and alveolar) epithelium, the capillary endothelium and pleural mesothelium; it contains basement membrane composed of collagen, elastin, proteoglycans, and fibronectin; it functions in the mechanical behavior of the lung, and forms a barrier to regulate the flow of plasma constituents from the capillaries to the airway and alveolar spaces uberon respiratory tube A tube in the respiratory system. Examples: bronchus, bronchiole, trachea. FMA:12224 UBERON:0000117 in GO lung development is part of respiratory tube development. This can lead to inconsistencies with other ontologies, e.g. VT. The GO structure may be better represented by a tree of tubes (see the FMA class) respiratory conducting tube segment of tracheobronchial tree segment of tracheobronchial tree tracheobronchial tree segment uberon lung bud BTO:0001643 EHDAA2:0004089 Structure derived from foregut that becomes a lung[GO]. UBERON:0000118 UMLS:C1514420 UMLS:C1514897 clarify successors - include bronchi? gemma pulmonalis gemma respiratoria lung bud primary lung bud respiratory diverticulum uberon neuron projection bundle A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. CARO:0001001 FBbt:00005099 UBERON:0000122 UBERON:0005163 funiculus nerve fiber bundle neural fiber bundle uberon neural nucleus A spatially aggregated collection of nerve cell bodies in the CNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections, and including nearby cells that share the same cell type, chemical phenotype, and connections. (CUMBO) AEO:0000136 Anatomical structure consisting of a discrete aggregate of neuronal soma[GO][GO_REF:0000021]. FMA:83686 Proposed CUMBO def from MM: A subcortical part of the nervous system consisting of a relatively compact group of cells that is distinguishable histologically that share a commonality of cytoarchitecture, chemoarchitecturel and connectivity. (comments: I put in 'subcortical' because I don't think we consider either the cerebellar cortex or cerebral cortex to be nuclei. Some people distinguish between a nucleus and a laminar structure (see Wikipedia definition). However, there are structures identified as nuclei that are laminar, e.g., lateral geniculate nucleus, although they are not laminated in all species. Also, I put in 'relatively compact' and 'distiguishable by histology' because we have groups of cells, e.g., cholinergic cell groups, doparminergic cell groups that are related on the 3 criteria but which we don't tend to consider nuclei because they don't occupy an easily defined territory. But all is open to debate. UBERON:0000125 nervous system nucleus neuraxis nucleus neuronal nucleus nucleus nucleus of CNS nucleus of neuraxis uberon cranial nerve nucleus FMA:54501 Nucleus that receives projections from or contains neurons that send projections through one of the cranial nerves UBERON:0000126 cranial neural nucleus nucleus nervi cranialis nucleus of cranial nerve uberon anterior region of body UBERON:0000153 uberon posterior region of body UBERON:0000154 uberon membranous layer A thin sheet or layer of pliable tissue, serving as a covering or envelope of a part, as the lining of a cavity, as a partition or septum, or to connect two structures. FMA:30322 FMA:82500 MESH:D008566 UBERON:0000158 membrane membranous organ component uberon intestine AAO:0000246 ANISEED:1235303 BSA:0000093 BTO:0000648 CALOHA:TS-0490 EFO:0000834 EMAPA:32874 EMAPA:35180 EV:0100071 FMA:7199 GAID:295 In zebrafish, No stomach, small intestine, or large intestine can be distinguished. However, differences can be found in the morphology of the mucosa columnar epithelial cells and the number of goblet cells, suggesting functional differentiation. The intestine has numerous folds that become progressively shorter in a rostral-to-caudal direction. Proportionally, these folds are significantly larger than the finger-like intestinal villi of mammals and other amniotes (Wallace et al. 2005). Columnar-shaped absorptive enterocytes are the most numerous in the zebrafish intestinal epithelium. Goblet cells are the second most populous epithelial cell type. MA:0000328 MA:0001524 MESH:A03.492.411 MIAA:0000043 Portion of the alimentary canal bounded anteriorly by the pyloric sphincter and posteriorly by the cloacal sphincter.[AAO] Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine. TAO:0001338 The tract of the alimentary canal. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] This class is probably too inclusive UBERON:0000160 UMLS:C0021853 VHOG:0000056 WBbt:0005772 XAO:0000129 ZFA:0001338 bowel galen:Intestine intestinal intestinal tract uberon orifice Anatomical conduit that connects two adjacent body spaces (or a body space with the space surrounding the organism)[FMA,modified]. FMA:3724 UBERON:0000161 anatomical orifice anatomical ostium hilum in FMA, this is an anatomical conduit *space*, rather than anatomical conduit ostium uberon cloaca A cloaca is apparently a primitive vertebrate feature because it occurs in most primitive gnathostomes and persists in the embryos of almost all vertebrates.[well established][VHOG] A common passage for fecal, urinary, and reproductive discharge in most lower vertebrates as well as the terminal end of the hindgut before division into rectum, bladder, and genital primordia in mammalian embryos. [TFD][VHOG] AAO:0000095 Anatomical structure which is the common receptacle for the alimentary canal, Wolffian ducts, oviducts, and the bladder.[AAO] Common chamber into which the intestines and excretory system opens. Arises during development in all vertebrates, but in many it becomes subdivided, lost or incorporated into other structures GAID:1206 Human beings only have an embryonic cloaca, which is split up into separate tracts during the development of the urinary and reproductive organs MESH:D002988 UBERON:0000162 UMLS:C0008987 VHOG:0001186 XAO:0000244 ZFA:0005781 adding df link to embryonic cloaca leads to a cycle in uberon-simple, as cloaca is a suberclass of embryonic cloaca cloacal cloacal chamber hindgut endoderm and proctodeal ectoderm. uberon vent embryonic cloaca EHDAA2:0000256 EHDAA:4895 EMAPA:27573 EMAPA:27638 UBERON:0000163 cloaca endoderm-lined chamber that develops as pouch-like dilation of the caudal end of the hindgut and receives the allantois ventrally and two mesonephric ducts laterally; caudally it ends blindly at the cloacal membrane formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm[MP]. this class represents the embryonic form of the cloaca, as found in both mammals and non-mammals. uberon primitive urogenital sinus EHDAA2:0004060 EHDAA:5029 EHDAA:5919 EMAPA:17211 EMAPA:17379 In mammals the lowly monotremes still have a cloaca. Higher types have done away with this structure and have a separate anal outlet for the rectum. The monotreme cloaca shows the initiation of this subdivision. The cloaca has such includes only the distal part, roughly comparable to the proctodeum. The more proximal part is divided into (1) a large dorsal passage into which the intestine opens, the coprodeum, and (2) a ventral portion, the urodeum with which the bladder connects. (...) the development of the placental mammals recapitulates in many respects the phylogenetic story. In the sexually indifferent stage of placental mammal there is a cloaca. While the indifferent stage still persists, a septum develops, and extends out to the closing membrane. This divides the cloaca into two chambers: a coprodeum continuous with the gut above, and a urodeum or urogenital sinus below.[well established][VHOG] The ventral part of the cloaca after its separation from the rectum, giving rise to the lower part of the bladder in both sexes, to the prostatic portion of the male urethra, and to the urethra and vestibule in the female. [TFD][VHOG] UBERON:0000164 UGS UMLS:C0231057 VHOG:0000414 fetal UGS sinus urogenitalis the term 'urogenital sinus' may refer to the primitive urogenital sinus present as a transient developmental structure in most mammals or it may refer to a condition in which an unseptated cloaca persists in animals longer than normal the ventral part of the cloaca remaining after septation of the rectum, which further develops into part of the bladder, part of the prostatic part of the male urethra and the urethra and vestibule in females uberon urogenital sinus mouth AAO:0010355 BTO:0001090 BTO:0004698 CALOHA:TS-1315 Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO] EFO:0000825 EHDAA2:0001326 EHDAA:542 EMAPA:16262 FBbt:00003126 FMA:49184 GAID:75 MA:0000341 MA:0002474 MAT:0000038 MESH:D009055 MIAA:0000038 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] OpenCyc:Mx4rvVidh5wpEbGdrcN5Y29ycA TADS:0000040 TAO:0000547 TAO:0000590 TGMA:0000131 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). UBERON:0000165 VHOG:0000280 VHOG:0000812 XAO:0003029 ZFA:0000547 ZFA:0000590 adult mouth cavital oralis cavitas oris cavum oris galen:Mouth 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 mouth cavity oral oral region oral vestibule regio oralis rima oris some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives stoma stomatodaeum trophic apparatus uberon vestibule of mouth vestibulum oris oral opening (...) 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 The orifice that connects the mouth to the exterior of the body. UBERON:0000166 mouth oral fissure oral orifice oral part of face uberon oral cavity AAO:0000053 AAO:0000960 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] BSA:0000107 CALOHA:TS-1315 EFO:0001975 EHDAA2:0001324 EHDAA:6970 EMAPA:17411 EMAPA:18399 EV:0100057 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] FMA:20292 HAO:0000669 TAO:0001027 TGMA:0000102 The cavity of the mouth, bounded by the jaw bones and associated structures (muscles and mucosa). [TFD][VHOG] UBERON:0000167 UMLS:C0226896 VHOG:0000188 WBbt:0005255 XAO:0000126 ZFA:0001027 bucca buccal cavity cavity of mouth uberon proximal-distal subdivision of colon A section dividing a colon along a proximal-distal axis. FMA:222905 UBERON:0000168 segment of colon uberon pair of lungs 1 1 1 1 FMA:68877 OpenCyc:Mx4rvVjKy5wpEbGdrcN5Y29ycA The pair of anatomical structures comprised of a left lung and right lung. UBERON:0000170 lungs lungs pair pulmones set of lungs uberon respiration organ EMAPA:17607 Organ that functions in gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms. SPD:0000428 TGMA:0001247 UBERON:0000171 apparatus respiratorius organ breathing organ gas exchange organ organ of apparatus respiratorius organ of respiratory system respiratory organ respiratory system organ uberon excreta A portion of organism substance that is the product of an excretion process that will be eliminated from the body. An excretion process is elimination by an organism of the waste products that arise as a result of metabolic activity AEO:0000184 BTO:0000491 EHDAA2_RETIRED:0003184 ENVO:02000022 FMA:9674 UBERON:0000174 UBERON:0000324 UBERON:0007550 excreted substance excretion galen:Excretion portion of excreted substance uberon waste substance blood 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] A fluid that is composed of blood plasma and erythrocytes. AAO:0000046 BTO:0000089 CALOHA:TS-0079 EFO:0000296 EHDAA2:0000176 EHDAA:418 EMAPA:16332 ENVO:02000027 EV:0100047 FMA:9670 GAID:965 Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO] MA:0000059 MESH:D001769 MIAA:0000315 OpenCyc:Mx4rvVjI8JwpEbGdrcN5Y29ycA 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] TAO:0000007 This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid. UBERON:0000178 UMLS:C0005767 VHOG:0000224 XAO:0000124 ZFA:0000007 galen:Blood portion of blood relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] uberon vertebrate blood whole blood haemolymphatic fluid 2009-04-08T04:38:19Z CARO:0000081 Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs. UBERON:0000179 blood or blood analog circulating fluid cjm uberon amnion A thin but tough extraembryonic membrane of reptiles, birds and mammals that lines the chorion and contains the fEtus and the amniotic fluid around it. [Biology_Online][VHOG] BTO:0000065 CALOHA:TS-0033 EHDAA2:0000116 EHDAA:136 EMAPA:16109 EV:0100122 FMA:80223 GAID:1298 MESH:A16.254.403.277 Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois.[well established][VHOG] UBERON:0000305 UMLS:C0002630 VHOG:0000721 amniotic the thin innermost layer of the extraembryonic membranes that contains the amniotic fluid; the membrane forms a closed sac in which the embryo and later, the fetus, is suspended and protected uberon blastula BILA:0000059 BTO:0000128 GAID:1294 MESH:A16.254.270.274 OGEM:000006 OpenCyc:Mx4rEetFnKP2EdqAAAACs4vPlg 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:0000307 UBERON:0007011 blastosphere blastula embryo uberon breast BTO:0000149 CALOHA:TS-2083 EV:0100124 FMA:9601 GAID:33 MESH:D001940 OpenCyc:Mx4rvVjV7ZwpEbGdrcN5Y29ycA The breasts of a female primate's body contain the mammary glands, which secrete milk used to feed infants. Both men and women develop breasts from the same embryological tissues. However, at puberty female sex hormones, mainly estrogens, promote breast development, which does not happen with men. As a result women's breasts become more prominent than men's. The upper ventral region of an animal's torso. UBERON:0000310 UMLS:C0006141 galen:Breast mamma mammary part of chest mammary region uberon duodenal mucosa A mucosa that is part of a duodenum [Automatically generated definition]. BTO:0000367 CALOHA:TS-0213 Doudenal mucosa Duodenal mucous membrane EMAPA:27235 FMA:14942 MA:0003207 UBERON:0000320 UBERON:0003348 duodenum mucosa mucosa of duodenum mucous membrane of duodenum uberon gastric gland BTO:0000503 EMAPA:27181 FMA:14919 The branched tubular glands found in the mucosa of the fundus and body of the stomach which contain parietal cells that secrete hydrochloric acid and zymogenic cells that produce pepsin. UBERON:0000325 uberon gut wall BTO:0000547 FMA:45653 The wall of the digestive tract. This encompasses all parts of the digestive tract with the exception of the lumen (cavity). UBERON:0000328 We model the digestive tract as consisting of two parts: the wall and the lumen. digestive tract wall uberon wall of alimentary tract wall of digestive tract wall of gut throat BTO:0000828 FMA:228738 In anatomy, the throat is the anterior part of the neck, in front of the vertebral column. It consists of the pharynx and larynx. An important feature of the throat is the epiglottis, a flap which separates the esophagus from the trachea and prevents inhalation of food or drink. The throat contains various blood vessels, various pharyngeal muscles, the trachea (windpipe) and the esophagus. The hyoid bone and the clavicle are the only bones located in the throat of mammals. It is sometimes considered a synonym for fauces. [WP,unvetted]. OpenCyc:Mx4rwQtO_JwpEbGdrcN5Y29ycA The hyoid bone and the clavicle are the only bones located in the throat of mammals. UBERON:0000341 UMLS:C0230069 gula gular uberon mucosa 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] AEO:0000199 BTO:0000886 CALOHA:TS-2031 EHDAA2_RETIRED:0003234 EV:0100382 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:85355 FMA:85358 GAID:297 MESH:D009092 OpenCyc:Mx4rvmKNOpwpEbGdrcN5Y29ycA UBERON:0000344 UMLS:C0026724 galen:Mucosa mucosa of organ mucosa of organ part mucosal mucosal region mucous membrane organ mucosa region of mucosa tunica mucosa uberon parenchyma EHDAA:3015 EHDAA:3905 EHDAA:3999 EHDAA:4005 EHDAA:6899 EHDAA:6903 EHDAA:6994 EHDAA:8086 EHDAA:9182 EHDAA:9190 EHDAA:9196 EHDAA:9202 Early in development the mammalian embryo has three distinct layers: ectoderm (external layer), endoderm (internal layer) and in between those two layers the middle layer or mesoderm. The parenchyma of most organs is of ectodermal (brain, skin) or endodermal origin (lungs, gastrointestinal tract, liver, pancreas). The parenchyma of a few organs (spleen, kidneys, heart) is of mesodermal origin. The stroma of all organs is of mesodermal origin FMA:45732 UBERON:0000353 UMLS:C0933845 functional part of an organ in the body. This is in contrast to the stroma, which refers to the structural tissue of organs, being exactly, connective tissues. parenchymal the FMA definition is more restrictive, and limits this to solid organs. This would seem to cause problems for the lung parenchyma, except FMA classifies Lung as solid rather than cavitated uberon blastocyst BTO:0001099 CALOHA:TS-0076 EFO:0000295 EMAPA:36035 EV:0100394 FMA:83041 GAID:1153 Gilbert fig11.32 has blastocyst has giving rise to ICM and trophoblast (which in this source is a synonym for trophectoderm) MESH:A16.254.085 The mammalian blastocyst is a hollow ball of cells containing two cell types, the inner cell mass and the trophectoderm[GO]. UBERON:0000358 UMLS:C1281743 blastocystis blastula uberon musculature of body AAO:0000307 Anatomical system that consists of the muscles of the body.[VSAO] BILA:0000088 BTO:0001369 BTO:0001485 EFO:0000801 EMAPA:35578 FBbt:00005069 FMA:72954 MA:0002888 MAT:0000025 MIAA:0000025 The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified]. UBERON:0000383 VSAO:0000033 XAO:0004042 consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77 muscle system muscle system of body muscular system musculature system muskelsystem set of all muscles set of muscles of body uberon vertebrate muscular system we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA serous gland A gland in which the principal secretory cells are serous secreting cells. BTO:0001837 FMA:62889 UBERON:0000409 glands that secrete watery albuminous material that often contains enzymes[MP:0008052]. uberon mucous gland A gland in which the principal secretory cells are mucus secreting cells. AAO:0010601 BTO:0001979 FMA:62888 In frogs and salamanders, this is the smaller of the two types of gland, the other being the granular (poison) gland. In these species the mucous gland is a cluster of cells that release secretion into a common duct[Kardong] UBERON:0000414 glandula mucosa muciparous gland mucous secreting gland mucus gland mucus-secreting gland uberon bodily secretion A portion of organism substance that is produced by exocrine glands. AEO:0001005 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:0002977 BTO:0002979 EMAPA:36535 FMA:9675 MA:0002504 MESH:D012634 UBERON:0000456 UBERON:0006540 UMLS:C1516992 exocrine gland fluid exocrine gland fluid or secretion exocrine gland fluid/secretion exocrine gland secretion external secretion galen:Secretion secreted substance secretion uberon uterine wall An anatomical wall that is part of a uterus [Automatically generated definition]. BTO:0003083 FMA:17560 UBERON:0000459 anatomical wall of uterus uberon uterus anatomical wall uterus wall wall of uterus organism substance AAO:0010839 AEO:0000004 BILA:0000004 CALOHA:TS-2101 CARO:0000004 EHDAA2:0003004 EMAPA:35178 FBbt:00007019 FMA:9669 HAO:0000004 MA:0002450 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. SPD:0000008 TAO:0001487 TGMA:0001824 UBERON:0000463 VHOG:0001726 XAO:0004001 ZFA:0001487 body fluid or substance body substance galen:BodySubstance organism substance portion of body substance portion of organism substance uberon anatomical space AAO:0010110 AEO:0000005 BILA:0000005 CARO:0000005 EHDAA2:0003005 FBbt:00007017 FMA:5897 HAO:0000005 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. TAO:0001668 TGMA:0001825 UBERON:0000464 UMLS:C0524461 VHOG:0001728 XAO:0003190 ZFA:0001643 anatomical spaces lumen lumen space space uberon material anatomical entity AAO:0010264 AEO:0000006 Anatomical entity that has mass. BILA:0000006 CARO:0000006 EHDAA2:0003006 FBbt:00007016 FMA:67165 HAO:0000006 TAO:0001836 TGMA:0001826 UBERON:0000465 VHOG:0001721 uberon immaterial anatomical entity AAO:0010265 AEO:0000007 Anatomical entity that has no mass. BILA:0000007 CARO:0000007 EHDAA2:0003007 FBbt:00007015 FMA:67112 HAO:0000007 TAO:0001835 TGMA:0001827 UBERON:0000466 VHOG:0001727 immaterial physical anatomical entity uberon anatomical system AAO:0000007 AEO:0000011 BILA:0000011 BSA:0000049 CALOHA:TS-2088 CARO:0000011 EHDAA2:0003011 EHDAA:392 EMAPA:16103 EV:0100000 FBbt:00004856 FMA:7149 HAO:0000011 MA:0000003 Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function. OpenCyc:Mx4rCWM0QCtDEdyAAADggVbxzQ TAO:0001439 TGMA:0001831 UBERON:0000467 UMLS:C0460002 VHOG:0001725 WBbt:0005746 WBbt:0005763 XAO:0003002 ZFA:0001439 anatomical systems body system connected anatomical system galen:AnatomicalSystem organ system system uberon multicellular organism AAO:0010026 AEO:0000191 Anatomical structure that is an individual member of a species and consists of more than one cell. BILA:0000012 BSA:0000038 BTO:0000042 CARO:0000012 EFO:0002906 EHDAA2:0003103 EHDAA2:0003191 EHDAA:1 EHDAA:9178 EMAPA:25765 EV:0100016 FBbt:00000001 FMA:256135 HAO:0000012 Koerper TADS:0000001 TAO:0001094 TGMA:0001832 TODO - split body and mc organism? body continues after death stage UBERON:0000468 VHOG:0000671 WBbt:0007833 XAO:0003004 ZFA:0001094 animal body galen:Organism multi-cellular organism ncithesaurus:Whole_Organism organism organismal uberon whole body whole organism cell part AAO:0010271 Anatomical structure that is a direct part of the cell. BILA:0000014 CARO:0000014 FBbt:00007012 FMA:86454 GO:0044464 HAO:0000014 NIF_Subcellular:sao-1337158144 OpenCyc:Mx4rwQwkcZwpEbGdrcN5Y29ycA TGMA:0001834 TODO - move metadata to GO and obsolete this class once homes have been found for existing children. Note the inconsistency between the usage of the label 'cell component' in GO and CARO UBERON:0000470 UMLS:C1178969 cell component uberon compound organ component AAO:0010017 AEO:0000019 BILA:0000019 CARO:0000019 EHDAA2:0003019 HAO:0000019 Multi-tissue structure that is part of a compound organ. TAO:0001489 TGMA:0001835 UBERON:0000471 XAO:0003039 ZFA:0001489 compound organ components 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 uberon female reproductive system BTO:0000083 By far, sexual reproduction is the more common pattern among living vertebrate forms and its widespread occurrence suggests that it is the plesiomorphic, or primitive, reproductive mode among the vertebrates.[well established][VHOG] CALOHA:TS-1303 EFO:0000969 EHDAA2:0000506 EHDAA:8116 EMAPA:17959 EV:0100110 FBbt:00004864 FMA:45663 GAID:364 HAO:0000324 MA:0000381 MESH:D005836 MIAA:0000028 OpenCyc:Mx4rvVipTZwpEbGdrcN5Y29ycA TGMA:0000635 The organs and associated structures associated with bearing offspring in a female animal. UBERON:0000474 UMLS:C0700038 VHOG:0000726 WBbt:0006748 WikipediaCategory:Female_reproductive_system XAO:0000156 female genital system female genital tract female genitalia female genitals female organism genitalia female organism reproductive system female reproductive tract genitalia of female organism gynaecological tissue reproductive system of female organism systema genitale femininum uberon organism subdivision AAO:0010053 AEO:0000032 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. BILA:0000032 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 OpenCyc:Mx4rvViAHJwpEbGdrcN5Y29ycA Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency TAO:0001308 TGMA:0001840 UBERON:0000475 UMLS:C0229962 VHOG:0001758 XAO:0003013 ZFA:0001308 anatomic region body part body region cardinal body part galen:BodyPart uberon acellular anatomical structure AAO:0010268 AEO:0000040 Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue. BILA:0000040 CARO:0000040 EHDAA2:0003040 FBbt:00007013 FMA:63863 HAO:0000040 TAO:0000382 TGMA:0001841 UBERON:0000476 XAO:0003162 ZFA:0000382 acellular anatomical structures uberon anatomical cluster AAO:0010009 AEO:0000041 Anatomical group that has its parts adjacent to one another. BILA:0000041 CARO:0000041 EHDAA2:0003041 FBbt:00007277 FMA:49443 HAO:0000041 TADS:0000605 TAO:0001478 TGMA:0001842 UBERON:0000477 VHOG:0001737 Will be obsoleted in CARO v2 [https://github.com/obophenotype/caro/issues/3] XAO:0003160 ZFA:0001478 uberon 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. AAO:0010020 AEO:0000042 BILA:0000042 CALOHA:TS-2119 CARO:0000042 EHDAA2:0003042 EHDAA:46 FBbt:00005835 FMA:85537 HAO:0000042 TAO:0000020 TGMA:0001843 UBERON:0000478 UMLS:C1282438 VHOG:0000292 XAO:0004005 ZFA:0000020 extra-embryonic structure extraembryonic structures extraembryonic tissue see also conceptus extraembryonic component in EHDAA2. uberon tissue AAO:0000607 AAO:0010054 AEO:0000043 BILA:0000043 CALOHA:TS-2090 CARO:0000043 EHDAA2:0003043 EMAPA:35868 FBbt:00007003 FMA:9637 HAO:0000043 MA:0003002 MESH:D014024 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. TAO:0001477 TGMA:0001844 UBERON:0000479 UMLS:C0040300 VHOG:0001757 WBbt:0005729 XAO:0003040 ZFA:0001477 changed label and definition to reflect CARO2 galen:Tissue portion of tissue simple tissue tissue portion uberon multi-tissue structure AAO:0010048 AEO:0000055 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. BILA:0000055 CARO:0000055 EHDAA2:0003055 FBbt:00007010 HAO:0000055 TAO:0001488 TGMA:0001847 UBERON:0000481 VHOG:0001762 XAO:0003037 ZFA:0001488 multi-tissue structures uberon epithelium 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 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]. TAO:0001486 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] UBERON:0000483 UMLS:C0014609 VHOG:0000387 XAO:0003045 ZFA:0001486 epithelial epithelial tissue portion of epithelium uberon simple columnar epithelium AAO:0010063 AEO:0000068 BILA:0000068 CARO:0000068 EHDAA2_RETIRED:0003068 FBbt:00007027 FMA:45567 HAO:0000068 TAO:0001496 UBERON:0000485 UMLS:C0836135 Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA] XAO:0004008 ZFA:0001496 columnar epithelium columnar epithlium epithelium simplex columnare simple columnar epithelia simple columnar epithelium uberon multilaminar epithelium AAO:0010059 AEO:0000069 BILA:0000069 BTO:0002074 CARO:0000069 EHDAA2:0003069 Epithelium that consists of more than one layer of epithelial cells.[CARO] 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:45562 HAO:0000069 TAO:0001494 UBERON:0000486 UMLS:C0682575 XAO:0004006 ZFA:0001494 laminated epithelium stratified epithelium uberon simple squamous epithelium AAO:0010066 AEO:0000070 BILA:0000070 BTO:0002073 CARO:0000070 EHDAA2:0003070 FMA:45565 HAO:0000070 TAO:0001498 UBERON:0000487 UMLS:C0836133 Unilaminar epithelium that consists of a single layer of squamous cells.[CARO] Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA] XAO:0004010 ZFA:0001498 epithelium simplex squamosum simple squamous epithelia uberon cavitated compound organ AAO:0010016 AEO:0000072 BILA:0000072 CARO:0000072 Compound organ that contains one or more macroscopic anatomical spaces. EHDAA2:0003072 FMA:55671 HAO:0000072 TAO:0001490 TGMA:0001857 UBERON:0000489 VHOG:0001730 XAO:0003165 ZFA:0001490 cavitated compound organs cavitated organ 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 uberon unilaminar epithelium AAO:0010062 AEO:0000073 BILA:0000073 BTO:0002073 CARO:0000073 EHDAA2:0003073 Epithelium that consists of a single layer of epithelial cells.[CARO] Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA] FMA:45561 HAO:0000073 TAO:0001495 UBERON:0000490 UMLS:C0682574 XAO:0004007 ZFA:0001495 consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable simple epithelium uberon unilaminar epithelia mucus CALOHA:TS-2144 ENVO:02000040 FMA:66938 GAID:1164 MESH:D009093 Mucus is a bodily fluid consisting of a slippery secretion of the lining of the mucous membranes in the body. It is a viscous colloid containing antiseptic enzymes (such as lysozyme) and immunoglobulins. Mucus is produced by goblet cells in the mucous membranes that cover the surfaces of the membranes. It is made up of mucins and inorganic salts suspended in water. OpenCyc:Mx4rvVjHq5wpEbGdrcN5Y29ycA UBERON:0000912 UMLS:C0026727 galen:Mucus mucoid mucous uberon interstitial fluid ENVO:02000042 FMA:9673 Interstitial fluid is a bodily fluid consisting of a solution which bathes and surrounds the cells of multicellular animals. It is the main component of the extracellular fluid, which also includes plasma and transcellular fluid. UBERON:0000913 intercellular fluid tissue fluid uberon thoracic segment of trunk EMAPA:35862 FMA:259209 MA:0000022 Subdivision of trunk that lies between the head and the abdomen. UBERON:0000915 anterior subdivision of trunk 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 thorax uberon upper body upper trunk abdomen BTO:0000020 CALOHA:TS-0001 EFO:0000968 EMAPA:35102 EV:0100011 FMA:9577 GAID:16 MA:0000029 MAT:0000298 MESH:A01.047 MIAA:0000298 OpenCyc:Mx4rvVjgyZwpEbGdrcN5Y29ycA The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column. UBERON:0000916 Vertebrate specific. In arthropods 'abdomen' is the most distal section of the body which lies behind the thorax or cephalothorax. If need be we can introduce some grouping class abdominal abdominopelvic region abdominopelvis adult abdomen belly celiac celiac region galen:Abdomen uberon embryo AAO:0011035 AEO:0000169 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. 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 OGEM:000001 Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo OpenCyc:Mx4rwP1ceZwpEbGdrcN5Y29ycA UBERON:0000922 UMLS:C0013935 VHOG:0001766 XAO:0000113 ZFA:0000103 developing organism developmental tissue embryonic embryonic organism uberon 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. AAO:0000480 BILA:0000035 BTO:0000556 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] EMAPA:36033 FBbt:00000110 FMA:69069 GAID:1303 MESH:A16.254.425 TAO:0001122 The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] UBERON:0000923 UMLS:C0920502 UMLS:C1708239 VHOG:0001223 XAO:0003011 ZFA:0001122 embryonic germ layer embryonic germ layers embryonic tissue germinal layer primary germ layer uberon ectoderm 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 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] TAO:0000016 The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] UBERON:0000924 UMLS:C0013574 VHOG:0000153 XAO:0000001 ZFA:0000016 ectodermal embryonic ectoderm uberon endoderm 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 Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. TAO:0000017 The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] UBERON:0000925 UMLS:C0014144 VHOG:0000154 XAO:0000090 ZFA:0000017 endodermal entoderm uberon mesoderm AAO:0000304 BILA:0000037 BTO:0000839 CALOHA:TS-0623 EFO:0001981 EHDAA2:0001128 EHDAA:124 EHDAA:160 EHDAA:168 EHDAA:183 EMAPA:16083 EV:0100006 FBbt:00000126 FMA:69072 GAID:522 MAT:0000174 MESH:A16.254.425.660 MIAA:0000174 Primary germ layer that is the middle of the embryonic germ layers.[AAO] TAO:0000041 The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] The middle germ layer of the embryo, between the endoderm and ectoderm. UBERON:0000926 UBERON:0003263 UMLS:C0025485 VHOG:0000152 XAO:0000050 ZFA:0000041 embryonic mesoderm entire mesoderm mesodermal mesodermal mantle 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 stomodeum Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO] 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. BTO:0004224 EHDAA2:0001929 EMAPA:16263 FBbt:00000439 FMA:295846 TAO:0001290 TGMA:0000135 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. UBERON:0000930 UMLS:C1514977 XAO:0000269 ZFA:0001290 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 mouth pit mouth primordium oral ectoderm oral pit primitive oral cavity stomatodeum stomodaeum stomodeal stomodeal-hypophyseal primordium 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 uberon proctodeum AAO:0011087 An inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[TAO] EHDAA2:0000121 EMAPA:25038 FBbt:00000123 Inward fold on the surface of the embryonic ectoderm that develops into an ectodermal terminal part of the digestive tract. Inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[AAO] TAO:0000066 UBERON:0000931 UMLS:C0231054 VHOG:0000139 XAO:0001019 ZFA:0000066 amnioproctodeal invagination anal pit anus porus embryonic proctodaeum proctodaeum proctodeal removed WBbt:0006795 'proctodeum' - junction between the alimentary and genital tracts in the male. uberon stomach AAO:0000579 ANISEED:1235297 An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium. BTO:0001307 CALOHA:TS-0980 EFO:0000837 EHDAA2:0001915 EHDAA:2993 EMAPA:17021 EV:0100070 FMA:7148 GAID:293 It appears that the stomach has an ancient origin. The stomach first appears in the fish lineage. The prevertebrate chordates do not have a true stomach, whereas the cartilaginous and bony fish do. Although most fish do have a true stomach, some fish species appear to have lost the stomach secondarily. The remaining vertebrate lineages do have a true stomach (at least in the adult animal), although there is great variation in the size and shape of the stomach.[well established][VHOG] MA:0000353 MAT:0000051 MESH:A03.492.766 MIAA:0000051 OpenCyc:Mx4rvVjlqpwpEbGdrcN5Y29ycA Portion of alimentary canal with increased circular and longitudinal smooth muscle. Bounded posteriorly by the pyloric sphincter. Mucosal lining has increased folding.[AAO] TAO:0002121 UBERON:0000945 UMLS:C0038351 VHOG:0000408 Ventricular We restrict this to the vertebrate specific structure - see the grouping class 'food storage organ' for analogous structures in other species. Teleosts: Zebrafish is functionally stomach-less, but may retain ontogenic footprint. Although the precise shape and size of the stomach varies widely among different vertebrates, the relative positions of the oesophageal and duodenal openings remain relatively constant. As a result, the organ always curves somewhat to the left before curving back to meet the pyloric sphincter. However, lampreys, hagfishes, chimaeras, lungfishes, and some teleost fish have no stomach at all, with the oesophagus opening directly into the intestine. The gastric lining is usually divided into two regions, an anterior portion lined by fundic glands, and a posterior with pyloric glands. Cardiac glands are unique to mammals, and even then are absent in a number of species. The distributions of these glands vary between species, and do not always correspond with the same regions as in man. Furthermore, in many non-human mammals, a portion of the stomach anterior to the cardiac glands is lined with epithelium essentially identical to that of the oesophagus. Ruminants, in particular, have a complex stomach, the first three chambers of which are all lined with oesophageal mucosa XAO:0000128 anterior intestine galen:Stomach gaster mesenteron stomach chamber uberon ventriculus cardial valve A membranous fold of the heart that prevents reflux of fluid BTO:0000564 EMAPA:17869 EV:0100024 Extensive conservation of valve developmental mechanisms also has been observed among vertebrate species including chicken, mouse, and human.[well established][VHOG] FMA:7110 GAID:176 MA:0000086 MESH:D006351 One of the four structures within the heart that prevent backflow of blood by opening and closing with each heartbeat. The valves include two semilunar valves, the aortic and pulmonary; the mitral or bicuspid valve; and the tricuspid valve. The valves permit blood flow in only one direction. [TFD][VHOG] OpenCyc:Mx4rv8oyuJwpEbGdrcN5Y29ycA Rector et al: One might be tempted to define 'heart valve' equivalently to 'valve in the heart', and 'valve' as a 'structure which functions as a valve'. But this combination results in the 'foramen ovale' being classified as a kind of 'heart valve', since it is undoubtedly located in the heart and functions as a valve TAO:0005065 UBERON:0000946 UMLS:C0018826 VHOG:0000818 XAO:0004126 ZFA:0005065 cardiac valve galen:HeartValve heart valve heart valve heart valves stomodaeal valve uberon valve of heart aorta AAO:0010213 All amniotes have a broadly similar arrangement to that of humans, albeit with a number of individual variations. In fish, however, there are two separate vessels referred to as aortas. The ventral aorta carries de-oxygenated blood from the heart to the gills; part of this vessel forms the ascending aorta in tetrapods (the remainder forms the pulmonary artery). A second, dorsal aorta carries oxygenated blood from the gills to the rest of the body, and is homologous with the descending aorta of tetrapods. The two aortas are connected by a number of vessels, one passing through each of the gills. Amphibians also retain the fifth connecting vessel, so that the aorta has two parallel arches BTO:0000135 CALOHA:TS-0046 EFO:0000265 EMAPA:18601 EV:0100027 FMA:3734 GAID:469 MA:0000062 MAT:0000035 MESH:D001011 MIAA:0000035 OpenCyc:Mx4rvVjvTpwpEbGdrcN5Y29ycA The main artery of the circulatory system which carries oxygenated blood from the heart to all the arteries of the body except those of the lungs.[AAO] The main trunk of the systemic arterial system that carries blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation This class is currently a mixed bag, encompassing (1) the entirety of the mammalian aorta together with (2) the developmental and phylogenetic homologs of its segments: the ventral aorta and dorsal aortae. UBERON:0000947 UMLS:C0003483 VHOG:0001523 When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG] XAO:0003010 aortic arteria maxima dorsal aorta galen:Aorta trunk of aortic tree trunk of systemic arterial tree uberon heart A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ. AAO:0010210 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] BILA:0000020 BTO:0000562 Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO] CALOHA:TS-0445 EFO:0000815 EHDAA2:0000738 EHDAA:420 EMAPA:16105 EV:0100018 FMA:7088 GAID:174 Herz@de MA:0000072 MAT:0000036 MESH:D006321 MIAA:0000036 OpenCyc:Mx4rvVjvDpwpEbGdrcN5Y29ycA Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO] TAO:0000114 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)" http://dx.doi.org/10.1101/gad.1485706 UBERON:0000948 UMLS:C0018787 VHOG:0000276 XAO:0000064 ZFA:0000114 branchial heart cardiac cardium chambered heart galen:Heart relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO] uberon vertebrate heart endocrine system AAO:0010279 Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO] Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity. CALOHA:TS-1301 EFO:0002969 EHDAA2:0002224 EMAPA:35306 EV:0100128 FBbt:00005068 FMA:9668 GAID:439 MA:0000012 MESH:D004703 Multicellular organisms have complex endocrine systems, allowing responses to environmental stimuli, regulation of development, reproduction, and homeostasis. Nuclear receptors (NRs), a metazoan-specific family of ligand-activated transcription factors, play central roles in endocrine responses, as intermediates between signaling molecules and target genes. The NR family includes ligand-bound and orphan receptors, that is, receptors with no known ligand or for which there is no ligand Pocket. Understanding NR evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...).[well established][VHOG] TAO:0001158 UBERON:0000949 UMLS:C0014136 VHOG:0000098 XAO:0000158 ZFA:0001158 endocrine endocrine glandular system endocrine system systema endocrinum uberon brain (...) 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 BTO:0000142 CALOHA:TS-0095 Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO] 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 MESH:D001921 MIAA:0000098 OpenCyc:Mx4rvVjT65wpEbGdrcN5Y29ycA PBA:3999 Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO] TAO:0000008 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]. 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) UBERON:0000955 UMLS:C0006104 UMLS:C1269537 VHOG:0000157 XAO:0000010 ZFA:0000008 encephalon galen:Brain http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=21 requires review for applicability to invertebrate structures, e.g. synganglion suprasegmental levels of nervous system suprasegmental structures synganglion the brain uberon medulla of organ FMA:61108 Middle part of an organ, surrounded by the cortex. UBERON:0000958 galen:Medulla medulla medullary this class is used in a very general sense uberon nerve of cervical vertebra BAMS:cern FMA:5859 Innervates: sternohyoid muscle, sternothyroid muscle, omohyoid muscle[WP] The cervical nerves are the spinal nerves from the cervical vertebrae. Although there are seven cervical vertebrae (C1-C7), there are eight cervical nerves (C1-C8). All nerves except C8 emerge above their corresponding vertebrae, while the C8 nerve emerges below the C7 vertebra. (In the other portions of the spine, the nerve emerges below the vertebra with the same name. Dorsal (posterior) distribution includes the greater occipital (C2) and third occipital (C3). Ventral (anterior) distribution includes the cervical plexus (C1-C4) and brachial plexus (C5-C8) [WP,unvetted]. UBERON:0000962 UMLS:C0228815 cervical nerve cervical nerve tree cervical spinal nerve nervus cervicalis uberon cornea AAO:0010344 BTO:0000286 CALOHA:TS-0171 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 EFO:0000377 EHDAA2:0000316 EHDAA:10199 EMAPA:17161 EV:0100341 FMA:58238 GAID:892 MA:0000266 MESH:D003315 OpenCyc:Mx4rvViBa5wpEbGdrcN5Y29ycA TAO:0000640 UBERON:0000964 UMLS:C0010031 VHOG:0000164 XAO:0000180 ZFA:0000640 cornea of camera-type eye corneal corneas the transparent anterior portion of the fibrous coat of the eye that serves as the chief refractory structure tunica cornea uberon lens of camera-type eye 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 OpenCyc:Mx4rvVj0fZwpEbGdrcN5Y29ycA RETIRED_EHDAA2:0000975 TAO:0000035 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] The lens is avascular and nourished by diffusion from the aqueous and vitreous This class excludes compound eye corneal lenses. Transparent part of camera-type eye that helps to refract light to be focused on the retina. UBERON:0000965 UMLS:C0023317 VHOG:0000169 XAO:0000008 ZFA:0000035 camera-type eye lens crystalline lens eye lens lens lens crystallina lenses ocular lens uberon retina AAO:0010352 BAMS:R BTO:0001175 CALOHA:TS-0865 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 EFO:0000832 EHDAA2:0001627 EHDAA:4757 EMAPA:17168 EV:0100348 FMA:58301 GAID:755 MA:0000276 MAT:0000142 MBA:304325711 MESH:D012160 MIAA:0000142 NIFSTD_RETIRED:birnlex_1156 Netzhaut OpenCyc:Mx4rvViTfpwpEbGdrcN5Y29ycA TAO:0000152 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] 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 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. UBERON:0000966 UMLS:C0035298 UMLS:C1278894 VHOG:0000229 XAO:0000009 ZFA:0000152 inner layer of eyeball retina of camera-type eye retinal retinas tunica interna of eyeball uberon eye An organ that detects light. BILA:0000017 BTO:0000439 CALOHA:TS-0309 EFO:0000827 EV:0100336 FBbt:00005162 GAID:69 MAT:0000140 MESH:D005123 MIAA:0000140 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, OpenCyc:Mx4rvViTvpwpEbGdrcN5Y29ycA 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) UBERON:0000970 light-detecting organ ocular optic uberon visual apparatus neck AEO:0000108 An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column. BTO:0000420 CALOHA:TS-2045 EFO:0000967 EHDAA2:0003108 EMAPA:35587 FMA:7155 GAID:86 MA:0000024 MAT:0000297 MESH:D009333 MIAA:0000297 OpenCyc:Mx4rvVjLF5wpEbGdrcN5Y29ycA UBERON:0000974 UMLS:C0027530 cervical collum galen:Neck neck (volume) 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. uberon pleura BTO:0001791 CALOHA:TS-2081 EFO:0001980 EMAPA:16775 EV:0100044 FMA:9583 GAID:360 In MA, is_a cavity lining (which we equate to parietal). In FMA, is_a (viscous) serous membrane (which includes mesothelium plus connective tissue). Note the MA structure should probably be associated with the mesothelium of pleura in FMA. JB/EHDAA2 argues the term 'pleura' is best used for the mesothelial lining (thus excluding connective tissue). See https://github.com/obophenotype/uberon/issues/86 MA:0000433 MESH:D010994 OpenCyc:Mx4rv3zwLZwpEbGdrcN5Y29ycA The invaginated serous membrane that surrounds the lungs (the visceral portion) and lines the walls of the pleural cavity (parietal portion). The serous membrane that covers the lungs and lines the pleural cavity. [Kaufman_MH_and_Bard_JBL, The_anatomical_basis_of_mouse_development_(1999)_San_Diego:_Academic_Press, p.264][VHOG] UBERON:0000977 UMLS:C0032225 VHOG:0000394 pleura pleural pleural tissue uberon wall of pleural sac leg BTO:0000721 CALOHA:TS-2206 EFO:0001411 EHDAA2:0000972 EHDAA:5151 EHDAA:6176 EHDAA:8289 EMAPA:17489 GAID:49 MA:0000047 MESH:D035002 Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] OpenCyc:Mx4rvViYzZwpEbGdrcN5Y29ycA The portion of the hindlimb that contains both the stylopod and zeugopod. The term leg can mean: [1] an appendage on which an animal walks [2] the entire hindlimb of a tetrapod [3] the segment of a human leg between knee and ankle (cf FMA) [4] the region of a hindlimb include the stylopod and zeugopod, but excluding the autopod. We define this class as [4], and thus 'leg' is compltely analagous to 'arm'. For [1], see the class 'locomotive weight-bearing appendage'. For [2] we use 'hindlimb'. For UBERON:0000978 VHOG:0000345 lower extremity tetrapod leg uberon we use the less open to misinterpretation 'hindlimb zeugopod'. Editor note: currently declared as overlapping foot, as AOs disagree over whether some ankle parts are in the leg or foot skeletal joint AEO:0000182 Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO] Anatomical cluster that consists of two or more adjacent skeletal structures, 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] BTO:0001686 CALOHA:TS-2023 EFO:0000948 EMAPA:35456 FMA:7490 GAID:102 MA:0000319 MAT:0000188 MESH:D007596 MIAA:0000188 OpenCyc:Mx4rvVjjdpwpEbGdrcN5Y29ycA RETIRED_EHDAA2:0003182 TAO:0000367 UBERON:0000982 UMLS:C0022417 VHOG:0001276 VSAO:0000101 XAO:0000171 ZFA:0001596 articular joint articulation galen:Joint joint joints uberon reproductive system AAO:0010258 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] 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] BILA:0000103 BTO:0000081 CALOHA:TS-1318 EFO:0000809 EHDAA2:0001603 EHDAA:5923 EMAPA:17381 EV:0100100 FBbt:00004857 FMA:7160 GAID:363 Geschlechtsorgan HAO:0000374 HAO:0000895 MA:0000326 MIAA:0000305 OpenCyc:Mx4rvVja4ZwpEbGdrcN5Y29ycA TAO:0000632 UBERON:0000990 UMLS:C1261210 VHOG:0000182 WBbt:0005747 XAO:0000142 ZFA:0000632 animal reproductive system consider splitting genitalia from reproductive system genital system genital tract genitalia organa genitalia reproductive tissue reproductive tract systemata genitalia uberon gonad AAO:0000213 Anatomical structure which produces gametes as well as certain sex hormones controlled by the pituitary gonadotropins.[AAO] BILA:0000123 BSA:0000079 BTO:0000534 EMAPA:16857 EMAPA:17383 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] FBbt:00004858 FMA xref is a 'general anatomical term' FMA:18250 GAID:368 HAO:0000379 MA:0002420 MESH:D006066 OpenCyc:Mx4rwQvdiZwpEbGdrcN5Y29ycA Reproductive organ that produces and releases eggs (ovary) or sperm (testis). TAO:0000413 The part of the reproductive system that produces and releases eggs (ovary) or sperm (testis).[TAO] UBERON:0000991 UMLS:C0018067 VHOG:0000397 WBbt:0005175 XAO:0003146 ZFA:0000413 gonada gonadal gonads uberon female gonad (...) while it is likely that Urbilateria lacked a complex somatic reproductive system, it is at present impossible to speculate on whether or not it possessed a true gonad, let alone any other somatic adaptations for reproduction (reference 1); Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved (reference 2).[uncertain][VHOG] AAO:0000371 BILA:0000125 BSA:0000080 BTO:0000975 CALOHA:TS-0730 EFO:0000973 EHDAA2:0001360 EHDAA:8124 EMAPA:17962 EV:0100111 Either of paired female reproductive organs involved in production of ova and female sex hormones.[AAO] FBbt:00004865 FMA:7209 Female reproductive organ.[TAO] GAID:367 MA:0000384 MESH:D010053 MIAA:0000125 OpenCyc:Mx4rvVi9QJwpEbGdrcN5Y29ycA Ovaries of some kind are found in the female reproductive system of many animals that employ sexual reproduction, including invertebrates. However, they develop in a very different way in most invertebrates than they do in vertebrates, and are not truly homologous. Many of the features found in human ovaries are common to all vertebrates, including the presence of follicular cells, tunica albuginea, and so on. However, many species produce a far greater number of eggs during their lifetime than do humans, so that, in fish and amphibians, there may be hundreds, or even millions of fertile eggs present in the ovary at any given time. In these species, fresh eggs may be developing from the germinal epithelium throughout life. Corpora lutea are found only in mammals, and in some elasmobranch fish; in other species, the remnants of the follicle are quickly resorbed by the ovary. In birds, reptiles, and monotremes, the egg is relatively large, filling the follicle, and distorting the shape of the ovary at maturity. Amphibians and reptiles have no ovarian medulla; the central part of the ovary is a hollow, lymph-filled space. The ovary of teleosts is also often hollow, but in this case, the eggs are shed into the cavity, which opens into the oviduct. Although most normal female vertebrates have two ovaries, this is not the case in all species. In birds and platypuses, the right ovary never matures, so that only the left is functional. In some elasmobranchs, the reverse is true, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo TAO:0000403 UBERON:0000992 UMLS:C0029939 VHOG:0000251 XAO:0000258 ZFA:0000403 female organism genitalia gonad female organism genitalia gonada female organism reproductive system gonad female organism reproductive system gonada female reproductive system gonad female reproductive system gonada genitalia of female organism gonad genitalia of female organism gonada gonad of female organism genitalia gonad of female organism reproductive system gonad of female reproductive system gonad of genitalia of female organism gonad of reproductive system of female organism gonada of female organism genitalia gonada of female organism reproductive system gonada of female reproductive system gonada of genitalia of female organism gonada of reproductive system of female organism ovarian ovaries ovarium ovary ovum-producing ovary reproductive system of female organism gonad reproductive system of female organism gonada the gonad of a female organism which contains germ cells uberon oviduct A passage through which ova leave the maternal body or pass to an organ communicating with the exterior of the body. [TFD][VHOG] A tube or collection of tubes in an animal from the ovaries to the outside of the body. AAO:0010533 BSA:0000083 BTO:0000980 EFO:0000974 EMAPA:18984 GAID:366 In all remaining vertebrates (i.e., coelacanths, lungfishes, amphibians, reptiles, birds, and mammals), the oviduct arises in ontogeny as a longitudinal, groovelike invagination of the coelomic epithelium on the lateral surface of the mesonephros.[well established][VHOG] MAT:0000126 MESH:D010057 MIAA:0000126 TAO:0000560 The only female vertebrates to lack oviducts are the jawless fishes. In these species, the single fused ovary releases eggs directly into the body cavity. The fish eventually extrudes the eggs through small genital pores towards the rear of the body[WP] UBERON:0000993 UMLS:C0029954 VHOG:0001136 XAO:0003052 ZFA:0000560 female reproductive tracts in birds divided into infundibulum, magnum, isthmus, uterus, and vagina ovarian duct ovarian tube oviducts sometimes oviduct is used interchangeably with follaopian tube. Here they are different - the oviduct connects the gonad to the outside in a variety of animals. The mammal-class fallopian tube is derived from the mullerian duct and connects the gonads/infubdibulum to the uterus tuba uterina tuba uterinae tubular parts of female reproductive system uberon uterine tube uterus An infundibulum, uterine tube, uterus, and vagina also differentiate along the oviducts of eutherian mammals.[well established][VHOG] BTO:0001424 CALOHA:TS-1102 EFO:0000975 EMAPA:29915 EV:0100113 FMA:17558 GAID:172 MA:0000389 MAT:0000127 MESH:D014599 MIAA:0000127 Most animals that lay eggs, such as birds and reptiles, have an oviduct instead of a uterus. In monotremes, mammals which lay eggs and include the platypus, either the term uterus or oviduct is used to describe the same organ, but the egg does not develop a placenta within the mother and thus does not receive further nourishment after formation and fertilization. Marsupials have two uteruses, each of which connect to a lateral vagina and which both use a third, middle 'vagina' which functions as the birth canal. Marsupial embryos form a choriovitelline 'placenta' (which can be thought of as something between a monotreme egg and a 'true' placenta), in which the egg's yolk sac supplies a large part of the embryo's nutrition but also attaches to the uterine wall and takes nutrients from the mother's bloodstream. OpenCyc:Mx4rvViojJwpEbGdrcN5Y29ycA The hollow muscular organ in female mammals in which the blastocyst normally becomes embedded and in which the developing embryo and fetus is nourished. Its cavity opens into the vagina below and into a uterine tube on either side. [TFD][VHOG] Two uteruses usually form initially in a female fetus, and in placental mammals they may partially or completely fuse into a single uterus depending on the species. In many species with two uteruses, only one is functional. Humans and other higher primates such as chimpanzees, along with horses, usually have a single completely fused uterus, although in some individuals the uteruses may not have completely fused [Wikipedia:Uterus] UBERON:0000995 UMLS:C0042149 VHOG:0001137 galen:Uterus the female muscular organ of gestation in which the developing embryo or fetus is nourished until birth uberon uterine vagina 'The distal end of the oviducts differentiates as a vagina in Metatheria and Eutheria.' Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective, Third Edition (2001) Orlando Fla.: Harcourt College Publishers, p.688 A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles[WP]. BTO:0000243 CALOHA:TS-1103 EFO:0000976 EMAPA:18986 EV:0100117 FMA:19949 GAID:381 MA:0000394 MAT:0000128 MESH:D014621 MIAA:0000128 OpenCyc:Mx4rvVj1B5wpEbGdrcN5Y29ycA Organ with organ cavity which connects the cervical canal of uterus to the vestibule of vagina.[FMA] The distal end of the oviducts differentiates as a vagina in Metatheria and Eutheria.[well established][VHOG] The genital canal in the female, leading from the opening of the vulva to the cervix of the uterus. [TFD][VHOG] UBERON:0000996 UMLS:C0042232 VHOG:0001138 distal oviductal region distal portion of oviduct galen:Vagina uberon vaginae vaginal skin epidermis (...) 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] 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] 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 TAO:0000105 The outer epithelial layer of the external integument of the body that is derived from the embryonic epiblast.[AAO] The outer epithelial layer of the skin that is superficial to the dermis. UBERON:0001003 UMLS:C0014520 VHOG:0000077 XAO:0000028 ZFA:0000105 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). epidermal epidermis relationship loss: subclass external integument structures (AAO:0000961)[AAO] skin uberon vertebrate epidermis respiratory system AAO:0000541 Atmungssystem BTO:0000203 CALOHA:TS-1319 EFO:0000804 EHDAA2:0001604 EHDAA:2203 EMAPA:16727 EV:0100036 FMA:7158 Functional system which consists of structures involved in respiration. GAID:78 MA:0000327 MAT:0000030 MESH:D012137 MIAA:0000030 OpenCyc:Mx4rvVjzFJwpEbGdrcN5Y29ycA TAO:0000272 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] UBERON:0001004 UMLS:C0035237 VHOG:0000202 XAO:0000117 ZFA:0000272 apparatus respiratorius apparatus respiratorius respiratory system systema respiratorium uberon respiratory airway An airway through which respiratory air passes in organisms. FMA:265130 This class generically groups trachea and analagous structures throughout metazoa. Consider renaming, as the term could be taken to mean lumen of tracheal system (e.g. in SNOMED). As a grouping class this is quite vague, as it is not clear where the airway begins and ends UBERON:0001005 airway airways uberon digestive system AAO:0000129 An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO] Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes. 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 UBERON:0001007 WBbt:0005748 XAO:0000125 ZFA:0000339 alimentary system alimentary tract digestive galen:DigestiveSystem gastrointestinal system gut 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 ncithesaurus:Digestive_System uberon renal system AAO:0010257 An anatomical system which consists of organs and tissues which produce, store, and excrete urine.[AAO] BILA:0000015 BTO:0001244 BTO:0003092 CALOHA:TS-1323 EFO:0000803 EHDAA2:0001601 EHDAA:5901 EMAPA:17366 EV:0100095 Evolution of vertebrate renal anatomy appears quite conservative when compared, for example, to evolution of respiratory and cardiovascular systems in vertebrates. Major anatomical changes in vertebrates kidneys separate those of birds and mammals from kidneys of lower vertebrates. General increase in animal size from fish to mammals is reflected by an increase in total number of nephrons per kidney, rather than by constant change in tubular dimensions.[well established][VHOG] FBbt:00005056 FMA:7159 GAID:391 In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels In various sources such as Encyclopedia Britannica, the excretory and urinary systems are indeed the same system (see wikipedia talk page); we merge two BTO classes here MA:0000325 MAT:0000027 MESH:D014551 MIAA:0000027 TADS:0000162 TAO:0000163 The renal system in an anatomical system that maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products.. This definition is inclusive of the organs of the vertebrate renal system, as well as the Malpighian tubules of insects, and allows for future incorporation of structures such as the antennal glands of crustaceans UBERON:0001008 UMLS:C1508753 VHOG:0000723 WBbt:0005736 XAO:0000143 ZFA:0000163 excretory system galen:UrinaryTract renal or urinary system renal system renal/urinary system systema urinaria systema urinarium uberon urinary system urinary tract circulatory system AAO:0000959 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] CALOHA:TS-2103 FBbt:00005057 OpenCyc:Mx4rvVjzG5wpEbGdrcN5Y29ycA UBERON:0001009 VHOG:0001248 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] 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]. systema cardiovasculare the cardiovascular system and the lymphatic system are parts of the circulatory system uberon adipose tissue AAO:0000001 AEO:000020 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] BTO:0001487 CALOHA:TS-0013 Connective tissue in which fat is stored.[TAO] EFO:0000790 EHDAA2:0003120 EMAPA:35112 EV:0100381 FMA:20110 GAID:920 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. MA:0000009 MAT:0000015 MESH:D000273 MIAA:0000015 OpenCyc:Mx4rvVjc_ZwpEbGdrcN5Y29ycA Portion of connective tissue composed of adipocytes enmeshed in areolar tissue TAO:0002134 Tissue that contains adipocytes, used for cushioning, thermal insulation, lubrication (primarily in the pericardium) and energy storage.[AAO] UBERON:0001013 UMLS:C0001527 VHOG:0001284 XAO:0003049 ZFA:0005345 adipose adipose bodyfat fat fat tissue fatty depot fatty tissue galen:FattyTissue in FMA this is dense irregular connective tissue relationship loss: subclass connective tissue proper (AAO:0000099)[AAO] uberon musculature A subdivision of the muscular system corresponding to a subdisivision of an organism. AAO:0011066 BTO:0000887 EFO:0001949 EMAPA:32715 EMAPA:35577 FMA:32558 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. MA:0000165 OpenCyc:Mx4rvVjmr5wpEbGdrcN5Y29ycA TAO:0000548 UBERON:0001015 UMLS:C0026845 VSAO:0005038 WBbt:0005737 ZFA:0000548 muscle group muscle system muscles muscles set musculature musculature system musculi set of muscles set of skeletal muscles uberon nervous system 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] AAO:0000324 Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO] BILA:0000079 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 Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG] OpenCyc:Mx4rvViT_pwpEbGdrcN5Y29ycA TAO:0000396 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]. UBERON:0001016 UMLS:C0027763 VHOG:0000402 WBbt:0005735 XAO:0000177 ZFA:0000396 nerve net nervous neural neurological system systema nervosum uberon central nervous system (...) 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 BTO:0000227 CALOHA:TS-0150 CNS EFO:0000908 EHDAA2:0000225 EHDAA:828 EMAPA:16470 EMAPA:16754 EV:0100163 FBbt:00005094 FMA:55675 GAID:570 MA:0000167 MAT:0000457 MESH:D002490 OpenCyc:Mx4rvzYt3pwpEbGdrcN5Y29ycA Part of the nervous system which includes the brain and spinal cord.[AAO] TAO:0000012 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). 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. UBERON:0001017 UMLS:C0927232 VHOG:0000293 XAO:0000215 ZFA:0000012 cerebrospinal axis neuraxis systema nervosum centrale uberon nerve fasciculus A slender neuron projection bundle[FBbt]; A bundle of anatomical fibers, as of muscle or nerve (American Heritage Dictionary 4th ed). BTO:0002191 EMAPA:36605 FBbt:00005101 FMA:12235 TGMA:0000088 UBERON:0001019 UMLS:C1185741 fascicle fasciculus nerve bundle nerve fasciculus nerve fiber tract neural fasciculus note FBbt class not disjoint from tract. Consider merging with 'neuron projection bundle' uberon nerve A portion of tissue which is a fasiculated group of axons.[TAO] AAO:0011070 AEO:0000137 An enclosed, cable-like bundle of axons in the peripheral nervous system originating in a nerve root in the central nervous system (or a condensed nervous structure) connecting with peripheral structures. BAMS:n BSA:0000098 BTO:0000925 BTO:0001027 CALOHA:TS-0772 EHDAA2:0003137 EHDAA:2851 EHDAA:3776 EHDAA:4657 EMAPA:32808 EMAPA:32815 EV:0100371 FBbt:00005105 FMA:65132 FMA:65239 GAID:747 GAID:758 MA:0000217 MA:0000228 MESH:D010525 OpenCyc:Mx4rwP3lkpwpEbGdrcN5Y29ycA TAO:0007009 UBERON:0001021 UMLS:C0027740 UMLS:C0031119 VHOG:0000901 XAO:0000204 XAO:0003047 ZFA:0007009 galen:Nerve nerves nervous neural subtree peripheral nerve uberon sensory system AAO:0000555 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] Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information. BAMS:SEN BILA:0000099 EFO:0000805 EHDAA2:0003094 EMAPA:16192 FBbt:00005827 FMA:75259 MA:0002442 MAT:0000031 MIAA:0000031 TAO:0000282 UBERON:0001032 VHOG:0001674 XAO:0003194 ZFA:0000282 note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs organa sensuum organa sensuum sense organ subsystem sense organs sense organs set sensory organ system sensory subsystem sensory systems set of sense organs uberon gustatory system AAO:0010577 BILA:0000143 EFO:0000830 FMA:7194 MA:0002446 MAT:0000275 MIAA:0000275 TAO:0001101 The sensory system for the sense of taste. The sensory system for the sense of taste[NIFSTD:nlx_anat_090803]. The sensory system used for the sense of taste.[AAO] UBERON:0001033 XAO:0003197 ZFA:0001101 gustatory gustatory organ system in ZFA and MA this is a subtype of sensory system. we should change sensory system to disambiguate parts and wholes taste system uberon foregut AAO:0011042 Anterior subdivision of a digestive tract. BILA:0000085 BTO:0000507 EHDAA2:0000557 EHDAA:520 EMAPA:16548 FBbt:00005379 FMA:45616 MA:0001526 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 TGMA:0001014 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] UBERON:0001041 UMLS:C0231051 VHOG:0000285 XAO:0000232 praeenteron proenteron uberon chordate pharynx (...) the earliest vertebrates possessed unjointed internal and external branchial arches, and musculature encircling the pharynx.[well established][VHOG] 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]. 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]. AAO:0000967 Anatomical cavity bounded by the derivatives of the branchial arches.[AAO] BTO:0001049 CALOHA:TS-0785 Consider generalizing to deuterostome pharynx EFO:0000836 EHDAA2:0001458 EHDAA:2947 EMAPA:16706 EV:0100065 FMA:46688 GAID:155 MA/FMA pharynx not part of digestive/alimentary system, we are consistent with this scheme MA:0000432 MESH:A03.867 OpenCyc:Mx4rvViv7ZwpEbGdrcN5Y29ycA 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]. TAO:0000056 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] UBERON:0001042 UMLS:C0031354 VHOG:0000462 XAO:0003227 ZFA:0000056 galen:Pharynx pharynx 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] uberon esophagus AAO:0000145 ANISEED:1235301 Anterior end of the alimentary canal lined with smooth muscle. Bounded anteriorly by a constriction in the pharynx. Bounded posteriorly by and increase in circular and/or longitudinal smooth muscle associated with the stomach.[AAO] BTO:0000959 CALOHA:TS-0700 EFO:0000835 EHDAA2:0001285 EHDAA:2937 EMAPA:16833 EV:0100069 FMA:7131 GAID:291 MA:0000352 MAT:0000048 MESH:A03.365 MIAA:0000048 OpenCyc:Mx4rvVj9Q5wpEbGdrcN5Y29ycA TAO:0000204 The few structural specializations in (adult lampreys) pharynx include complex valves on the external gill openings that direct the tidal flow, and the division of the ancestral pharynx into an oesophagus and a respiratory pharynx.[well established][VHOG] Tube that connects the pharynx to the stomach. In mammals, the oesophagus connects the buccal cavity with the stomach. The stratified squamous non-keratinised epithelium lining the buccal cavity is continued through the pharynx down into the oesophagus. The lowest part of the oesophagus (ca. 2 cm) is lined with gastric mucosa and covered by peritoneum. The main body of the oesophagus is lined with small, simple mucous glands. Each gland opens into the lumen by a long duct which pierces the muscularis mucosae (Wilson and Washington, 1989). A sphincter is situated at the point where the oesophagus enters the stomach to prevent gastro-oesophageal reflux, i.e. to prevent acidic gastric contents from reaching stratified epithelia of the oesophagus, where they can cause inflammation and irritation (Wilson and Washington, 1989; Brown et al., 1993). UBERON:0001043 UMLS:C0014876 VHOG:0000450 XAO:0000127 ZFA:0000204 esophageal esophagus NOT part of gut in MA. part of gut in ZFA. part_of gut (via UGIT) in FMA. Consider splitting. Interspecies: The human oesophagus is 25 cm long and has a diameter of ca. 2 cm. Only little information was found on the oesophagus in rat, rabbit and pig. The oesophagus of rat (75 x 2 mm) and rabbit has no mucous glands and the cardia of the stomach has a well-developed sphincter, which prevents them from vomiting (Hebel and Stromberg, 1988; Manning et al., 1994). Morphologically the oesophagus is similar in man and pig; both are omnivores and have a non-keratinised epithelium, submucous glands and similar membrane enzymes. Like in humans, pigs can suffer from reflux oesophagitis and stress ulceration of the oesophagus. The pig oesophagus may therefore be a good model for investigation compared to the human oesophagus (Christie et al., 1995) galen:Esophagus gullet oesophagus uberon saliva-secreting gland A gland that produces the saliva. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-25, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] BTO:0001203 CALOHA:TS-0892 EFO:0000859 EHDAA2:0001775 EHDAA:7987 EMAPA:17751 EV:0100059 FBbt:00005382 FMA:9597 GAID:937 In air-feeding animals, the lack of water column to lubricate the food has been compensated for by the evolution of the salivary glands. These glands are present only in amniotes and are controlled by the parasympathetic system.[well established][VHOG] MA:0000346 MAT:0000079 MESH:D012469 MIAA:0000079 OpenCyc:Mx4rvVjl5ZwpEbGdrcN5Y29ycA The salivary glands in mammals are exocrine glands, glands with ducts, that produce saliva. They also secrete amylase, an enzyme that breaks down starch into maltose. In other organisms such as insects, salivary glands are often used to produce biologically important proteins like silk or glues, and fly salivary glands contain polytene chromosomes that have been useful in genetic research. The salivary glands of some species are modified to produce enzymes; salivary amylase is found in many, but by no means all, bird and mammal species (including humans, as noted above). Furthermore, the venom glands of poisonous snakes, Gila monsters, and some shrews, are modified salivary glands UBERON:0001044 UMLS:C0036098 VHOG:0000376 currently we define saliva and salivary glands very generally in functional terms but it may be more appropriate to split this class. From WP: In most vertebrates, saliva does not contain any enzymes, consisting of mucus and water only, and its primary function is to moisten food while eating. As a result, true salivary glands are rarely found in fish or aquatic tetrapods, although there are often individual mucus-secreting cells. Amphibians have a single salivary gland, the intermaxillary gland, located in the forward part of the palate. Reptiles and birds normally have only very small glands on the lips, palate, and base of the mouth, although there are some birds with large glands, which produce a sticky saliva that helps in nest-building. The distinct parotid, submandibular, and sublingual glands are only developed in mammals. galen:SalivaryGland glandulae salivariae saliva-secreting exocrine glands of the oral cavity[GO] salivary gland uberon midgut BILA:0000086 BTO:0000863 EFO:0001950 EHDAA2:0001185 EHDAA:983 EMAPA:16255 FBbt:00005383 FMA:45617 In humans: originates from the foregut at the opening of the bile duct into the duodenum and continues through the small intestine and much of the large intestine until the transition to the hindgut about two-thirds of the way through the transverse colon MA:0001564 Middle subdivision of a digestive tract[CJM]. In vertebrates: The middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine[GO]. Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. We may explicitly make this a developmental class TGMA:0001036 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] UBERON:0001045 UMLS:C0231052 VHOG:0000290 XAO:0000103 in FMA this represents an embryonic region. mesenteron uberon hindgut AAO:0011052 BILA:0000087 BTO:0000510 EHDAA2:0000779 EHDAA:975 EMAPA:16715 FBbt:00005384 FMA:45618 MA:0001527 Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future (vertebrates have some contribution from NC - https://github.com/obophenotype/uberon/wiki/The-neural-crest). We may explicitly make this a developmental class TGMA:0001020 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] The caudalmost subdivision of a digestive tract. UBERON:0001046 UMLS:C0231053 VHOG:0000459 XAO:0000104 in FMA this class has no children. In MA it has a single child hindgut epithelium metenteron the caudal portion of the primitive digestive tube of the embryo uberon primordium AEO:0000171 BTO:0001886 EFO:0001652 EHDAA2:0003171 FBbt:00005495 FMA:86589 MAT:0000482 Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt, Hartenstein, V. (2004)]. UBERON:0001048 UMLS:C0678727 XAO:0003043 bud future organ placode primordia rudiment uberon 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] AAO:0010617 BTO:0001057 CALOHA:TS-2371 DHBA:10154 EHDAA2:0001254 EHDAA:2869 EHDAA:908 EMAPA:16164 EMAPA:16530 EMAPA:16757 FMA:293882 Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO] 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]. MAT:0000069 MIAA:0000069 TAO:0001135 The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][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 UBERON:0001049 UMLS:C0231024 VHOG:0000307 XAO:0003204 ZFA:0001135 neural primordium presumptive central nervous system tubus neuralis uberon rectum AAO:0010401 BTO:0001158 CALOHA:TS-1180 EFO:0000848 EHDAA2:0001592 EHDAA:5836 EMAPA:17896 EV:0100081 FMA:14544 GAID:311 In the lungfish, sharks and rays the rectum opens into the cloaca which also receives wastes (urine) from the kidneys and material from the reproductive organs. In bony fish the rectum reaches the outside environment through the anus, which is normally situated just in front the urinary and reproductive openings. However in some fish the digestive tract may be curled back on itself, and in the Electric Eel (Electrophorus electricus) the anus is situated in the fish's throat. -- http://www.earthlife.net/fish/digestion.html MA:0000336 MAT:0000050 MESH:A03.492.411.495.767 MIAA:0000050 OpenCyc:Mx4rvVjaU5wpEbGdrcN5Y29ycA The terminal portion of the large intestine between the ileo-pelvic colon and the anus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] UBERON:0001052 UMLS:C0034896 VHOG:0001751 XAO:0000238 galen:Rectum intestinum rectum rectal rectal sac terminal portion of intestine terminal portion of large intestine the terminal portion of the intestinal tube, terminating with the anus uberon anatomical entity AAO:0010841 AEO:0000000 BILA:0000000 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:0000000 EHDAA2:0002229 FBbt:10000000 FBbt_root:00000000 FMA:62955 HAO:0000000 MA:0000001 TAO:0100000 TGMA:0001822 UBERON:0001062 UMLS:C1515976 XAO:0000000 ZFA:0100000 uberon ventral pancreatic duct A duct joining the pancreas to the common bile duct to supply pancreatic juices which aid in digestion provided by the exocrine pancreas. The pancreatic duct joins the common bile duct just prior to the ampulla of Vater, after which both ducts perforate the medial side of the second portion of the duodenum at the major duodenal papilla. BTO:0002362 EHDAA2:0001396 EHDAA:6905 EMAPA:17510 FMA:16003 GAID:337 MA:0000126 MESH:D010183 RETIRED_EHDAA2:0002177 These data show that ducts within the zebrafish pancreas originally arise in situ from isolated progenitor cells rather than arising from reiterative branching of the pancreatic epithelium. This process of pancreatic duct formation in zebrafish may be analogous to the mechanism of duct formation in the mammalian mammary and salivary glands. (...) A related mechanism of duct formation has also been proposed to occur within the mammalian pancreatic epithelium.[uncertain][VHOG] UBERON:0001064 UBERON:0005627 UMLS:C0030288 Upon reaching its final destination, the ventral pancreatic bud fuses with the much larger dorsal pancreatic bud. At this point of fusion, the main ducts of the ventral and dorsal pancreatic buds fuse, forming the duct of Wirsung, the main pancreatic duct. VHOG:0000256 canal of Wirsung chief pancreatic duct duct of Wirsung ductus pancreatis ventralis hepaticopancreatic duct in EHDAA2 this is an epithelium, in FMA the wall consists of epithelium and connective tissue main pancreatic duct pancreatic duct uberon posterior vena cava A vein that carries deoxygenated blood from the lower half of the body into the right atrium of the heart. AAO:0011083 BTO:0002682 EHDAA2:0000611 EMAPA:18416 FMA:10951 GAID:548 MA:0000480 MESH:D014682 Phylogenetic modifications within this basic pattern of arteries and veins are largely correlated with functional changes. In the transition from water to land, gills gave way to lungs, accompanied by the establishment of a pulmonary circulation. In some fishes and certainly in tetrapods, the cardinal veins become less involved in blood return. Instead, the composite, prominent postcava (posterior vena cava) arose to drain the posterior part of the body and the precava (anterior vena cava) developed to drain the anterior part of the body.[well established][VHOG] Trunk of systemic vein which is formed by the union of the right common iliac vein and the left common iliac vein and terminates in the right atrium[FMA]. UBERON:0001072 UMLS:C0042458 VHOG:0001194 XAO:0000388 caudal vena cava galen:InferiorVenaCava inferior caval vein inferior vena cava postcava posterior vena cava uberon vena cava inferior skin of head A zone of skin that is part of a head [Automatically generated definition]. FMA:12166 FMA:24756 MA:0000582 TODO - distinguish between entire skin of region and arbitrary zone of skin on region UBERON:0001084 UMLS:C0205029 adult head zone of skin head skin head zone of skin uberon zone of skin of adult head zone of skin of head urine BTO:0001419 CALOHA:TS-1092 EFO:0001939 EMAPA:36554 ENVO:00002047 Excretion that is the output of a kidney FMA:12274 GAID:1189 MA:0002545 MAT:0000058 MESH:D014556 MIAA:0000058 OpenCyc:Mx4rvVjGppwpEbGdrcN5Y29ycA UBERON:0001088 UMLS:C0042036 galen:Urine kidney excreta from some taxa (e.g. in aves) may not be liquid uberon synovial fluid BTO:0001339 CALOHA:TS-0996 ENVO:02000039 FMA:12277 GAID:265 MA:0002544 MESH:D013582 Portion of organism substance that is a clear fluid that occupies the space in synovial joints.[TAO] TAO:0005154 Transudate contained in the synovial cavity of joints, and in the cavity of tendon sheaths and bursae. UBERON:0001090 UMLS:C0039097 ZFA:0005154 galen:SynovialFluid joint fluid uberon diaphragm A thin musculomebranous barrier that separates the abdominal and thoracic cavities. Often used for breathing control BTO:0000341 CALOHA:TS-0198 EFO:0000937 EHDAA2:0003495 EMAPA:17701 EV:0100376 FMA:13295 GAID:158 MA:0001904 MAT:0000502 MESH:D003964 OpenCyc:Mx4rvVivz5wpEbGdrcN5Y29ycA The diaphragm is a skeletal muscle that is responsible for contraction and expansion of the lungs[GO]. The existence of some membrane separating the pharynx from the stomach can be traced widely among the chordates. Thus amphioxus possesses an atrium by which water exits the pharynx, which has been argued (and disputed) to be homologous to structures in ascidians and hagfishes.[3] The mammals are characterized by a diaphragm, which separates the thoracic portion of the body cavity from the abdominal region and assists in drawing air into the lungs and forcing it out. Modern reptiles lack a muscular diaphragm and it is reasonable to suppose that the diaphragm developed as a new device that made possible a large degree of oxygen intake for active animals. The change may have taken place during the transition from reptile to mammal (...).[well established][VHOG] The urochordate epicardium separates digestive organs from the pharynx and heart, but the anus returns to the upper compartment to discharge wastes through an outgoing siphon (Thoracic_diaphragm#Comparative_anatomy_and_evolution) UBERON:0001103 UMLS:C0011980 VHOG:0000713 barrier between thoracic and abdominal cavities; stop gastric contents from refluxing into the oesophagus breathing control diaphragm muscle diaphragm of thorax midriff originate from the cervical somites, likely C3-C5[PMID:23586979] phren phrenic thoracic diaphragm uberon lobe of liver EMAPA:18306 FMA:13361 MA:0000360 Traditional gross anatomy divided the liver into four lobes based on surface features. The falciform ligament is visible on the front (anterior side) of the liver. This divides the liver into a left anatomical lobe, and a right anatomical lobe. UBERON:0001113 UMLS:C0447541 hepatic lobe liver lobe lobus hepatis some work needs to be done to ensure the child terms of this class have correct isa/partof placement. in MA they are subclasses, in FMA they are parts uberon right lobe of liver 2nd lobe EHDAA2:0001008 EHDAA:4001 EMAPA:18311 FMA:13362 MA:0000363 Portion of the liver which develops on the fish's right side adjacent to the gall bladder.[TAO] TAO:0005173 The right lobe is much larger than the left; the proportion between them being as six to one. It occupies the right hypochondrium, and is separated from the left lobe on its upper surface by the falciform ligament; on its under and posterior surfaces by the left sagittal fossa; and in front by the umbilical notch. It is of a somewhat quadrilateral form, its under and posterior surfaces being marked by three fossæ: the porta and the fossæ for the gall-bladder and inferior vena cava, which separate its left part into two smaller lobes; the quadrate and caudate lobes. [WP,unvetted]. This class was created automatically from a combination of ontologies UBERON:0001114 UMLS:C0227481 VHOG:0001424 ZFA:0005173 gall bladder lobe liver right lobe lobus hepaticus dexter lobus hepatis dexter right hepatic lobe right liver lobe second lobe uberon left lobe of liver EHDAA2:0001000 EHDAA:3995 EMAPA:18307 FMA:13363 MA:0000361 Portion of the liver which develops on the fish's left side.[TAO] TAO:0005172 The left lobe is smaller and more flattened than the right. It is situated in the epigastric and left hypochondriac regions. Its upper surface is slightly convex and is moulded on to the diaphragm; its under surface presents the gastric impression and omental tuberosity. [WP,unvetted]. This class was created automatically from a combination of ontologies UBERON:0001115 UMLS:C0227486 VHOG:0001423 ZFA:0005172 left hepatic lobe left liver lobe liver left lobe lobus hepaticus sinister lobus hepatis sinister uberon parathyroid gland AAO:0010545 Any one of several small structures, usually four, attached to the dorsal surfaces of the lateral lobes of the thyroid gland. [TFD][VHOG] BTO:0000997 CALOHA:TS-0745 EFO:0000862 EMAPA:32812 EV:0100134 Either of the two pairs of small, spherical, encapsulated glands which develop from ventral growths of the third and fourth pharyngeal pouches and are closely associated with the external jugular veins. Calcitonin and parathyroid hormone are secreted by these glands.[AAO] FMA:13890 GAID:452 In humans and chick it emerges from pouches 3 and 4, but in mice it is exclusively generated by the third pouch MA:0000128 MAT:0000082 MESH:D010280 MIAA:0000082 Parathyroid glands are found in all adult tetrapods, although they vary in their number, and in their exact position. Mammals typically have four parathyroids, while other groups typically have six. Fish do not possess parathyroid glands, although the ultimobranchial glands, which are found close to the oesophagus, may have a similar function and could even be homologous with the tetrapod parathyroids. Even these glands are absent in the most primitive vertebrates, the jawless fish, but as these species have no bone in their skeletons, only cartilage, it may be that they have less need to regulate calcium metabolism. The conserved homology of genes and calcium-sensing receptors in fish gills with those in the parathryroid glands of birds and mammals is recognized by evolutionary developmental biology as evolution-using genes and gene networks in novel ways to generate new structures with some similar functions and novel functions[WP] The evolution of the tetrapods, and the shift from an aquatic to a terrestrial environment, was believed to have required new controls for regulating calcium homeostasis, and thus the evolution of parathyroid glands (...) both the tetrapod parathyroid and the gills of fish contribute to the regulation of extracellular calcium levels. It is therefore reasonable to suggest that the parathyroid gland evolved as a result of the transformation of the gills into the parathyroid glands of tetrapods and the transition from an aquatic to a terrestrial environment. This interpretation would also explain the positioning of the parathyroid gland within the pharynx in the tetrapod body. Were the parathyroid gland to have emerged de novo with the evolution of the tetrapods it could, as an endocrine organ, have been placed anywhere in the body and still exert its effect.[well established][VHOG] The parathyroid gland is an endocrine gland for secretion of parathyroid hormone, usually found as a pair, embedded in the connective tissue capsule on the posterior surface of the thyroid gland. Parathyroid regulates calcium and phosphorous metabolism. UBERON:0001132 UMLS:C0030518 VHOG:0001188 XAO:0000167 epithelial body parathyroid parathyroid secreting cell table 13.1 of Kardong is used to create the taxon-specific developmental relationships here, although some omissions are made for simplicity. uberon cardiac muscle tissue AAO:0010245 AEO:0000142 BILA:0000134 BTO:0000199 CALOHA:TS-0440 EHDAA2:0003142 EMAPA:32688 FMA:14068 Muscle tissue composed of cardiac muscle cells, forming the muscles of the heart[ZFA,modified]. TAO:0005280 UBERON:0001133 UBERON:0007096 ZFA:0005280 cardiac muscle cardiac muscle muscle tissue cardiac muscle textus muscularis cardiac musculature check relationship with myocardium. part_of in MA - but we also have a more specific class 'cardiac muscle tissue of myocardium'. Check ncit galen:CardiacMuscle galen:CardiacMuscleTissue 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 ncithesaurus:Heart_Muscle 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 skeletal muscle tissue EMAPA:32716 FMA:14069 MA:0002439 Muscle tissue that consists primarily of skeletal muscle fibers. Muscle, composed of long cylindrical, multinucleated cells that attaches to the skeleton via tendons.[TAO] TODO - add skeletal muscle organ? See GO:0060538 skeletal muscle organ development. Todo - group FBbt:00005073 - somatic muscle. 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] Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm[FMA] UBERON:0001134 UMLS:C0242692 skeletal muscle skeletal muscle system somatic muscle uberon smooth muscle tissue (...) 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] A non-striated muscle that is composed of spindle-shaped cells. Smooth muscle usually is organized into sheets that line cavitated organs.[TAO] AAO:0010244 AEO:0000141 BTO:0001260 CALOHA:TS-0943 EFO:0000889 EHDAA2:0003141 EMAPA:32717 EV:0100378 FBbt:00003525 FMA:14070 GAID:167 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. Involuntary muscle tissue consisting of uninucleate spindle-shaped fibers.[AAO] MA:0000166 MAT:0000303 MESH:D009130 MIAA:0000303 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]. OpenCyc:Mx4rvvSS3pwpEbGdrcN5Y29ycA TAO:0005274 UBERON:0001135 UMLS:C1267092 VHOG:0001246 WBbt:0005781 XAO:0000175 ZFA:0005274 galen:SmoothMuscle galen:SmoothMuscleTissue involuntary muscle non-striated muscle smooth muscle textus muscularis levis; textus muscularis nonstriatus textus muscularis nonstriatus uberon visceral muscle visceral muscle tissue mesothelium 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 Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. http://en.wikipedia.org/wiki/ 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). UBERON:0001136 UMLS:C0086610 uberon dorsum 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.. BTO:0001713 CALOHA:TS-2223 EFO:0001405 FMA:14181 GAID:30 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 MESH:A01.176 OpenCyc:Mx4rvVkEU5wpEbGdrcN5Y29ycA UBERON:0001137 UMLS:C0004600 back back of body proper dorsal dorsal part of organism galen:Back uberon cystic duct Duct that connects the gall bladder and the common bile duct.[TAO] EHDAA2:0000333 EHDAA:3045 EMAPA:16841 FMA:14539 GAID:290 MA:0000355 MESH:A03.159.183.419 OpenCyc:Mx4rveBeC5wpEbGdrcN5Y29ycA TAO:0005166 The duct of the gallbladder which joins the common hepatic duct, thus forming the common biliary duct. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] UBERON:0001152 UMLS:C0010672 VHOG:0000213 ZFA:0005166 ductus cysticus galen:CysticDuct the tubular structure that conducts gall bladder contents from the gall bladder to the common bile duct uberon caecum A cecum is present in most amniote species, and also in lungfish, but not in any living species of amphibian. In reptiles, it is usually a single median structure, arising from the dorsal side of the large intestine. Birds typically have two paired ceca, as, unlike other mammals, do hyraxes. Most mammalian herbivores have a relatively large cecum, hosting a large number of bacteria, which aid in the enzymatic breakdown of plant materials such as cellulose; in many species, it is considerably wider than the colon. In contrast, obligatory carnivores, whose diets contain little or no plant material, have a reduced cecum, which is often partially or wholly replaced by the vermiform appendix. Many fish have a number of small outpocketings, called pyloric ceca, along their intestine; despite the name they are not homologous with the cecum of amniotes, and their purpose is to increase the overall area of the digestive epithelium.[2] Some invertebrates, such as squid,[3] may also have structures with the same name, but these have no relationship with those of vertebrates. A pouch in the digestive tract that connects the ileum with the ascending colon of the large intestine. It is separated from the ileum by the ileocecal valve, and is the beginning of the large intestine. It is also separated from the colon by the cecocolic junction. BTO:0000166 CALOHA:TS-0122 EFO:0000850 EHDAA2:0000206 EHDAA:3913 EMAPA:35197 EV:0100397 FMA:14541 GAID:307 Kardong: in some herbivorous lizards, a cecum is present between small and large intestines MA:0000334 MESH:A03.492.411.495.209 MIAA:0000288 OpenCyc:Mx4rve6u4JwpEbGdrcN5Y29ycA UBERON:0001153 UMLS:C0007531 VHOG:0001559 blind intestine blindgut caeca caecal caecum ceca cecum galen:Cecum intestinum caecum intestinum crassum caecum intestinum crassum cecum uberon vermiform appendix A blind-ended tube connected to the cecum, from which it develops embryologically[WP]. A comparative anatomical approach reveals three apparent morphotypes of the cecal appendix, as well as appendix-like structures in some species that lack a true cecal appendix. Cladistic analyses indicate that the appendix has evolved independently at least twice (at least once in diprotodont marsupials and at least once in Euarchontoglires), shows a highly significant (P < 0.0001) phylogenetic signal in its distribution, and has been maintained in mammalian evolution for 80 million years or longer.[well established][VHOG] BTO:0000084 CALOHA:TS-1267 EFO:0000849 EHDAA2:0000588 EMAPA:35140 EV:0100076 EV:0100080 FMA:14542 GAID:308 MA:0001540 MAT:0000287 MESH:A03.492.411.495.209.290 MIAA:0000287 OpenCyc:Mx4rvVjGgJwpEbGdrcN5Y29ycA Organ with organ cavity which is continuous proximally with the cecum and distally terminates in the tip of the appendix. Examples: There is only one appendix[FMA:14542]. UBERON:0001154 UMLS:C0003617 VHOG:0001306 apex of caecum apex of cecum appendiceal appendix appendix vermiformis appendix vermiformis caecal appendix cecal appendix galen:AppendixVermiformis uberon vermix colon AAO:0010400 Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] BTO:0000269 CALOHA:TS-0158 EFO:0000361 EMAPA:18939 EV:0100079 FMA:14543 GAID:309 In mammals, the colon consists of four sections: the ascending colon, the transverse colon, the descending colon, and the sigmoid colon[WP] In zebrafish, the posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates[ZFIN] Last portion of the large intestine before it becomes the rectum. MA:0000335 MAP:0000001 MAT:0000526 MESH:A03.492.411.495.356 OpenCyc:Mx4rvgLEM5wpEbGdrcN5Y29ycA TAO:0000706 TODO - abstract this such that it legitimately covers all vertebrates The last portion of the digestive system, it extracts water and salt from solid wastes before they are eliminated from the body.[AAO] The posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates. Wallace et al, 2005.[TAO] UBERON:0001155 UMLS:C0009368 VHOG:0000648 XAO:0000243 ZFA:0000706 colonic galen:Colon hindgut it extracts water and salt from solid wastes before they are eliminated from the body[WP] large bowel posterior intestine uberon ascending colon BTO:0000270 CALOHA:TS-0057 EFO:0000843 EMAPA:35151 FMA:14545 MA:0001541 MAT:0000311 MIAA:0000311 OpenCyc:Mx4rv3H0FZwpEbGdrcN5Y29ycA Section of colon which is distal to the cecum and proximal to the transversecolon.[FMA,modified] UBERON:0001156 UMLS:C0227375 colon ascendens galen:AscendingColon in MA, this is a subclass of colon spiral colon uberon transverse colon BTO:0000272 CALOHA:TS-2052 EFO:0000844 EMAPA:35880 FMA:14546 MA:0001543 MAT:0000312 MIAA:0000312 OpenCyc:Mx4rvg7qyJwpEbGdrcN5Y29ycA The proximal-distal subdivision of colon that runs transversely across the upper part of the abdomen, from the right to the left colic flexure. Continuous with the descending colon[BTO,modified]. UBERON:0001157 UMLS:C0227386 colon transversum galen:TransverseColon uberon descending colon BTO:0000641 CALOHA:TS-2010 EFO:0000845 EMAPA:35285 FMA:14547 MA:0001542 MAT:0000313 MIAA:0000313 OpenCyc:Mx4rwHsNhpwpEbGdrcN5Y29ycA The portion of the colon between the left colic flexure and the sigmoid colon at the pelvic brim; the portion of the descending colon lying in the left iliac fossa is sometimes called the iliac colon. UBERON:0001158 UMLS:C0227389 colon descendens galen:DescendingColon uberon sigmoid colon BTO:0000645 CALOHA:TS-2044 EFO:0000846 EMAPA:36391 FMA:14548 MAT:0000314 MESH:A03.492.411.495.356.668 MIAA:0000314 OpenCyc:Mx4rwHX_-5wpEbGdrcN5Y29ycA The part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about 40 cm. in length, and normally lies within the pelvis, but on account of its freedom of movement it is liable to be displaced into the abdominal cavity. UBERON:0001159 UMLS:C0227391 UMLS:C0682612 colon sigmoideum galen:SigmoidColon pelvic colon sigmoid colon sigmoid flexure uberon body of stomach BTO:0000505 EMAPA:35810 FMA:14560 MA:0002559 The body of stomach is the part of the stomach that lies between the fundus above and the pyloric antrum below; its boundaries are poorly defined[GO]. UBERON:0001161 UMLS:C0227230 corpus gastricum corpus gastricum (ventriculare) corpus ventriculare corpus ventriculi galen:GastricCorpus gastric body gastric corpus stomach body uberon we include this as zone of stomach even though it is not distinguished by gland type pyloric antrum BTO:0001732 EFO:0002555 EMAPA:17891 FMA:14579 GAID:332 MA:0001624 MESH:A03.492.766.716 UBERON:0001165 UMLS:C0034193 antrum antrum of Willis antrum of stomach antrum pylori antrum pyloricum galen:PyloricAntrum gastric antrum stomach antrum stomach pyloric antrum the area at the bottom of the stomach on the caudal side of the pyloric canal that contains gastrin-producing G cells, which stimulate acid production, and the luminal pH-sensitive population of somatostatin-producing D cells uberon pylorus Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] BTO:0001146 EHDAA2:0001580 EHDAA:4860 EMAPA:17631 FMA:14581 GAID:333 MA:0002560 MESH:A03.492.766.799 The orifice which allows the passage from the stomach into the intestine. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] UBERON:0001166 UMLS:C0034196 VHOG:0000420 We follow Kardong in defining stomach regions by glands galen:Pylorus pars pylorica pars pylorica gastricae pyloric pyloric part of stomach pyloric region stomach pyloric region the stomach tissue region surrounding and controlling the distal outlet of the stomach, which opens into the duodenum uberon valvula pylori wall of stomach EMAPA:35826 FMA:14582 MA:0002692 UBERON:0001167 anatomical wall of stomach anatomical wall of ventriculus galen:WallOfStomach gastric wall stomach anatomical wall stomach wall the layered structure that makes up the stomach, typiclly consists of a serous coat, a muscular coat, a mucous membrane, and other tissue layers in between uberon ventriculus anatomical wall ventriculus wall wall of ventriculus wall of small intestine An anatomical wall that is part of a small intestine [Automatically generated definition]. EMAPA:35785 FMA:14615 MA:0002696 UBERON:0001168 UMLS:C1519375 anatomical wall of small bowel anatomical wall of small intestine small bowel anatomical wall small bowel wall small intestinal wall small intestine anatomical wall small intestine wall uberon wall of small bowel portal lobule FMA:14653 MA:0002498 The triangular region on the periphery of the liver lobules that contain a bile duct and a terminal branch of the hepatic artery and portal vein, and may also include a lymphatic vessel. UBERON:0001171 UMLS:C0682620 uberon hepatic acinus EMAPA:35497 FMA:14654 MA:0002496 The functional unit of the liver, consisting of a mass of hepatocytes from adjacent liver lobules aligned around the hepatic arterioles and portal venules just as they anastomose into sinusoids. UBERON:0001172 UMLS:C0227519 liver acinus portal acinus uberon biliary tree A complex network of conduits that begins with the canals of Hering (intralobar bile duct) and progressively merges into a system of interlobular, septal, and major ducts which then coalesce to form the extrahepatic bile ducts, which finally deliver bile to the intestine, and in some species to the gallbladder. AAO:0011020 EMAPA:35172 FMA:14665 Hollow tree organ, the organ parts of which consist of the bile ducts.[AAO] The path in many species is as follows: Bile canaliculi -> Canals of Hering (intralobar bile duct) -> interlobular bile ducts -> intrahepatic bile ducts -> left and right hepatic ducts merge to form -> common hepatic duct *exits liver* and joins -> cystic duct (from gall bladder) forming -> common bile duct -> joins with pancreatic duct -> forming ampulla of Vater -> enters duodenum [WP] UBERON:0001173 UMLS:C0005423 XAO:0000455 biliary tract uberon common bile duct Digestive system duct that collects bile from the hepatic bile duct and the cystic duct.[TAO] EHDAA2:0000303 EHDAA:3981 EMAPA:17201 FMA:14667 GAID:282 MA:0001631 MESH:D003135 TAO:0005165 The duct formed by the union of the common hepatic and cystic ducts. [Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, adapted_from_Dorian_AF][VHOG] UBERON:0001174 UMLS:C0009437 VHOG:0000214 ZFA:0005165 ductus choledochus ductus choledochus (biliaris) galen:CommonBileDuct the part of the biliary tree formed by the union of the cystic duct and the common hepatic duct uberon common hepatic duct EMAPA:19101 FMA:14668 GAID:286 MA:0002660 MESH:D006500 Predominantly extrahepatic bile duct which is formed by the junction of the right and left hepatic ducts, which are predominantly intrahepatic, and, in turn, joins the cystic duct to form the common bile duct[GAID]. The common hepatic duct is the duct formed by the convergence of the right hepatic duct (which drains bile from the right functional lobe of the liver) and the left hepatic duct (which drains bile from the left functional lobe of the liver). The common hepatic duct then joins the cystic duct coming from the gallbladder to form the common bile duct[WP]. TODO - MA distinguishes between bile duct, hepatic duct, common bile duct and common hepatic duct. in FMA hepatic duct and common hepatic duct are the same. Common is part of extra-hepatic part The duct which conveys the bile from the liver and unites with the cystic duct to form the common bile duct. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] UBERON:0001175 UMLS:C0019149 VHOG:0000220 ductus hepaticus communis hepatic duct uberon right hepatic duct EHDAA2:0001727 EHDAA:3992 EMAPA:32797 FMA:14669 MA:0001639 The duct that drains bile from the right half of the liver and joins the left hepatic duct to form the common hepatic duct. The duct which drains bile from the right half of the liver and unites with the left hepatic duct to form the common hepatic duct. [adapted_from_http://www.medterms.com/script/main/art.asp?articlekey=26032][VHOG] UBERON:0001176 UMLS:C0227557 VHOG:0000217 ductus hepaticus dexter uberon left hepatic duct EHDAA2:0000941 EHDAA:3990 EMAPA:32795 FMA:14670 MA:0001638 The duct that drains bile from the left half of the liver and joins the right hepatic duct to form the common hepatic duct. The duct which drains bile from the left half of the liver and unites with the right hepatic duct to form the common hepatic duct. [adapted_from_http://www.medterms.com/script/main/art.asp?articlekey=26032][VHOG] UBERON:0001177 UMLS:C0227560 VHOG:0000218 ductus hepaticus sinister uberon visceral peritoneum EMAPA:16592 FMA:14703 TAO:0005132 The inner layer of peritoneum that is wrapped around organs located inside the intraperitoneal space. UBERON:0001178 VHOG:0001528 ZFA:0005132 uberon visceral serous membrane of peritoneum peritoneal cavity Anatomical cavity bounded by visceral and parietal peritoneum BTO:0001782 EHDAA2:0001446 EMAPA:16138 FMA:14704 GAID:24 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] MA:0000054 MESH:A01.047.025.600.678 The potential space between the parietal and visceral layers of the peritoneum, which are normally in contact. The peritoneal cavity is divided into the greater and lesser sac. The greater sac is the peritoneal cavity, and the lesser sac is the omental bursa. [TFD][VHOG] UBERON:0001179 UMLS:C1704247 VHOG:0000852 cavitas peritonealis saccus serosus peritonei uberon renal artery AAO:0010223 Artery which supplies blood via branches to the gonads, oviducts, and kidneys.[AAO] BTO:0001165 EFO:0002552 EHDAA2:0004100 EHDAA:5321 EHDAA:8594 EMAPA:28373 FMA:14751 GAID:507 MA:0002035 MESH:D012077 One of two laterally paired arteries that supplies the kidneys. These are large arteries that branch from the dorsal aorta in primitive vertebrates. OpenCyc:Mx4rveOFHpwpEbGdrcN5Y29ycA RETIRED_EHDAA2:0001600 TAO:0000420 The renal arteries normally arise off the side of the abdominal aorta, immediately below the superior mesenteric artery, and supply the kidneys with blood. Each is directed across the crus of the diaphragm, so as to form nearly a right angle with the aorta. The renal arteries carry a large portion of total blood flow to the kidneys. Up to a third of total cardiac output can pass through the renal arteries to be filtered by the kidneys. The arterial supply of the kidneys is variable and there may be one or more renal arteries supplying each kidney. It is located above the renal vein. It has a radius of approximately 0.25cm, 0.26 cm at the root. The measured mean diameter can differ depending on the imaging method used. For example, the diameter was found to be 5.04 ± 0.74 mm using ultrasound, but 5.68 ± 1.19 mm using angiography. [WP,unvetted].[Wikipedia] UBERON:0001184 UMLS:C0035065 ZFA:0000420 arteria renalis galen:RenalArtery renal arterial tree renal arteries renal arteries vary widely even in humans. Sub-structures should be checked for taxon variability. uberon hepatic artery An artery that supplies the liver. Artery that supplies blood to the liver.[TAO] BTO:0004307 EMAPA:17859 FMA:14769 GAID:496 MA:0001963 MESH:D006499 OpenCyc:Mx4rvzKtFpwpEbGdrcN5Y29ycA TAO:0005161 UBERON:0001193 UMLS:C0019145 ZFA:0005161 arteria hepatica arteria hepatica propria currently defined in a generic fashion. galen:HepaticArtery uberon mucosa of stomach BTO:0001308 CALOHA:TS-0404 EMAPA:35817 FMA:14907 GAID:321 MA:0002683 MESH:A03.492.766.440 Magenschleimhaut OpenCyc:Mx8NhB4rvcD6KJwpEbGdrcN5Y29ycB4rvmKNOpwpEbGdrcN5Y29ycB4rvVj5FpwpEbGdrcN5Y29ycB4rvVjlqpwpEbGdrcN5Y29ycA The gastric mucosa is the mucous membrane layer of the stomach which contains the glands and the gastric pits. In men it is about 1 mm thick and its surface is smooth, soft, and velvety. It consists of epithelium, lamina propria, and the muscularis mucosae. In its fresh state, it is of a pinkish tinge at the pyloric end and of a red or reddish-brown color over the rest of its surface. In infancy it is of a brighter hue, the vascular redness being more marked. It is thin at the cardiac extremity, but thicker toward the pylorus. During the contracted state of the organ it is thrown into numerous plaits or rugae, which, for the most part, have a longitudinal direction, and are most marked toward the pyloric end of the stomach, and along the greater curvature. These folds are entirely obliterated when the organ becomes distended. When examined with a lens, the inner surface of the mucous membrane presents a peculiar honeycomb appearance from being covered with funnel-like depressions or foveolae of a polygonal or hexagonal form, which vary from 0.12 to 0.25 mm. in diameter. These are the ducts of the gastric glands, and at the bottom of each may be seen one or more minute orifices, the openings of the gland tubes. Gastric glands are simple or branched tubular glands that emerge on the deeper part of the gastric foveola, inside the gastric areas and outlined by the folds of the mucosa. There are three types of glands: cardiac glands (in the proximal part of the stomach), oxyntic glands (the dominating type of gland), and pyloric glands. The cardiac glands mainly contain mucus producing cells. The bottom part of the oxyntic glands is dominated by zymogen (chief) cells that produce pepsinogen (an inactive precursor of the pepsin enzyme). Parietal cells, which secrete hydrochloric acid are scattered in the glands, with most of them in the middle part. The upper part of the glands consist of mucous neck cells; in this part the dividing cells are seen. The pyloric glands contain mucus-secreting cells. Several types of endocrine cells are found in all regions of the gastric mucosa. In the pyloric glands contain gastrin producing cells (G cells); this hormone stimulates acid production from the parietal cells. ECL (enterochromaffine-like) cells, found in the oxyntic glands release histamine, which also is a powerful stimulant of the acid secretion. The A cells produce glucagon, which mobilizes the hepatic glycogen, and the enterochromaffin cells that produce serotonin, which stimulates the contraction of the smooth muscles. The surface of the mucous membrane is covered by a single layer of columnar epithelium . This epithelium commences very abruptly at the cardiac orifice, where there is a sudden transition from the stratified epithelium of the esophagus. The epithelial lining of the gland ducts is of the same character and is continuous with the general lining of the stomach. [WP,unvetted][Wikipedia:Gastric_mucosa]. The mucosal layer that lines the stomach. UBERON:0001199 UMLS:C0017136 galen:GastricMucosa gastric mucosa gastric mucous membrane mucosa of organ of stomach mucosa of organ of ventriculus mucosa of ventriculus mucous membrane of stomach mucous membrane of ventriculus organ mucosa of stomach organ mucosa of ventriculus stomach mucosa stomach mucosa of organ stomach mucous membrane stomach organ mucosa tunica mucosa (gaster) tunica mucosa gastricae tunica mucosa gastris uberon ventriculus mucosa ventriculus mucosa of organ ventriculus mucous membrane ventriculus organ mucosa pyloric sphincter (...) the adult Xenopus stomach exhibits both glandular and aglandular regions and a distinct pyloric sphincter similar to that of the amniotic vertebrates (...).[uncertain][VHOG] A strong ring of smooth muscle at the end of the pyloric canal which lets food pass from the stomach to the duodenum. It receives sympathetic innervation from the celiac ganglion[WP]. AAO:0011093 EMAPA:19251 FMA:14916 MA:0002952 OpenCyc:Mx4rvly2ZZwpEbGdrcN5Y29ycA UBERON:0001202 UMLS:C0227238 VHOG:0001466 XAO:0000457 pyloric valve uberon mucosa of small intestine A mucosa that is part of a small intestine [Automatically generated definition]. BTO:0001259 CALOHA:TS-0941 EMAPA:35780 FMA:14933 MA:0002686 UBERON:0001204 UMLS:C0227261 mucosa of organ of small bowel mucosa of organ of small intestine mucosa of small bowel mucous membrane of small bowel mucous membrane of small intestine organ mucosa of small bowel organ mucosa of small intestine small bowel mucosa small bowel mucosa of organ small bowel mucous membrane small bowel organ mucosa small intestinal mucosa small intestine mucosa small intestine mucosa of organ small intestine mucous membrane small intestine organ mucosa tunica mucosa (intestinum tenue) tunica mucosa intestini tenuis uberon renal pelvis A funnel shaped proximal portion of the ureter that is formed by convergence of the major calices [MP]. CALOHA:TS-2230 EMAPA:17948 FMA:15575 GAID:426 In this ontology, the renal pelvis is represented as the area of part-overlap between the kidney and the ureter MA:0000374 MESH:D007682 UBERON:0001224 UMLS:C0227666 galen:RenalPelvis kidney pelvis p. renallis pelvis of ureter pyelum uberon cortex of kidney BTO:0001166 CALOHA:TS-0503 EMAPA:17952 FMA:15581 GAID:424 In the adult metanephros, it forms a continuous smooth outer zone with a number of projections that extend down between the pyramids. It contains the renal corpuscles and the renal tubules except for parts of the loop of Henle which descend into the renal medulla. It also contains blood vessels and cortical collecting ducts. The renal cortex is the part of the kidney where ultrafiltration occurs.[WP] MA:0000372 MESH:D007672 Outer cortical portion of the kidney, between the renal capsule and the renal medulla. UBERON:0001225 UMLS:C0022655 cortex renalis galen:CortexOfKidney kidney cortex renal cortex uberon renal corpuscle A mass of arterial capillaries enveloped in a capsule and attached to a tubule in the kidney[BTO] A tuft of capillaries found in a Bowman's capsule in which waste products are filtered from the blood and urine formation is initiated. Paired highly vascularized structures of the pronephros, responsible for blood filtration.[XAO] BTO:0000333 CALOHA:TS-1317 EMAPA:28236 EMAPA:35726 EV:0100385 FMA:15625 MA:0000376 Malpighian corpuscle TAO:0005281 The part of the nephron that filters blood.[TAO] Together, the Bowmans capsule and the glomerulus comprise the definitive renal corpuscle. http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron UBERON:0001229 UMLS:C0227635 VHOG:0001262 ZFA:0005281 corpusculum renale corpusculum renis cortical renal corpuscle kidney corpuscle malphighian corpuscle malphigian corpuscle the structure containing the glomerular capsule and the glomerulus that serves as the initial blood-filtering component of a nephron uberon glomerular capsule A cup-like sac at the expanded beginning of a tubular component of a nephron that contains the glomerulus AAO:0010526 Anatomical structure found in the kidney consisting of an expanded end of a kidney tubule surrounding a glomerulus and is the major site of filtration.[AAO] BTO:0002297 Bowman's capsule Bowmans capsule EMAPA:27973 EMAPA:28257 FMA:15626 Fluids from blood in the glomerulus are collected in the Bowman's capsule and further processed along the nephron to form urine. This process is known as ultrafiltration[WP]. KUPO:0001001 MA:0001660 Mueller capsule Muellerian capsule One fold of the S-shaped body gives rise to Bowman's capsule[GUDMAP] TAO:0005254 TAO:0005310 UBERON:0001230 UMLS:C0524448 ZFA:0005254 ZFA:0005310 bowman's capsule capsula glomerularis capsula glomeruli malphigian capsule pronephric glomerular capsule renal glomerular capsule uberon collecting duct of renal tubule BTO:0000761 CALOHA:TS-0860 EMAPA:28407 EV:0100391 FMA:15628 GAID:434 MA:0000371 MESH:D007685 Renal duct that collects the output from renal tubules.[TAO] TAO:0005294 The collecting duct is a portion of the nephron through which water flows, moving passively down its concentration gradient UBERON:0001232 ZFA:0005294 arcuate renal tubule collecting duct collecting duct system collecting tubule in ISBN10:0073040584 (Vertebrates, Kardong), the nephron is adjacent to the collecting tubule, consistent with FMA, but not GO. Wikipedia says: Many sources include the connecting tubule as part of the collecting duct system. However, the embryological origin is more similar to the nephron than it is to the rest of the collecting duct (which derives from the ureteric bud), and other sources therefore classify the connecting tubule with the nephron junctional tube kidney collecting duct kidney collecting tubule renal collecting tubule tubulus renalis arcuatus tubulus renalis colligens uberon ureteric tree adrenal cortex AAO:0011009 All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues (medulla), but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] BTO:0000045 CALOHA:TS-0015 EFO:0000237 EMAPA:18427 EV:0100136 FMA:15632 GAID:447 Kardong states that mammals are the first to have distinct cortext and medulla, but this contradicts XAO MA:0000118 MAT:0000494 MESH:D000302 UBERON:0001235 UMLS:C0001613 VHOG:0001481 XAO:0000165 adrenal gland cortex cortex (glandula suprarenalis) cortex glandulae suprarenalis cortex of adrenal gland cortex of suprarenal gland suprarenal suprarenal cortex the thick outer layer of the adrenal gland that produces and secretes steroid hormones such as corticosterone, estrone and aldosterone uberon adrenal medulla AAO:0011010 All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues (medulla), but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] BTO:0000049 CALOHA:TS-0018 EFO:0000852 EMAPA:18428 EV:0100137 FMA:15633 GAID:451 MA:0000119 MAT:0000495 MESH:D019439 UBERON:0001236 UMLS:C0001629 VHOG:0001378 XAO:0000166 adrenal central medulla adrenal gland medulla chromaffin cells medulla (glandula suprarenalis) medulla glandulae suprarenalis medulla of adrenal gland medulla of glandula suprarenalis medulla of suprarenal gland suprarenal medulla the inner portion of the adrenal gland that consists mainly of chromaffin cells which produce, store and secrete neurotransmitters such as epinephrine and norepinephrine uberon intestinal mucosa BTO:0000642 EMAPA:35440 FMA:15695 GAID:296 MA:0001537 MESH:A03.492.411.369 The innermost membrane of the four coats of the intestinal wall, the other three being the submucosa, muscular layers, and serosa. (Berk et al., Gastroenterology, 4th ed, v.3, p1479) UBERON:0001242 UMLS:C0021839 bowel mucosa bowel mucosa of organ bowel mucous membrane bowel organ mucosa intestine mucosa intestine mucosa of organ intestine mucous membrane intestine organ mucosa mucosa of bowel mucosa of intestine mucosa of organ of bowel mucosa of organ of intestine mucous membrane of bowel mucous membrane of intestine organ mucosa of bowel organ mucosa of intestine tunica mucosa intestini uberon anus BTO:0001680 CALOHA:TS-2005 EV:0100082 FBbt:00003148 FMA:15711 GAID:312 In the lungfish, sharks and rays the rectum opens into the cloaca which also receives wastes (urine) from the kidneys and material from the reproductive organs. In bony fish the rectum reaches the outside environment through the anus, which is normally situated just in front the urinary and reproductive openings. However in some fish the digestive tract may be curled back on itself, and in the Electric Eel (Electrophorus electricus) the anus is situated in the fish's throat. -- http://www.earthlife.net/fish/digestion.html MA:0000331 MESH:A03.492.411.495.767.288 OpenCyc:Mx4rvVjaEZwpEbGdrcN5Y29ycA Orifice at the opposite end of an animal's digestive tract from the mouth. Its function is to expel feces, unwanted semi-solid matter produced during digestion, which, depending on the type of animal, may be one or more of: matter which the animal cannot digest, such as bones; food material after all the nutrients have been extracted, for example cellulose or lignin; ingested matter which would be toxic if it remained in the digestive tract; and dead or excess gut bacteria and other endosymbionts. TADS:0000066 TGMA:0001279 UBERON:0001245 UMLS:C0003461 WBbt:0005364 anal anal opening anal orifice galen:Anus opening of terminal part of digestive tract proctodeum uberon interlobular bile duct FMA:15767 MA:0002668 The canals that carry bile in the liver between the intralobular ducts and the biliary ductules; interlobular bile ducts are part of the interlobular portal triad. UBERON:0001246 UMLS:C0227515 interlobular ductule uberon urinary bladder A saccular organ in which urine accumulates before discharge from the body. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] AAO:0000623 Anatomical structure which consists of a membranous sac used to temporarily store urine until it is excreted from the body.[AAO] BTO:0001418 CALOHA:TS-1090 EFO:0000290 EHDAA2:0000174 EHDAA:9328 EMAPA:18321 EV:0100098 FMA:15900 GAID:0000004 In tetrapods, the urinary bladder arises as an outpocketing of the cloaca. (...) The tetrapod urinary bladder appears first among amphibians and is present in Sphenodon, turtles, most lizards, ostriches among birds, and all mammals.[well established][VHOG] MA:0000380 MAT:0000122 MESH:A05.810.161 MIAA:0000122 OpenCyc:Mx4rvVjMmZwpEbGdrcN5Y29ycA The urinary bladder evolved in tetrapods. Birds to not possess a true urinary bladder, although Palaeognathae have an undifferentiated cloacal outpocketing that serves a similar function[https://github.com/obophenotype/uberon/issues/454] UBERON:0001255 UMLS:C0005682 VHOG:0000740 XAO:0000154 bladder distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP]. galen:UrinaryBladder uberon urocyst vesica vesica urinaria vesical wall of intestine An anatomical wall that is part of a intestine [Automatically generated definition]. BTO:0000647 EMAPA:35181 EMAPA:35444 FMA:15949 MA:0001525 MA:0002693 UBERON:0001262 UMLS:C1708548 anatomical wall of bowel anatomical wall of intestine bowel anatomical wall bowel wall bowel wall intestinal wall intestine anatomical wall intestine wall uberon wall of bowel we place two MA classes here due to the official ncit2ma mapping to intestinal wall tissue; not clear how bowel and intestine are different pancreatic acinus EMAPA:35651 FMA:16011 MA:0002417 The secretory units of the exocrine pancreas, where fluid containing digestive enzymes is produced; consists of a group of secretory cells surrounding a luminal space that connects to the pancreatic duct. UBERON:0001263 UMLS:C0227578 acinus pancreaticus pancreas acinus pancreatic acinar pancreatic acini uberon pancreas AAO:0010112 An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes[GO]. As a secretory organ serving exocrine and endocrine functions, the pancreas is specific to the vertebrates[PMID:16417468] Hagfishes and lampreys are unique in the complete separation of their endocrine pancreas (islet or- gan) and their exocrine pancreas (50). The endocrine and exocrine pancreas are coassociated in crown gnathostomes (50). In Branchiostoma and Ciona, there is no diverticulum as there is in hagfishes, lampreys, and gnathostomes, only dispersed insulin-secreting cells in the walls of the gastrointestinal tract (51, 52) BTO:0000988 CALOHA:TS-0736 EFO:0000855 EHDAA2:0001367 EHDAA:6893 EMAPA:17503 EV:0100092 FMA:7198 GAID:334 In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG] MA:0000120 MAT:0000075 MESH:D010179 MIAA:0000075 OpenCyc:Mx4rvVimZZwpEbGdrcN5Y29ycA Organ which secretes a fluid containing enzymes that aid in the digestion of food.[AAO] TAO:0000140 The mature pancreas of higher vertebrates and mammals comprises two major functional units: the exocrine pancreas, which is responsible for the production of digestive enzymes to be secreted into the gut lumen, and the endocrine pancreas, which has its role in the synthesis of several hormones with key regulatory functions in food uptake and metabolism. The exocrine portion constitutes the majority of the mass of the pancreas, and contains only two different cell types, the secretory acinar cells and the ductular cells. The endocrine portion, which comprises only 1-2% of the total mass, contains five different cell types, which are organized into mixed functional assemblies referred to as the islets of Langerhans The zebrafish does not have a discrete pancreas. Exocrine pancreatic tissue can be found scattered along the intestinal tract. The acinar structure of the exocrine pancreas is very similar to that of mammals and comprises cells with a very dark, basophilic cytoplasm UBERON:0001264 UMLS:C0030274 VHOG:0000050 XAO:0000136 ZFA:0000140 galen:Pancreas pancreatic uberon pelvic girdle region FMA:16581 Subdivision of lower limb or fin which links the limb/fin to the body[FMA,modified]. There is only one instance of the pelvic girdle region per organism.[VSAO] The organism subdivision that includes the pelvic girdle skeleton and associated soft tissue. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Examples: There are only two instances in an organism, right and left pectoral girdle regions. UBERON:0001271 UMLS:C0684083 VSAO:0000304 girdle - pelvic pelvic girdle this class describes the subdivision of the limb/fin, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831). See also comments on obo-anatomy mail list. Note that even though the class includes soft tissue it is more restrictive than 'pelvis' which also includes structures in cavities etc. TODO this needs to be better documented uberon epithelium of stomach BTO:0000500 CALOHA:TS-2068 EHDAA2:0001918 EMAPA:17023 FMA:17091 MA:0001610 The epithelial layer of the stomach . UBERON:0001276 VHOG:0001433 epithelial tissue of stomach epithelial tissue of ventriculus epithelium of ventriculus gastric epithelium in FMA this is classified as simple columnar, MA divides this into squamous and glandular stomach epithelial tissue stomach epithelium uberon ventriculus epithelial tissue ventriculus epithelium portal triad A multi-organ-part structure that consists of three vessels of the portal lobule including the bile duct, a terminal branch of the hepatic artery and portal vein, and may also include a lymphatic vessel FMA:17523 MA:0002499 The misnomer 'portal triad' traditionally has included only the first three structures, and was named before lymphatic vessels were discovered in the structure. It can refer both to the largest branch of each of these vessels running inside the hepatoduodenal ligament, and to the smaller branches of these vessels inside the liver. UBERON:0001279 UMLS:C0227514 trias hepatica trias hepatica uberon liver parenchyma AAO:0010405 EHDAA2:0001004 EHDAA:2201 EMAPA:17203 FMA:17540 MA:0000366 The functional units of the liver including the lobules. UBERON:0001280 UBERON:0003223 VHOG:0000539 XAO:0000454 hepatic parenchyma hepatic parenchyme liver parenchyme parenchyma of liver the (liver) tubular structure (dual layered parenchyma) appears to be conserved among all embryonic vertebrates (...) it is not unlikely that all vertebrate livers share the same fundamental functional unit.[well established][VHOG] uberon intralobular bile duct FMA:17545 MA:0002669 Note that this is part of the intrahepatic bile duct in MA, as this class is more alike the tree in FMA. Note also that SCT has canal of Hering and Entire IBduct as the only sibling terms under 'Structure of intralobular bile duct' (i.e. the CoH is the only part of the entire IBduct) UBERON:0001282 UMLS:C0227517 canal of Hering canal of Herring canals of Hering cholangiole duct of Herring ductus interlobularis bilifer intrahepatic bile ductule the tubules located between the bile canaliculi and interlobular bile ducts near the outer edge of a classic liver lobule uberon nephron BTO:0000924 CALOHA:TS-1312 EMAPA:28491 EMAPA:35592 EV:0100384 FMA:17640 Functional unit of the kidney that filters waste.[TAO] GAID:428 In the avian kidney, three types of nephron are identified: mammalian-type nephrons with long and short loops of Henle, and reptilian type nephrons (Gambaryan, 1992) MA:0000375 MESH:D009399 TAO:0002153 The basic functional unit of the kidney. its chief function is to regulate the concentration of water and soluble substances like sodium salts by filtering the blood, reabsorbing what is needed and excreting the rest as urine. A nephron eliminates wastes from the body, regulates blood volume and blood pressure, controls levels of electrolytes and metabolites, and regulates blood pH. Its functions are vital to life and are regulated by the endocrine system by hormones such as antidiuretic hormone, aldosterone, and parathyroid hormone.[WP] UBERON:0001285 UMLS:C0027713 ZFA:0005282 kidney terms require review for cross-vertebrate compatibility and developmental relationships. mature nephron nephroneum tubulus renalis uberon endometrium Animals that have estrous cycles reabsorb the endometrium if conception does not occur during that cycle. Animals that have menstrual cycles shed the endometrium through menstruation instead BTO:0001422 CALOHA:TS-0276 EFO:0000980 EMAPA:29917 EV:0100115 FMA:17742 GAID:377 MA:0000390 MAT:0000319 MESH:D004717 MIAA:0000319 The maternal part of the placenta (of eutherian mammals) is the vascularized and glandular uterine lining, or endometrium.[well established][VHOG] The mucous membrane lining the uterus. [TFD][VHOG] UBERON:0001295 UMLS:C0014180 VHOG:0001285 endometrial in FMA this is subdivided into basal and outer the glandular mucous membrane lining of the uterine cavity that is hormonally responsive during the estrous/menstrual cycle and during pregnancy tunica mucosa (endometrium) tunica mucosa uteri uberon uterine endometrium uterine mucosa uterine mucous membrane sciatic nerve A large nerve that supplies nearly the whole of the skin of the leg, the muscles of the back of the thigh, and those of the leg and foot. It begins in the lower back and runs through the buttock and down the lower limb. BTO:0001221 CALOHA:TS-0899 EFO:0001417 EHDAA2:0001779 EHDAA:5659 EMAPA:18577 FMA:19034 GAID:852 MA:0001172 MESH:D012584 OpenCyc:Mx4rv7MlDJwpEbGdrcN5Y29ycA UBERON:0001322 UMLS:C0036394 VHOG:0000894 ischiadic nerve ischiatic nerve mouse sciatic nerve origins predominantly from the third lumbar (L3) and L4 spinal nerves, unlike the L4 and L5 in rats - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2700063/ nervus ischiadicus nervus sciaticus uberon anal region Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] EFO:0000847 EHDAA2:0000122 EHDAA:2931 EMAPA:16831 MA:0000329 MAT:0000042 MIAA:0000042 The anus and surrounding regions. Encompasses both internal and external regions, where present UBERON:0001353 UMLS:C0230120 VHOG:0000395 WBbt:0006919 posterior posterior end of organism uberon cerebrospinal fluid A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord. BTO:0000237 CALOHA:TS-0130 CSF EFO:0000329 EHDAA2:0004441 ENVO:02000029 EV:0100311 FMA:20935 GAID:1181 In vertebrates, at early stages of Central Nervous System (CNS) development, the architecture of the brain primordium reveals the presence of the cavity of brain vesicles, which is filled by Embryonic Cerebro-Spinal Fluid (E-CSF). (...) Rat and chick E-CSF proteomes are similar, although rat is more complex in certain groups of proteins, e.g., apolipoproteins, which may be involved in the control of neural diversity, and has soluble enzymes present, just like adult human CSF, but unlike chick E-CSF, revealing phylogenetic brain differences between these groups of vertebrates.[uncertain][VHOG] MA:0002503 MAT:0000499 MESH:A12.207.268 Portion of organism substance that is a clear fluid that occupies the subarachnoid space and the ventricular system around and inside the brain.[TAO] TAO:0002184 UBERON:0001359 UMLS:C0007806 VHOG:0001278 ZFA:0001626 cerebral spinal fluid liquor cerebrospinalis spinal fluid the FMA def states that this is subarachnoid spaces only. ZFA def states subarachnoid spaces and brain ventricles, but not SC (and has part_of to brain). Circulation: It circulates from the lateral ventricles to the foramen of Monro (Interventricular foramen), third ventricle, aqueduct of Sylvius (Cerebral aqueduct), fourth ventricle, foramen of Magendie (Median aperture) and foramina of Luschka (Lateral apertures), subarachnoid space over brain and spinal cord. It should be noted that the CSF moves in a pulsatile manner throughout the CSF system with nearly zero net flow. CSF is reabsorbed into venous sinus blood via arachnoid granulations. uberon parietal peritoneum AAO:0010816 EMAPA:16591 FMA:21451 Peritoneum attached to the abdominal wall.[AAO] TAO:0005131 The outer layer of peritoneum that is attached to the abdominal and pelvic walls. UBERON:0001366 UBERON:0004459 VHOG:0001527 ZFA:0005131 parietal serous membrane of peritoneum peritoneal cavity lining uberon skin of limb A zone of skin that is part of a limb [Automatically generated definition]. EMAPA:32726 FMA:23100 MA:0000694 UBERON:0001419 UMLS:C1282135 limb skin limb zone of skin uberon zone of skin of limb skeletal system AAO:0000566 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. Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO] BTO:0001486 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] CALOHA:TS-1320 EFO:0000806 EHDAA2:0003168 EMAPA:35773 FMA:23881 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 MA:0000018 OpenCyc:Mx4rvVi1rpwpEbGdrcN5Y29ycA Skelettsystem System that provides physical support to the organism.[AAO] TAO:0000434 UBERON:0001434 UMLS:C0037253 VHOG:0001254 VSAO:0000027 XAO:0003060 ZFA:0000434 https://github.com/obophenotype/uberon/wiki/The-skeletal-system set of all bones and joints skeletal skeleton system uberon hindlimb skeleton AAO:0000217 EHDAA2:0002226 EMAPA:32633 FMA:24144 Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] OpenCyc:Mx4rvZcKkZwpEbGdrcN5Y29ycA Skeletal structure of the paired, posterior appendages.[AAO] Subdivision of skeleton consisting of all skeletal elements in an hindlimb region. TOOD - find a home for: FMA:24140 UBERON:0001441 VHOG:0001255 VSAO:0000152 XAO:0003062 bones of lower limb free lower limb skeleton hind limb skeleton hind-limb skeleton hindlimb skeleton lower limb skeleton ossa membri inferioris relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO] set of bones of lower limb skeleton of free lower limb skeleton of lower limb uberon chest BTO:0001368 CALOHA:TS-1039 EFO:0000965 EV:0100010 FMA:24216 present in FMA1, but gone in subsequent versions FMA:9576 GAID:91 MA:0000031 MAT:0000295 MESH:A01.911 MIAA:0000295 OpenCyc:Mx4rvVikFZwpEbGdrcN5Y29ycA Subdivision of trunk proper, which is demarcated from the neck by the plane of the superior thoracic aperture and from the abdomen internally by the inferior surface of the diaphragm and externally by the costal margin and associated with the thoracic vertebral column and ribcage and from the back of the thorax 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; together with the abdomen and the perineum, it constitutes the trunk proper[FMA]. UBERON:0001443 UMLS:C0817096 UMLS:C1527391 anterolateral part of thorax front of thorax galen:Chest galen:Thorax pectoral pectus thoracic thoracic body wall thorax uberon ventral part of thoracic region subdivision of head FMA:24218 UBERON:0001444 XAO:0000040 head region head subdivision region of head uberon skeleton of pes EHDAA2:0002228 FMA:24222 Subdivision of skeleton that is the collection of all skeletal elements in a pes, which is the distal section of the posterior hindlimb skeleton consisting of the mesopodium, the metapodium and the acropodium (e.g. including the ankle, sole, and toes)[Phenoscape]. UBERON:0001445 VSAO:0005021 foot region skeleton foot skeleton here 'pes' includes both the ankle region, metatarsals and acropodial region https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern pedal skeleton pes pes skeleton posterior autopodium posterior autopodium skeleton set of bones of foot skeleton of foot uberon face 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). BTO:0003369 CALOHA:TS-2216 EMAPA:32763 FMA:24728 GAID:64 HAO:0000316 MA:0002473 MESH:D005145 OpenCyc:Mx4rvVi5GZwpEbGdrcN5Y29ycA 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]. 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) UBERON:0001456 UMLS:C0015450 facia/facies facial galen:Face uberon visage skin of lip A zone of skin that is part of a lip [Automatically generated definition]. FMA:24764 MA:0001579 UBERON:0001458 UMLS:C0222101 lip skin lip zone of skin skin of lips uberon zone of skin of lip hip BTO:0001457 CALOHA:TS-2226 EFO:0001929 EHDAA2:0000783 EHDAA:5153 EHDAA:6178 EMAPA:17490 FMA:24964 GAID:47 MA:0000045 MESH:D006615 OpenCyc:Mx4rvVjhy5wpEbGdrcN5Y29ycA See notes for shoulder. in BTO this is part of the abdomen - this creates an inconsistency if limb and abdomen are spatially disjoint The hip region is located lateral to the gluteal region (i.e. the buttock), inferior to the iliac crest, and overlying the greater trochanter of the thigh bone. In adults, three of the bones of the pelvis have fused into the hip bone which forms part of the hip region. The hip joint, scientifically referred to as the acetabulofemoral joint (art. coxae), is the joint between the femur and acetabulum of the pelvis and its primary function is to support the weight of the body in both static (e.g. standing) and dynamic (e.g. walking or running) postures. [WP,modified]. The pelvic girdle is never joined by contributions of dermal bone. From its first appearance in placoderms, the pelvic girdle is exclusively endoskeletal. It arose from pterygiophores, perhaps several times, in support of the fin.[well established][VHOG] UBERON:0001464 UMLS:C0019552 VHOG:0000346 coxa coxal galen:Hip hip region regio coxae uberon lymphatic vessel A network of blunt ended vessels lacking direct connection to the blood vascular system. These vessels collect and drain fluids and macromolecules from interstitial spaces throughout the animal. They derive from a subpopulation of endothelial cells and have walls that are much thinner than the blood carrying vessels. Lymphatic vessels are usually classified as either superficial or deep.[TAO] A vessel that contains or conveys lymph, that originates as an interfibrillar or intercellular cleft or space in a tissue or organ, and that if small has no distinct walls or walls composed only of endothelial cells and if large resembles a vein in structure[BTO]. A vessel that contains or conveys lymph.[AAO] AAO:0011005 BTO:0000752 CALOHA:TS-2102 EFO:0000873 EMAPA:35532 FMA:30315 MA:0000138 MAT:0000443 OpenCyc:Mx4rwA1fYZwpEbGdrcN5Y29ycA TAO:0005105 Tetrapods have evolved distinct lymphatic systems, in which lymphatic capillaries help drain most of the tissues of the body.[well established][VHOG] UBERON:0001473 UMLS:C0229889 VHOG:0001249 XAO:0000375 lymph vessel uberon vas lymphaticum bone element AAO:0000047 AEO:0000082 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] 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 OpenCyc:Mx4rvViDlpwpEbGdrcN5Y29ycA OpenCyc:Mx4rvVkCG5wpEbGdrcN5Y29ycA 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. Skeletal element that is composed of bone tissue.[VSAO] TAO:0001514 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] UBERON:0001474 UMLS:C0262950 VHOG:0001190 VSAO:0000057 XAO:0000169 ZFA:0001514 bone bone element bone organ bones galen:Bone relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] uberon articular capsule An articular capsule (or joint capsule) is an envelope surrounding a synovial joint. [WP,unvetted]. FMA:34836 GAID:263 MA:0001519 MESH:D017746 UBERON:0001484 UMLS:C0206207 capsula articularis capsulae articulares check ncita fibrous capsule of joint galen:JointCapsule joint capsule joint fibrous capsule uberon skin of leg A zone of skin that is part of a leg [Automatically generated definition]. EMAPA:18156 EMAPA:18159 FMA:37828 MA:0000674 UBERON:0001511 UMLS:C0222279 leg skin leg zone of skin uberon zone of skin of leg descending aorta EMAPA:18606 FMA:3784 MA:0002571 OpenCyc:Mx4rv4EE35wpEbGdrcN5Y29ycA The descending aorta is the portion of the aorta in a two-pass circulatory system from the arch of aorta to the point where it divides into the common iliac arteries[GO]. The descending aorta is part of the aorta, the largest artery in the body. The descending aorta is the part of the aorta beginning at the aortic arch that runs down through the chest and abdomen. The descending aorta is divided into two portions, the thoracic and abdominal, in correspondence with the two great cavities of the trunk in which it is situated. Within the abdomen, the descending aorta branches into the two common iliac arteries which serve the legs. [WP,unvetted]. UBERON:0001514 UMLS:C0011666 aorta descendens pars descendens aortae pars descendens aortae results from fusion of left and right dorsal aortae uberon abdominal aorta Abdominal part of aorta: the distal part of the descending aorta, which is the continuation of the thoracic part and gives rise to the inferior phrenic, lumbar, median sacral, superior and inferior mesenteric, middle suprarenal, renal, and testicular or ovarian arteries, and celiac trunk[BTO]. The abdominal aorta is the largest artery in the abdominal cavity. As part of the aorta, it is a direct continuation of descending aorta(of the thorax). [WP,unvetted]. BTO:0002976 EFO:0002524 EMAPA:17856 FMA:3789 GAID:470 MA:0000474 MESH:D001012 Many of the branches of the abdominal aorta in mammals may be branches of the dorsal aorta in other vertebrates OpenCyc:Mx4rvYhWCZwpEbGdrcN5Y29ycA UBERON:0001516 UMLS:C0003484 abdominal part of aorta abdominal part of aorta aorta abdominalis descending abdominal aorta galen:AbdominalAorta pars abdominalis aortae pars abdominalis aortae uberon digestive tract A tube extending from the mouth to the anus. AAO:0010023 BILA:0000083 BTO:0000511 BTO:0000545 EHDAA2:0000726 EHDAA:518 EMAPA:16247 FBbt:00003125 FMA also has a term 'gastrointestinal tract', but this includes the liver. FMA:45615 MA:0000917 OpenCyc:Mx4rvVi0GpwpEbGdrcN5Y29ycA TAO:0000112 TGMA:0001819 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] UBERON:0001555 UMLS:C0017189 VHOG:0000309 WBbt:0005743 ZFA:0000112 alimentary canal alimentary tract digestive canal digestive tube enteric tract galen:AlimentaryTract gut gut tube uberon 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 we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509 lower urinary tract FMA:45659 MA:0002636 Subdivision of urinary system which consists of the urinary bladder and the urethra. UBERON:0001556 galen:LowerUrinaryTract uberon upper respiratory tract EHDAA2:0002136 EMAPA:17669 FMA:45661 MA:0000442 OpenCyc:Mx4rtT2HwgJMEdyAAADggVbxzQ Some specify that the glottis (vocal cords) is the defining line between the upper and lower respiratory tracts;[2] yet even others make the line at the cricoid cartilage. The FMA includes nose, nasopharynx, oropharynx and larynx[WP] The segment of the respiratory tract that starts proximally with the nose and ends distally with the cricoid cartilage, before continuing to the trachea. UBERON:0001557 VHOG:0000406 uberon lower respiratory tract EHDAA2:0001036 EMAPA:16738 FMA:45662 MA:0000435 OpenCyc:Mx4rQRqjUgAKEdyHxgDggVfs8g The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified] UBERON:0001558 VHOG:0000382 uberon cheek A fleshy subdivision of one side of the face bounded by an eye, ear and the nose. BTO:0001754 FMA:46476 GAID:65 In many animals the inside of the cheek is lined with mucous membrane covered with stratified squamous epithelium and supplied with secretions from buccal glands. MA:0002475 MESH:D002610 OpenCyc:Mx4rvVi5WZwpEbGdrcN5Y29ycA Surface structure that includes the scales, skin, and muscles that are located ventral and posterior to the eye.[TAO] TAO:0002113 UBERON:0001567 UMLS:C0007966 buccae buccal galen:Cheek jowl uberon ciliary muscle BTO:0000654 Bowman`s muscles EMAPA:35240 FMA:49151 MA:0001269 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]. UBERON:0001605 UMLS:C0559230 ciliaris musculus ciliaris musculus ciliarus uberon coronary artery An artery that supplies the myocardium. BTO:0000290 CALOHA:TS-0176 EFO:0002551 EMAPA:19160 EMAPA:25968 EV:0100383 FMA:49893 MA:0002453 OpenCyc:Mx4rvoL56ZwpEbGdrcN5Y29ycA UBERON:0001621 UMLS:C0205042 VHOG:0001557 ZFA:0005812 coronary arterial tree coronary vessel galen:CoronaryArtery uberon muscle organ AAO:0011066 EMAPA:32715 EV:0100146 FMA:5022 GAID:131 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] MA:0000015 OpenCyc:Mx4rv2kf-5wpEbGdrcN5Y29ycA 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] TAO:0005145 UBERON:0001630 VHOG:0001245 XAO:0000172 ZFA:0005145 galen:Muscle muscle muscular uberon artery AAO:0010211 AEO:0000208 An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition]. 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 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. OpenCyc:Mx4rvVjknZwpEbGdrcN5Y29ycA Part of the circulatory system composed of blood vessels which carry oxygenated blood away from the heart to the rest of the body.[AAO] TAO:0000005 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] UBERON:0001637 UMLS:C0003842 VHOG:0001251 XAO:0000114 ZFA:0000005 arterial arterial subtree arterial system arterial tree organ part arterial vessel arteries galen:Artery uberon vein AAO:0010212 AEO:0000209 Any of the tubular branching vessels that carry blood from the capillaries toward the heart. 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 OpenCyc:Mx4rvVjkWpwpEbGdrcN5Y29ycA Part of the circulatory system composed of blood vessels which carry blood from other organs, tissues, and cells to the heart.[AAO] TAO:0000082 TODO - check with MA - vein vs venous blood vessel 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] UBERON:0001638 UMLS:C0042449 VHOG:0001743 XAO:0000115 ZFA:0000082 galen:Vein uberon vascular element vena venae venous subtree venous tree organ part venous vessel ear AAO:0011014 BTO:0000368 Both vertebrate and invertebrate auditory organs are thought to have evolved from primitive mechanosensors, but the nature of the ancestral structure and the evolutionary trajectories followed in distinct animal lineages remain unknown. In particular, we do not know how many types of mechanosensor existed in the protostome-deuterostome ancestor from which insects and vertebrates evolved or whether the PDA had an auditory organ.[well established][VHOG] CALOHA:TS-1165 EFO:0000826 EHDAA2:0000423 EHDAA:502 EMAPA:16193 EV:0100353 FMA:52780 GAID:62 MA:0000236 MAT:0000138 MESH:D004423 MIAA:0000138 OpenCyc:Mx4rvViXS5wpEbGdrcN5Y29ycA OpenCyc:Mx4rvVjL05wpEbGdrcN5Y29ycA Sense organ in vertebrates that is specialized for the detection of sound, and the maintenance of balance. Includes the outer ear and middle ear, which collect and transmit sound waves; and the inner ear, which contains the organs of balance and (except in fish) hearing. Also includes the pinna, the visible part of the outer ear, present in some mammals. The organ of hearing and of equilibrium. [TFD][VHOG] UBERON:0001690 UMLS:C0013443 UMLS:C0521421 VHOG:0000330 XAO:0000189 auditory apparatus auricular auris galen:Ear uberon neurocranium AAO:0010153 Anatomical cluster that consists of the cartilages and bones that surround the brain.[TAO] EHDAA2:0000243 EMAPA:17681 FMA:53672 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 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:0000317 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:0001580 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]. UBERON:0001703 XAO:0003170 ZFA:0001580 brain box brain case brain pan braincase neurocranial uberon nail A horn-like keratin structure covering the dorsal aspect of the terminal phalanges of fingers and toes[WP]. A primate's nail consists of the unguis alone; the subunguis has disappeared BTO:0001719 CALOHA:TS-2034 EFO:0000956 EMAPA:35580 EV:0100159 FMA:54326 GAID:1320 MA:0002703 MAT:0000158 MESH:D009262 MIAA:0000158 OpenCyc:Mx4rvVjJv5wpEbGdrcN5Y29ycA The nails of humans and the claws are moth are highly similar. Both species have a proximal nail fold, cuticle, nail matrix, nail bed, nail plate, and hyponychium. Distinguishing features are the shape of the nail and the presence of an extended hyponychium in the mouse [PMC3579226] UBERON:0001705 UMLS:C0027342 Use this class for both the nails of primates and the homologous claws of mammals such as mouse. VHOG:0001361 XAO:0003103 claw galen:Nail nail/claw talon uberon jaw skeleton AAO:0000988 BTO:0001749 EMAPA:35455 FMA:54396 GAID:214 MA:0001905 MESH:D007568 OpenCyc:Mx4rvVjjEZwpEbGdrcN5Y29ycA Skeletal and cartilage elements of the first pharyngeal arch.[TAO] Subdivision of skeleton which includes upper and lower jaw skeletons. TAO:0001227 TODO - move ZFA:0001227 (it is the entire jaw skeleton). There are cellular contributions from all three embryonic germ layers: pharyngeal mesoderm, endoderm and neural crest that migrates out of the ectoderm (Noden, 1983). UBERON:0001708 UMLS:C0022359 ZFA:0001227 anterior splanchnocranium galen:Jaw 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 jaw jaw cartilage jaws mandibular arch mandibular arch skeleton oral jaw skeleton pharyngeal arch 1 skeleton uberon visceral arch 1 lower jaw region AAO:0000272 EFO:0003660 EHDAA2:0001018 EHDAA:7995 EMAPA:17906 FMA:59398 Inferior mandibular arch located on the anterior and lateral sides of the skull.[AAO] MESH:D008334 Note isa/partof difference MA/FMA See notes for jaw w.r.t skeletal element vs subdivision of head Subdivision of head that consists of the lower jaw skeletal elements plus associated soft tissue (skin, lips, muscle)[cjm]. 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] UBERON:0001710 VHOG:0000453 lower part of mouth mandibular part of mouth mandibular series ncithesaurus:Lower_Jaw uberon eyelid A fold of skin that covers and protects part of the eyeball. Examples: upper eyelid, lower eyelid, nictitating membrane BTO:0002241 Consider adding 'eye surface', like MA EHDAA2:0000487 EHDAA:9037 EMAPA:17829 EV:0100338 FMA divides this into skin, fascia, conjunctiva FMA:54437 GAID:72 In humans the upper and lower eyelid consists of the following layers, starting anteriorly: (1) skin, (2) a layer of subcutaneous connective tissue, (3) a layer of striated muscle fibres of the orbicularis muscle, (4) a layer of submuscular connective tissue, (5) a fibrous layer, including the tarsal plates, (6) a layer of smooth muscle, (7) the palpebral conjunctiva. MA:0000268 MESH:D005143 OpenCyc:Mx4rvVi4m5wpEbGdrcN5Y29ycA UBERON:0001711 UMLS:C0015426 VHOG:0000016 blephara blepharic blepharon eye lid palpebra palpebrae palpebral uberon cranial ganglion BTO:0000106 EFO:0000902 EMAPA:16659 FMA:54502 Ganglion which is located in the head.[TAO] MA:0000213 MA:0000214 MAT:0000200 MIAA:0000200 TAO:0000013 UBERON:0001714 UBERON:0003213 UBERON:0026601 VHOG:0000076 XAO:0000027 ZFA:0000013 cranial ganglia cranial ganglion cranial ganglion part of peripheral nervous system cranial ganglion/nerve cranial nerve ganglion cranial neural ganglion cranial neural tree organ ganglion ganglion of cranial nerve ganglion of cranial neural tree organ head ganglion presumptive cranial ganglia the groups of nerve cell bodies associated with the twelve cranial nerves uberon tongue A mobile mass of muscular tissue that is covered with mucous membrane, occupies much of the cavity of the mouth, forms part of its floor, bears the organ of taste, and assists in chewing and swallowing. [TFD][VHOG] A muscular organ in the floor of the mouth. AAO:0010360 BTO:0001385 CALOHA:TS-1050 EFO:0000833 EHDAA2:0002062 EHDAA:9144 EMAPA:17185 EV:0100058 FMA:54640 GAID:816 MA:0000347 MAT:0000040 MESH:D014059 MIAA:0000040 Many species of fish have small folds at the base of their mouths that might informally be called tongues, but they lack a muscular structure like the true tongues found in most tetrapods Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle.[well established][VHOG] Muscular organ in the floor of the mouth.[FEED] OpenCyc:Mx4rvVjmJ5wpEbGdrcN5Y29ycA_53KXLq9EdqAAAACs6hnmQ TAO:0005333 The tongue has contributions from all pharyngeal arches which changes with time. The tongue initially begins as swelling rostral to foramen cecum, the median tongue bud.. tongue muscles derive from the somites - http://php.med.unsw.edu.au/embryology/index.php?title=Tongue_Development#Pharyngeal_Arch_Contributions The tongue is the movable, muscular organ on the floor of the mouth of most vertebrates, in many other mammals is the principal organ of taste, aids in the prehension of food, in swallowing, and in modifying the voice as in speech[GO][GO:0043586]. UBERON:0001723 UMLS:C0040408 VHOG:0000419 XAO:0000446 ZFA:0005333 glossal glossus in MA the tongue is part of the oral region, which in uberon is treated as the oral opening. consider revising oral opening - oral region equivalence. lingual uberon tonsillar ring FMA:55070 MA:0000752 UBERON:0001735 UMLS:C0459892 Waldeyer's ring Waldeyer's tonsillar ring anulus lymphoideus pharyngis oropharyngeal lymphoid tissue pharyngeal lymphatic ring pharyngeal lymphoid ring the circular lymphoid tissue formed by the lingual, pharyngeal, and facial tonsils uberon larynx (In anura) a dorsal pair of arytenoid cartilages (...), which support vocal cords, and a ventral pair (often fused) of cricoid cartilage (...). These cartilages are regarded as derivatives of posterior visceral arches of ancestors. Together they constitute the larynx, a structure characteristic of tetrapods. (...) (In mammals) Paired arytenoid cartilages help support and control the vocal cords. The cricoid cartilage is single. Two additional cartilages are present that are lacking in other vertebrates: a large ventral thyroid cartilage (...) and a cartilage in the epiglottis.[well established][VHOG] A continuation of the pharynx that is involved in breathing, sound production, and protecting the trachea against food aspiration. AAO:0000268 An anatomical cluster consisting of the epiglottus, the arytenoid cartilages, the thyroid cartilage, the cricoid cartilage and the muscles, membranes, and ligaments connecting them, and also of the mucosal covering these structures.[FEED] Anatomical structure consisting of a narrowly triangular chamber supported by a series of semicircular cartilages in which part of the sound-production system is located.[AAO] BTO:0001208 CALOHA:TS-0532 EFO:0000838 EHDAA2:0004063 EMAPA:18333 EV:0100039 FMA:55097 GAID:108 Kehlkopf@ge MA:0000414 MAT:0000187 MESH:D007830 MIAA:0000187 OpenCyc:Mx4rvViOnZwpEbGdrcN5Y29ycA UBERON:0001737 UMLS:C0023078 VHOG:0001279 XAO:0003081 galen:Larynx laryngeal uberon lymphoid tissue BTO:0000753 CALOHA:TS-0584 FMA:55220 GAID:342 MA:0002436 MESH:D008221 Portion of connective tissue with various types of white blood cells enmeshed in it, most numerous being the lymphocytes[WP]. UBERON:0001744 UMLS:C0024296 galen:LymphoidTissue lymphatic tissue lymphocytic tissue uberon vagus nerve 10n AAO:0010475 BAMS:10n BAMS:Xn BTO:0003472 CN-X Cranial nerve that branches into the lateral (to body sense organs) and the intestino-accessorial (to the skin, muscles of shoulder, hyoid, larynx, gut, lungs, and heart). EFO:0002549 FMA:5731 GAID:721 HBA:9337 MA:0001106 MBA:917 MESH:D014630 Nerve consisting of branchiomotor and visceral efferent fibers which branch and innervate the smooth muscles and glands of the heart, lungs, esophagus, and stomach as well as some throat muscles. Sensory fibers supply mucosa of the mouth and pharynx.[AAO] OpenCyc:Mx4rviHk2ZwpEbGdrcN5Y29ycA TAO:0000453 UBERON:0001759 UMLS:C0042276 UMLS:C1305910 VHOG:0000737 Vagus nerve [X] We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG] XAO:0003097 ZFA:0000453 cranial nerve X galen:VagusNerve http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=702 nerve X nervus vagus nervus vagus [x] pneuomgastric nerve tenth cranial nerve uberon vagal nerve vagus vagus X nerve vagus nerve or its root vagus nerve tree uvea CALOHA:TS-2228 EMAPA:35901 FMA:58103 GAID:912 MA:0002480 MESH:D014602 TODO - check child terms, isa vs partof. See also MA:0001284 ! tunica vasculosa plexus UBERON:0001768 UMLS:C0042160 pars iridica retinae the pigmented middle of the three concentric layers that make up an eye, consisting of the iris, ciliary body and choroid[WP,edited]. tunica vasculatis oculi tunica vasculosa bulbi tunica vasculosa of eyeball uberon uvea uveal uveal tract vascular layer of eyeball iris AAO:0010347 BTO:0000653 CALOHA:TS-0491 EFO:0004245 EMAPA:19154 EV:0100345 FMA:58235 GAID:917 MA:0000273 MESH:D007498 OpenCyc:Mx4rvVjbppwpEbGdrcN5Y29ycA TAO:0001238 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] 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] 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] UBERON:0001769 UMLS:C0022077 VHOG:0000101 XAO:0000185 ZFA:0001238 anterior uvea irides iridial irises the adjustable membrane, composed of the stroma and pigmented epithelium, located just in front of the crystalline lens within the eye uberon corneal epithelium BTO:0000287 CALOHA:TS-0173 EFO:0001917 EHDAA2:0000319 EMAPA:17162 FMA:58263 GAID:895 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 MA:0001243 MESH:D019573 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] TAO:0002187 UBERON:0001772 UMLS:C0459875 ZFA:0001683 anterior corneal epithelium anterior endothelium of cornea cornea epithelial tissue cornea epithelium e. anterius corneae endothelium anterius corneae endothelium camerae anterioris bulbi endothelium corneale epithelial tissue of cornea epithelium anterius (cornea) epithelium anterius corneae epithelium corneæ anterior layer epithelium of cornea epithelium posterius corneae external epithelium of cornea the smooth stratified squamous epithelium that covers the outer surface of the cornea uberon sclera AAO:0010354 BTO:0001606 Disease notes: implicated in rheumatoid arthritis. EMAPA:19027 EV:0100342 FMA:58269 GAID:911 MA:0000280 MESH:D012590 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]. Opaque fibrous outer layer of the eyeball[ZFA,Kardong,WP]. OpenCyc:Mx4rv7yR55wpEbGdrcN5Y29ycA Seko et al demonstrate chondrogenic potential and identify this as connective tissue[doi:10.1371/journal.pone.0003709]. 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] UBERON:0001773 UMLS:C0036410 VHOG:0001274 XAO:0000183 ZFA:0005563 continuous with the dura mater and the cornea; The sclera forms the posterior five-sixths of the connective tissue coat of the globe. in fish, reptiles and monotremes the connective tissue of the sclera is skeletal scleral scleral capsule uberon skeletal muscle of trunk A skeletal muscle organ that is part of the trunk region. AAO:0000611 EMAPA:35888 FMA:58274 MA:0000514 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. 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'. TAO:0000473 UBERON:0001774 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 ciliary body AAO:0010341 BTO:0000260 CALOHA:TS-0694 EMAPA:19065 EV:0100346 FMA:58295 GAID:916 MA:0000264 MESH:D002924 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] UBERON:0001775 UMLS:C0008779 VHOG:0000102 XAO:0000186 anterior uvea ciliary bodies corpus ciliare ocular ciliary body the thickened portion of the vascular tunic, which lies between the choroid and the iris, composed of ciliary muscle and ciliary processes uberon optic choroid BTO:0001829 CALOHA:TS-2054 EMAPA:19077 EV:0100347 FMA:58298 GAID:913 MA:0000263 MESH:D002829 MP treats posterior uvea and optic choroid as distinct TAO:0005229 UBERON:0001776 UMLS:C0008520 VHOG:0001568 ZFA:0005229 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 chorioid choroid choroid coat choroidal choroidea choroidea eye choroid optic choroid posterior uvea uberon 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]. spinal nerve AAO:0011101 Any of the paired nerves emerging from the spinal cord, each attached to the cord by two roots: ventral and dorsal, and passing out between the vertebrae. [TFD][VHOG] BAMS:spin BTO:0000870 EHDAA2:0001898 EMAPA:16989 FMA:5858 GAID:841 MA:0000233 MESH:D013127 OpenCyc:Mx4rwK_iFJwpEbGdrcN5Y29ycA UBERON:0001780 UMLS:C0037941 VHOG:0000824 XAO:0003101 backbone nerve nerve of backbone nerve of spinal column nerve of spine nerve of vertebral column nervi spinales spinal column nerve spinal nerve tree spinal nerves spine nerve the any of the paired peripheral nerves formed by the union of the dorsal and ventral spinal roots from each spinal cord segment[MP,modified] uberon vertebral column nerve layer of retina AAO:0010353 Any of the layers that make up the retina[MP]. EMAPA:35742 FMA:58617 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:0001319 UBERON:0001781 UMLS:C0459649 XAO:0000266 retina layer retina neuronal layer retinal layer retinal neuronal layer uberon cranial nerve AAO:0000108 BAMS:cran BTO:0001104 Cranial nerves are nerves that emerge directly from the brain, in contrast to spinal nerves, which emerge from segments of the spinal cord. EHDAA2:0000323 EMAPA:17264 FMA:5865 GAID:802 HBA:9299 MA:0000215 MBA:967 MESH:D003391 OpenCyc:Mx4rvWvJVpwpEbGdrcN5Y29ycA See https://github.com/obophenotype/mouse-anatomy-ontology/issues/6 TAO:0000641 Twelve pairs of cranial nerves exit/enter the cranium through openings in the skull. The nerves contain efferent axons with motor and glandular functions, as well as afferent axons from cranial ganglia with sensory functions. The nerves are numbered in a rostral to caudal sequence, with the exception of the lateral line nerves.[TAO] UBERON:0001785 UMLS:C0010268 UMLS:C1269897 VHOG:0000279 We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...).[well established][VHOG] XAO:0000429 XAO:0003089 ZFA:0000641 classified as neural tree organ, not nerve in FMA. CN II poses a challenge here as it is not strictly a nerve, yet is expected to be classified under CN. cranial nerves cranial neural tree organ nervus cranialis uberon anterior segment of eyeball EMAPA:36594 FMA:58865 MA:0002484 MESH:D000869 UBERON:0001801 UMLS:C0003153 ZFA:0005566 anterior eye segment anterior segment eye anterior segment of eye anterior segment of the eye any of the parts of the eye that lie in front of, or ventral to, the lens (inclusive) eye anterior segment segmentum anterius (bulbus oculi) segmentum anterius bulbi oculi uberon posterior segment of eyeball EMAPA:36595 FMA:58868 MA:0002485 UBERON:0001802 UMLS:C0278450 ZFA:0005567 any of the parts of the eye that lie in back of, or dorsal to, the lens (but not inclusive) eye posterior segment posterior eye segment posterior segment eye posterior segment of eye posterior segment of the eye segmentum posterius (bulbus oculi) segmentum posterius bulbi oculi uberon nerve plexus AEO:0000138 Anatomical junction where subdivisions of two or more neural trees interconnect with one another to form a network through which nerve fibers of the constituent nerve trees become regrouped; together with other nerve plexuses, nerves and ganglia, it constitutes the peripheral nervous system. Examples: cervical nerve plexus, brachial nerve plexus, sacral nerve plexus[FMA]. BTO:0000205 EHDAA2:0003138 EHDAA:3780 FMA:5901 MA:0002407 UBERON:0001810 UMLS:C0501403 in FMA this is a subtype of junction rather than tissue plexus uberon spinal nerve plexus EHDAA2:0001899 EMAPA:16987 FMA:5903 MA:0000235 To reach the muscles, dermatomes, and other structures of the limbs, some of the neurons in the spinal nerves come together in the plexus at the base of the limb. Such plexuses occur in all gnathostomes, and they reach their highest complexity among mammals and birds in which the cervical plexus supplies many ventral neck muscles, the brachial plexus supplies the pectoral appendage, a lumbosacral plexus supplies the pelvic appendage, and a coccygeal plexus supplies some of the pelvic muscles.[well established][VHOG] UBERON:0001813 UMLS:C0228603 VHOG:0000925 an intermingling of fiber fascicles from adjacent spinal nerves to form a network. plexus nervorum spinalium plexus of spinal nerves somatic nerve plexus spinal nerve plexus uberon lumbosacral nerve plexus An arrangement of nerve fibers, running from the spine that travels to the pelvic appendage where it innervates skin and muscle. BAMS:lsp EHDAA2:0001040 EHDAA:4673 EMAPA:17587 FMA:5907 GAID:849 MA:0001181 MESH:D008160 OpenCyc:Mx4rvzYo75wpEbGdrcN5Y29ycA UBERON:0001815 UMLS:C0024093 VHOG:0000926 lumbosacral plexus plexus lumbosacralis plexus lumbosacralis uberon major salivary gland FMA:59788 MA:0002478 One of the three largest glands of the oral cavity that secrete most of the saliva, including the parotid, submandibular, and sublingual glands. There are 3 pairs of major salivary glands in human and mouse UBERON:0001829 UMLS:C0930553 galen:MajorSalivaryGland uberon parotid gland A mammalian salivary gland located caudal to the ear. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-22, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] AAO:0010095 BTO:0001004 CALOHA:TS-0748 EFO:0002558 EMAPA:18537 EV:0100060 FMA:59790 GAID:938 MA:0001585 MESH:D010306 OpenCyc:Mx4rvqwyg5wpEbGdrcN5Y29ycA The most common oral glands in mammals are the salivary glands. There are usually three primary pairs of salivary glands, named for their approximate positions: mandibular (submandibular or submaxillary), sublingual, and parotid.[well established][VHOG] The mouse parotid, exorbital lacrimal gland and exocrine pancreas have similar histological appearances[ISBN10:0123813611] The parotid gland is the largest of the salivary glands. It is found wrapped around the mandibular ramus, and it secretes saliva through Stensen's duct into the oral cavity, to facilitate mastication and swallowing. [WP,unvetted]. UBERON:0001831 UMLS:C0030580 VHOG:0000308 galen:ParotidGland glandula parotidea parotid uberon lip BTO:0001647 CALOHA:TS-0558 EMAPA:32839 FMA:59816 GAID:76 MA:0000343 MESH:D008046 One of the two fleshy folds which surround the opening of the mouth. OpenCyc:Mx4rvVi4U5wpEbGdrcN5Y29ycA Surface structure that is one of the two fleshy folds surrounding the opening of the mouth.[TAO] TAO:0007006 UBERON:0001833 UMLS:C0023759 VHOG:0000677 ZFA:0007006 galen:Lip labia oris labial lips uberon saliva A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions. BTO:0001202 CALOHA:TS-0891 EMAPA:36536 ENVO:02000036 FMA:59862 GAID:1167 MA:0002507 MAT:0000444 MESH:D012463 OpenCyc:Mx4rvVjJ95wpEbGdrcN5Y29ycA UBERON:0001836 UMLS:C0036087 We classify a wide variety of not necessarily homologous fluids here. In humans, the saliva is a turbid and slightly viscous fluid, generally of an alkaline reaction, and is secreted by the parotid, submaxillary, and sublingual glands. In the mouth the saliva is mixed with the secretion from the buccal glands. In man and many animals, saliva is an important digestive fluid on account of the presence of the peculiar enzyme, ptyalin galen:Saliva sailva normalis saliva atomaris saliva molecularis salivary salivary gland secretion uberon semicircular canal AAO:0011098 BTO:0003383 CALOHA:TS-2164 EMAPA:32832 EV:0100365 FMA:60186 Fluid-filled toroidal spaces, arranged orthogonally to each other in the ear, that detect angular accelerations. (See Anatomical Atlas entry for semicircular canals by T. Whitfield.)[TAO] GAID:776 In gnathostomes, each membranous labyrinth has three semicircular ducts that connect with a chamber known as the utriculus. These ducts are sometimes called canals, but technically the term semicircular canal applies to the spaces in the osseus labyrinth in which the semicircular ducts lie.[uncertain][VHOG] MA divides this into osseous and duct. In FMA, this is systemically part of the bony labyrinth. Note this is an anatomical space in ZFA. The MA treatment has advantages for representing the neuroepithelium, which should not be part of bone. Also check duct vs canal MA:0000249 MESH:D012665 One of three half-circular, interconnected tubes located inside each ear[WP]. TAO:0000431 UBERON:0001840 UMLS:C0036622 VHOG:0001144 XAO:0000198 ZFA:0000431 canalis semicircularis detects angular acceleration ductus semicirculares scc semicircular canals semicircular ducts uberon lateral semicircular canal EHDAA2:0000920 EHDAA:7790 EMAPA:17821 FMA:60193 MA:0001208 One of three fluid-filled toroidal spaces, arranged orthogonally to each other in each ear, that detect angular acceleration. (See Anatomical Atlas entry for semicircular canals by T. Whitfield.)[TAO] TAO:0000220 UBERON:0001843 ZFA:0000220 detects angular acceleration horizontal semicircular canal lateral semicircular canals lateral semicircular duct relationship loss: develops_from lateral semicircular canal primordium (TAO:0000232)[TAO] uberon internal ear AAO:0000238 BTO:0000630 CALOHA:TS-0478 Complex labyrinthine structure that comprises sensory endorgans specialized for vestibular, auditory, and acoustico-vestibular sensation. EFO:0001363 EHDAA2:0000831 EHDAA:504 EMAPA:16194 EV:0100361 FMA:60909 GAID:871 MA:0000237 MAT:0000145 MESH:D007758 MIAA:0000145 OpenCyc:Mx4rwJ8SsJwpEbGdrcN5Y29ycA TAO:0000217 The auditory (hearing) and vestibular (balance) organ of the fish, equivalent to the inner ear of amniotes. (See Anatomical Atlas entry for ear by T. Whitfield.)[TAO] The labyrinth, or inner ear, evolved very early in vertebrate history and, with many variations in configuration but none of basic design and function, has been retained by all vertebrates.[well established][VHOG] UBERON:0001846 UMLS:C0022889 UMLS:C1268973 VHOG:0000284 XAO:0000192 ZFA:0000217 auris interna galen:InnerEar inner ear labyrinth otocyst uberon membranous labyrinth A system of communicating epithelial sacs and ducts within the bony labyrinth, containing the endolymph. [TFD][VHOG] AAO:0011060 EHDAA2:0000899 EHDAA:4698 EMAPA:17815 EV:0100367 FMA:61022 MA:0000242 Organ with organ cavity which consists of the vestibular labyrinth and the cochlear labyrinth. The membranous labyrinth is lodged within the bony labyrinth and has the same general form; it is, however, considerably smaller and is partly separated from the bony walls by a quantity of fluid, the perilymph.[FMA, WP] The labyrinth, or inner ear, evolved very early in vertebrate history and, with many variations in configuration but none of basic design and function, has been retained by all vertebrates.[well established][VHOG] UBERON:0001849 UBERON:0010113 UMLS:C0458700 VHOG:0000729 XAO:0000194 inner ear has parts membranous and osseuous/bony labyrinth. it's not clear where the EMAPA term 'labyrinth' belong, we place them here for now labyrinthus membranaceus uberon cortex EFO:0000383 EHDAA:9344 FMA:61109 Outermost layer of an organ[WP]. UBERON:0001851 cortex cortex of organ cortical galen:Cortex this class is used more generically than in FMA, and includes e.g. cortex of hair uberon cerebral hemisphere AAO:0010480 BAMS:HEM BTO:0000231 CALOHA:TS-2007 DMBA:15739 EFO:0002521 EMAPA:16653 FMA:61817 Hemispheric regions MA:0000133 MBA:403 One of two bilateral, largely symmetrical organ subdivisions within the telencephalon which contain the cerebral cortex and cerebral white matter.[FMA] OpenCyc:Mx4rvigx5ZwpEbGdrcN5Y29ycA Part of the telencephalon consisting of either of the two smooth, elongated halves of the cerebrum.[AAO] The presence of paired evaginated hemispheres and olfactory bulbs in both agnathan and gnathostome radiations suggests that such hemispheres were also present in the common ancestor.[well established][VHOG] UBERON:0001869 UMLS:C0228174 UMLS:C0242202 VHOG:0001639 cerebrum galen:CerebralHemisphere hemisphere hemispherium cerebri http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=241 medial amygdalar nucleus nucleus amygdaloideus medialis nucleus medialis amygdalae telencephalic vesicle uberon temporal lobe BAMS:TL BAMS:Temporal_lobe BTO:0001355 Boundary notes: It is bounded dorsally by the lateral fissure and posteriorly by an arbitrary border shared with the occipital lobe. [Wikipedia:Temporal_lobe] CALOHA:TS-1020 DHBA:12139 EFO:0000917 EMAPA:18797 EV:0100169 FMA:61825 GAID:635 HBA:4132 Lower lateral part of the cerebral hemisphere. (MSH) MAT:0000508 MESH:A08.186.211.730.885.213.863 OpenCyc:Mx4rwQLi-ZwpEbGdrcN5Y29ycA UBERON:0001871 UMLS:C0039485 UMLS:C1268978 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=125 lobus temporalis temporal cortex uberon phrenic nerve A nerve that arises from the caudal cervical nerves and is primarily the motor nerve of the diaphragm but also sends sensory fibers to the pericardium. A nerve that arises from the caudal cervical nerves and is primarily the motor nerve of the diaphragm but also sends sensory fibers to the pericardium. [TFD][VHOG] BAMS:phn BTO:0001063 EHDAA:4677 EMAPA:17813 FMA:6191 GAID:848 MA:0001170 MESH:D010791 OpenCyc:Mx4rvtmdUJwpEbGdrcN5Y29ycA UBERON:0001884 UMLS:C0031774 VHOG:0000728 diaphragmatic nerve nervus phrenicus phrenic uberon choroid plexus A network formed by blood vessels and the tela choroidea which secretes CSF into the ventricular spaces. A tuft of capillaries that project into the ventricles of the brain and secretes cerebral spinal fluid. The choroid plexus is covered by a cuboidal epithelium which maintains the integrity of the blood-brain barrier.[TAO] BAMS:CHP BAMS:GHP BAMS:chp BAMS:chpl BTO:0000258 CALOHA:TS-0145 CP EFO:0001915 EMAPA:32741 FMA:61934 Fringe of the tela choroidea of the brain ventricles[MP] GAID:607 MA:0000823 MBA:108 MESH:D002831 TAO:0001443 TODO - check relationship to ventricle. Check subclass - ZFA says vasculature. Note that FMA:61934 (choroid plexus of cerebral hemisphere) has exact synonym 'choroid plexus' but it is not clear that this belongs here, as the fourth ventricle is not in the cerebral hemisphere UBERON:0001886 UMLS:C0008524 VHOG:0001377 ZFA:0001443 chorioid plexus choroid plexus of cerebral hemisphere choroidal plexus choroideus plexus choroideus uberon ventricular choroid plexus forebrain AAO:0010147 BAMS:FB BAMS:Forebrain BTO:0000478 CALOHA:TS-0380 DHBA:10156 DMBA:15566 EFO:0000909 EHDAA2:0000556 EHDAA:3470 EMAPA:16895 FB FMA:61992 In craniate embryos, neural expression of Distal-less-related genes is exclusively in the forebrain (...). Because the major neural expression domain of amphioxus AmphiDll is in the anterior three-fourths of the cerebral vesicle, we suggest that this region of the neural tube is homologous to parts of the craniate forebrain. This conclusion is strongly supported by three-dimensional, computer-assisted reconstruction of the neural tube of amphioxus based on serial transmission electron microscopy. At the neuroanatomical level, a number of detailed homologies are indicated between the anterior three-fourths of the amphioxus cerebral vesicle and the diencephalic region of the craniate forebrain. If one assumes that the amphioxus condition fairly represents the nervous system of the proximate ancestor of the craniates, one can suggest that they evolved from a creature that had the beginnings of a forebrain.[well established][VHOG] MA:0000170 MAT:0000105 MESH:D016548 MIAA:0000105 Most anterior of the three regions of the brain consisting of the telencephalon and diencephalon.[AAO] TAO:0000109 The most anterior region the brain including both the telencephalon and diencephalon. The most anterior region the brain including both the telencephalon and diencephalon. Kimmel et al, 1995.[TAO] UBERON:0001890 UMLS:C0085140 VHOG:0000383 XAO:0000011 ZFA:0000109 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=27 prosencephalic prosencephalon relationship loss: develops_from forebrain neural tube (TAO:0007041)[TAO] uberon midbrain AAO:0010149 BAMS:MES BM:MB BTO:0000138 CALOHA:TS-0630 DHBA:10648 DMBA:16649 EFO:0000919 EHDAA2:0001162 EHDAA:3694 EMAPA:16974 EV:0100242 FMA:61993 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] HBA:9001 MA:0000207 MAT:0000106 MB MBA:313 MESH:D008636 MIAA:0000106 Middle part of the brain composed of the optic tectum and penducular region.[AAO] OpenCyc:Mx4rvsBUqpwpEbGdrcN5Y29ycA RETIRED_EHDAA2:0001104 TAO:0000128 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] 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]. UBERON:0001891 UMLS:C0025462 VHOG:0000069 XAO:0000014 ZFA:0000128 developmental relationships need revised http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=462 mesencephalic mesencephalon part of brainstem in ABA - we reject this in favor of ISBN10:0471888893 which has an implicit overlaps relationships uberon telencephalon AAO:0010479 BAMS:CB BAMS:CH BAMS:IV BAMS:Tel BM:Tel BTO:0000239 CALOHA:TS-1018 DHBA:10158 EFO:0000912 EHDAA2:0001982 EMAPA:16652 EMAPA:16910 EV:0100165 FMA:62000 From an evolutionary standpoint, the telencephalon is the most recent brain structure: the amphioxus does not have this structure as a morphological entity. Overt telencephalon is present in the hagfish and lamprey to receive numerous input fibers from various parts of the CNS, similar to gnathostomes.[well established][VHOG] GAID:621 HBA:4007 In mammals the cortex covers almost the whole of the cerebral hemispheres. In ray-finned fishes the inner surfaces of the lateral and ventral regions of the cerebrum bulge up into the ventricles. In the amniotes, the cerebrum becomes increasingly large and complex. In reptiles, the paleopallium is much larger than in amphibians, and its growth has pushed the basal nuclei into the central regions of the cerebrum. In the most primitive living vertebrates, the hagfishes and lampreys, the cerebrum is a relatively simple structure receiving nerve impulses from the olfactory bulb. MA:0000183 MAT:0000421 MBA:567 MESH:D013687 MIAA:0000421 Organ component of neuraxis that has as its parts the cerebral cortex, cerebral white matter, basal ganglia, septum and fornix, as well as subcortical gray and white matter structures[FMA:62000]. PBA:128011350 Part of the forebrain consisting of paired olfactory bulbs and cerebral hemispheres. Part of the forebrain consisting of paired olfactory bulbs and cerebral hemispheres.[AAO] TAO:0000079 The anterior and dorsal forebrain neuromere, includes the olfactory bulb. Kimmel et al, 1995.[TAO] The cerebrum of birds has evolved along different lines to that of mammals, although they are similarly enlarged, by comparison with reptiles. However, this enlargement is largely due to the basal ganglia, with the other areas remaining relatively primitive in structure. UBERON:0001893 UMLS:C0039452 VHOG:0000283 XAO:0000012 ZFA:0000079 cerebral cerebrum dolphins are the only species (other than humans) to have cerebra accounting for as much as 2 percent of their body weight. endbrain http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=31 relationship loss: develops_from presumptive telencephalon (TAO:0000571)[TAO] supratentorial region telenencephalic uberon metencephalon Anterior part of the hindbrain ventral to the cerebellum[NIFSTD:birnlex_965]. BAMS:Met BTO:0000673 CALOHA:TS-2029 DHBA:10655 EHDAA2:0001149 EHDAA:5498 EMAPA:17071 FMA:62003 GAID:594 HBA:4833 MA:0000197 MESH:D020540 Rostral segment of the hindbrain that has as its parts the pons (where present) and the cerebellum[WP,modified]. The anterior of two brain vesicles formed by specialization of the rhombencephalon in the developing embryo. It gives rise to cerebellum and pons. [TFD][VHOG] The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG] UBERON:0001895 UMLS:C0376353 UMLS:C1516904 VHOG:0000741 epencephalon epencephalon-2 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=543 the terms metencephalon and myelencephalon are only meaningful in mammals and birds[Neuroanatomy of the Zebrafish Brain]. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata and thus these are not distinguished in ZFA[ZFA]. uberon medulla oblongata AAO:0010486 BAMS:MY BAMS:Md BM:Me BTO:0000041 CALOHA:TS-0607 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] 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 OpenCyc:Mx4rvVjxSJwpEbGdrcN5Y29ycA OpenCyc:Mx4rwCqnXJwpEbGdrcN5Y29ycA 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] TAO:0000545 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] UBERON:0001896 UMLS:C0025148 UMLS:C1269575 VHOG:0000181 XAO:0003100 ZFA:0000545 bulb bulbus http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=698 medulla medulla oblonzata metepencephalon uberon endothelium of artery AAO:0011013 An endothelium that is part of an artery [Automatically generated definition]. BTO:0004757 EMAPA:35148 FMA:62116 MA:0000707 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] UBERON:0001917 UMLS:C1179025 VHOG:0001215 Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] XAO:0000357 arterial endothelium artery endothelium uberon midbrain tegmentum 'tegmentum' is used generically for the ventral part of the brainstem (ISBN10:0471888893). 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 BAMS:MTg BTO:0003388 DHBA:12195 EFO:0000921 EHDAA2:0004475 EMAPA:18215 FMA:62393 HBA:9002 MA:0000212 MAT:0000452 MTg TAO:0000160 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] UBERON:0001943 UMLS:C0039441 VHOG:0001367 Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN10:0471888893]. 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]. XAO:0004271 ZFA:0000160 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=491 mesencephalic tegmentum tegmentum tegmentum mesencephali tegmentum mesencephalicum tegmentum of midbrain uberon regional part of spinal cord A multi-tissue structure that is part of a spinal cord. UBERON:0001948 UMLS:C1268166 spinal cord part uberon mucosa-associated lymphoid tissue FMA:62819 MA:0000140 MALT UBERON:0001961 UMLS:C0599921 diffuse system of small concentrations of lymphoid tissue found in various sites of the body such as the gastrointestinal tract, thyroid, breast, lung, salivary glands, eye, and skin[WP]. Mucosal-associated lymphoid tissue is typically found as nodules associated with mucosal epithelia with distinct internal structures including B- and T-zones for the activation of lymphocytes[GO]. epithelio-lymphoid tissue mucosa associated lymphatic tissue mucosa associated lymphoid tissue mucosa-associated lymphoid tissue mucosal-associated lymphatic tissue mucosal-associated lymphoid tissue todo - add part relationships to specific layers uberon gut-associated lymphoid tissue FMA:62820 GALT MA:0000136 Mucosa-associated lymphoid tissue in digestive tract. includes Peyer's patches, appendix, and solitary lymph nodules[GO]. UBERON:0001962 UMLS:C0596638 gut associated lymphoid tissue guts of jawless fish contains cells with lymphocyte-like morphology (Mayer 2002). phylogenetic relationships to be added uberon blood plasma BTO:0000131 CALOHA:TS-0800 EFO:0001905 EMAPA:35690 FMA:62970 GAID:1178 MA:0002501 MAT:0000052 MESH:D010949 MIAA:0000052 OpenCyc:Mx4rEg4ZYrIbEduAAAAOpmP6tw The liquid component of blood, in which erythrocytes are suspended. UBERON:0001969 UMLS:C0032105 blood plasm plasma portion of blood plasma portion of plasma uberon bile BTO:0000121 CALOHA:TS-1172 ENVO:02000023 FMA:62971 GAID:1157 In many species, bile is stored in the gallbladder and upon eating is discharged into the duodenum. MA:0002513 MESH:D001646 UBERON:0001970 UMLS:C0005388 aids the process of digestion of lipids in the small intestine bile salts function to emulsify dietary fats and facilitate their intestinal absorption elimination of cholesterol fel galen:Bile gall major excretory route for potentially harmful exogenous lipophilic substances many hormones and pheromones are excreted in bile, and contribute to growth and development of the intestine in some species and provide attractants for the weaning of non-human vertebrates protects the organism from enteric infections by excreting immune globulin A (IgA), inflammatory cytokines, and stimulating the innate immune system in the intestine uberon vital aqueous secretion of the liver that is formed by hepatocytes and modified down stream by absorptive and secretory properties of the bile duct epithelium. venule BTO:0002626 EMAPA:35917 FMA:63130 MA:0000071 MESH:A07.231.432.952 Multi-tissue structure part of the blood vasculature formed by the anastomosis of capillaries. Venules carry blood toward the heart.[TAO] One of the minute vessels that collect deoxygenated blood from the capillary plexuses returns it to the veins TAO:0005315 UBERON:0001979 UMLS:C0042520 VHOG:0001765 ZFA:0005315 uberon venula arteriole AAO:0010253 BTO:0001997 EMAPA:35146 FMA:63182 MA:0000063 MESH:D001160 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] TAO:0002138 The smallest division of the artery located between the muscular arteries and the capillaries[GO]. UBERON:0001980 UMLS:C0003847 VHOG:0001763 ZFA:0005255 arteriola uberon blood vessel A vessel through which blood circulates in the body. AAO:0011004 AEO:0000207 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] BTO:0001102 CALOHA:TS-0080 EFO:0000817 EHDAA2:0003252 EHDAA:240 EMAPA:32743 EMAPA:35993 FMA:50722 FMA:63183 FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX GAID:169 MA:0000060 MAT:0000393 MESH:D001808 OpenCyc:Mx4rvVjxlpwpEbGdrcN5Y29ycA TAO:0002137 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] UBERON:0001981 UMLS:C0005847 VHOG:0001250 XAO:0001011 ZFA:0005314 annelids have blood vessels, but this class is not applicable to annelids. consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus region of vascular tree organ uberon vas sanguineum vascular element vascular tree organ region capillary AAO:0010252 Any of the smallest blood vessels connecting arterioles with venules. Any of the tiny blood vessels connecting the arterioles to the venules.[AAO] BTO:0002045 CALOHA:TS-2006 EFO:0001906 EMAPA:35198 EV:0100035 FMA:63194 MA:0000065 MESH:A07.231.432.410 OpenCyc:Mx4rvWEU-5wpEbGdrcN5Y29ycA TAO:0005250 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] UBERON:0001982 UMLS:C0935624 VHOG:0001253 XAO:0000116 ZFA:0005250 blood capillary capillaries lack tunica media and tunica adventitia; only the endothelial wall of the tunica intima belongs capillary vessel not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element uberon endothelium A layer of epithelium that lines the heart, blood vessels (endothelium, vascular), lymph vessels (endothelium, lymphatic), and the serous cavities of the body[MESH]. Simple squamous epithelium which lines blood and lymphatic vessels and the heart[FMA] BTO:0000393 CALOHA:TS-0278 EFO:0002548 FMA:63916 GAID:520 MESH:D004727 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) UBERON:0001986 UMLS:C0014257 endothelial galen:Endothelium uberon fibrocartilage A mixture of white fibrous tissue and cartilaginous tissue in various proportions. It owes its flexibility and toughness to the former of these constituents, and its elasticity to the latter. It is the only type of cartilage that contains type I collagen in addition to the normal type I[Wikipedia:Fibrocartilage]I Cartilage (tissue) which consists of chondrocytes and collagen, the intercellular matrix of which is an amorphous gel without a well-defined perichondrium[FMA:64784]. Cartilage tissue intermediate between hyaline cartilage and dense connective tissue; contains of abundant collagen fibers; chondrocytes often arranged in columns. Cartilage tissue intermediate between hyaline cartilage and dense connective tissue; contains of abundant collagen fibers; chondrocytes often arranged in columns.[VSAO] FMA:64784 MA:0000108 The white fibrocartilages admit of arrangement into four groups-interarticular, connecting, circumferential, and stratiform -- WP. EDITOR NOTE: TODO add mineralized UBERON:0001995 UMLS:C0684077 VSAO:0000103 XAO:0004028 fibrocartilage tissue fibrocartilaginous galen:Fibrocartilage stratified cartilage tissue uberon portal vein A vein that conducts blood from the digestive organs, spleen, pancreas, and gallbladder to the liver[BTO]. BTO:0001792 CALOHA:TS-0814 EHDAA2:0001485 EHDAA:6510 EMAPA:17349 FMA:66645 GAID:540 MA:0002198 MESH:D011169 OpenCyc:Mx4rv_bem5wpEbGdrcN5Y29ycA UBERON:0002017 UMLS:C0032718 VHOG:0000656 XAO:0000392 galen:PortalVein portal venous tree organ part uberon gray matter A nervous system structure composed primarily of nerve cell bodies (somas). May also include dendrites and the initial unmyelinated portion of axons. AEO:0001012 EHDAA2:0003136 EHDAA2_RETIRED:0004658 FMA:67242 HBA:4006 MA:0001112 Multi-tissue comprised of neurons, dendrites, axon terminals, glial cells, and capillaries.[TAO] OpenCyc:Mx4rwDdKMpwpEbGdrcN5Y29ycA TAO:0002197 UBERON:0002020 UMLS:C0018220 VHOG:0001768 ZFA:0001681 gray mater gray matter gray matter of neuraxis grey matter grey matter of neuraxis grey substance grisea neuronal grey matter substantia grisea uberon hindbrain AAO:0010150 BAMS:HB BTO:0000672 CALOHA:TS-0457 DHBA:10653 DMBA:16808 EFO:0000923 EHDAA2:0000746 EHDAA:3514 EHDAA:6487 EMAPA:16916 FMA:67687 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] MA:0000195 MAT:0000107 MBA:1065 MESH:D012249 MIAA:0000107 Posterior part of the brain consisting of the cerebellum and medulla oblongata.[AAO] TAO:0000029 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] 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]. UBERON:0002028 UMLS:C0035507 UMLS:C1522180 VHOG:0000070 XAO:0000015 ZFA:0000029 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=540 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 relationship loss: develops_from hindbrain neural tube (TAO:0007043)[TAO] rhombencephalic rhombencephalon uberon striated muscle tissue AAO:0010762 AEO:0000140 CALOHA:TS-2047 EHDAA2:0003140 EMAPA:36390 FMA:67905 MA:0002438 Muscle tissue that contains fibers that are divided by transverse bands into striations. OpenCyc:Mx4rwAoze5wpEbGdrcN5Y29ycA UBERON:0002036 UMLS:C1331262 Voluntary muscle tissue arranged in bundles of fibers.[AAO] WBbt:0005779 galen:StriatedMuscle striated muscle uberon cerebellum AAO:0010485 BAMS:CB BAMS:Cb BM:CB BTO:0000232 CALOHA:TS-0125 DHBA:10656 Dorsal part of the hindbrain that coordinates muscle movement, posture, and balance.[AAO] EFO:0000327 EHDAA2:0000232 EMAPA:17787 EV:0100293 FMA:67944 GAID:595 HBA:4696 However, although the lamprey possesses a region comparable to the cerebellum and display expression of LjFgf8/17 at the MHB (midbrain hindbrain boundary), it does not have Purkinje cells and cerebellar nuclei, as well as components of the rhombic lip-derived cerebellar and pre-cerebellar systems. It is noteworthy that the latter structures require specific expression of Pax6 in the rhombic lip of the gnathostome hindbrain. Interestingly, the lamprey rhombic lip does not express Pax6. Thus, it is tempting to speculate that in vertebrate evolution the rostral hindbrain is incapable of differentiating into the cerebellum before the co-option of Pax6 in that region. In other words, cerebellum has been brought about as an evolutionary innovation in gnathostomes, based on exaptation of MHB, rhombic lip, and some regulatory gene expression already present in the vertebrate common ancestor.[well established][VHOG] MA:0000198 MAT:0000110 MBA:512 MESH:D002531 MIAA:0000110 OpenCyc:Mx4rvl1eipwpEbGdrcN5Y29ycA Part of the metencephalon that lies in the posterior cranial fossa behind the brain stem. It is concerned with the coordination of movement[MESH]. A large dorsally projecting part of the brain concerned especially with the coordination of muscles and the maintenance of bodily equilibrium, situated between the brain stem and the back of the cerebrum , and formed in humans of two lateral lobes and a median lobe[BTO]. Brain structure derived from the anterior hindbrain, and perhaps including posterior midbrain. The cerebellum plays a role in somatic motor function, the control of muscle tone, and balance[ZFA]. Specialized brain region derived from the dorsal metencephalon (anterior hindbrain, and perhaps including posterior midbrain) and becoming distinctive late in the segmentation period. Kimmel et al, 1995.[TAO] TAO:0000100 The absence of a cerebellum in hagfishes and lampreys appears to be the only exception [to the rule that vertebrates possess the same number of brain divisions]. Both hagfishes and lampreys do possess a thin band of cells located medial to the lateral line centers of the medulla (Ronan and Northcutt, 1998), which has been interpreted as a primitive cerebellum (Larsell, 1967), but more recent experimental studies (Kishida et al., 1987; Weigle and Northcutt, 1998) fail to support Larsell's claim[http://icb.oxfordjournals.org/content/42/4/743.full] UBERON:0002037 UMLS:C0007765 UMLS:C1268981 VHOG:0000024 XAO:0003098 ZFA:0000100 almost all AOs agree that the cerebellum is part of the hindbrain (sometimes specifically part of the metencephalon, which, when present, is part of the hindbrain). However, ABA has cerebellum and brain stem as partof siblings, with the hindbrain part of the brainstem cerebellar corpus cerebelli epencephalon-1 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=643 infratentorial region parencephalon uberon thyroid gland (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (2) a groove in the pharyngeal floor known as the endostyle, or a thyroid gland derived from part of the endostyle (...).[well established][VHOG] A two-lobed endocrine gland found in all vertebrates, located in front of and on either side of the trachea in humans, and producing various hormones, such as triiodothyronine and calcitonin[BTO]. AAO:0010544 BTO:0001379 CALOHA:TS-1047 EFO:0000861 EHDAA2:0002028 EHDAA:2148 EHDAA:2975 EMAPA:17068 EV:0100133 Either of paired structures located in the throat which develop from the ventral wall of the pharynx and excretes hormones involved in the morphological and functional changes during metamorphosis as well as influencing other tissues.[AAO] FMA:9603 GAID:465 In fish, it is usually located below the gills and is not always divided into distinct lobes. However, in some teleosts, patches of thyroid tissue are found elsewhere in the body, associated with the kidneys, spleen, heart, or eyes In larval lampreys, the thyroid originates as an exocrine gland, secreting its hormones into the gut, and associated with the larva's filter-feeding apparatus. In the adult lamprey, the gland separates from the gut, and becomes endocrine, but this path of development may reflect the evolutionary origin of the thyroid. For instance, the closest living relatives of vertebrates, the tunicates and Amphioxus, have a structure very similar to that of larval lampreys, and this also secretes iodine-containing compounds (albeit not thyroxine) In tetrapods, the thyroid is always found somewhere in the neck region. In most tetrapod species, there are two paired thyroid glands - that is, the right and left lobes are not joined together. However, there is only ever a single thyroid gland in most mammals, and the shape found in humans is common to many other species MA:0000129 MAT:0000081 MESH:D013961 MIAA:0000081 OpenCyc:Mx4rvVjLT5wpEbGdrcN5Y29ycA UBERON:0002046 UMLS:C0040132 VHOG:0000418 XAO:0000162 galen:ThyroidGland glandula thyroidea thyroid uberon lung AAO:0000275 AAO:0010567 BTO:0000763 CALOHA:TS-0568 EFO:0000934 EHDAA2:0001042 EHDAA:1554 EHDAA:2205 EMAPA:16728 EV:0100042 Either of two organs which allow gas exchange absorbing oxygen from inhaled air and releasing carbon dioxide with exhaled air.[AAO] FMA:7195 GAID:345 Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata. (...) In actinopterygian fishes, apart from Cladistia, the ventral intestinal pocket migrates dorsally and becomes the swim-bladder, a mainly hydrostatical organ (reference 1); Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung (reference 2).[well established][VHOG] MA:0000415 MAT:0000135 MESH:D008168 MIAA:0000135 OpenCyc:Mx4rvVjKy5wpEbGdrcN5Y29ycA Respiration organ that develops as an oupocketing of the esophagus. Snakes and limbless lizards typically possess only the right lung as a major respiratory organ; the left lung is greatly reduced, or even absent. Amphisbaenians, however, have the opposite arrangement, with a major left lung, and a reduced or absent right lung [WP] UBERON:0002048 UMLS:C0024109 VHOG:0000310 XAO:0000119 galen:Lung pulmo pulmonary respiration organ in all air-breathing animals, including most tetrapods, a few fish and a few snails. In mammals and the more complex life forms, the two lungs are located in the chest on either side of the heart. Their principal function is to transport oxygen from the atmosphere into the bloodstream, and to release carbon dioxide from the bloodstream into the atmosphere. This exchange of gases is accomplished in the mosaic of specialized cells that form millions of tiny, exceptionally thin-walled air sacs called alveoli. // Avian lungs do not have alveoli as mammalian lungs do, they have Faveolar lungs. They contain millions of tiny passages known as para-bronchi, connected at both ends by the dorsobronchi uberon vasculature An interconnected tubular multi-tissue structure contains fluid that is actively transported around the organism[ZFA]. Examples: vasculature of lung, vasculature of face. BTO:0003718 FMA:69050 TAO:0005249 UBERON:0002049 ZFA:0005249 see also: vascular system. Consider merging? uberon vascular vascular network embryonic structure AAO:0000138 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] BILA:0000034 BTO:0000174 CALOHA:TS-2110 EFO:0000461 FBbt:00004208 FMA:69067 GAID:407 MESH:D004628 RETIRED_EHDAA2:0003169 TAO:0001105 UBERON:0002050 UMLS:C0013948 VSAO:0000178 XAO:0003042 ZFA:0001105 developing embryonic structure developing structure embryonale Struktur embryonic anatomical structure embryonic structures in FMA embryo is_a embryonic structure uberon endocardial cushion (Cardiac valve formation in vertebrates) In response to a myocardial signal, endocardial cells at chamber boundaries take on a mesenchymal character, delaminate and migrate into the cardiac jelly. There, they form an endocardial cushion that is later remodelled into a valve.[well established][VHOG] AV cushion EHDAA2:0000434 EHDAA2:0004028 EHDAA:2586 EMAPA:16696 FMA:70302 GO graph seems to suggest this is an endothelium. WP: The endocardial cushions are thought to arise from a subset of endothelial cells that undergo epithelial to mesenchymal transformation, a process whereby these cells break cell-to-cell contacts and migrate into the cardiac jelly (towards to interior of the heart tube). Latest (2010-06-01) new def suggested for GO, added above. Note that EHDAA2 has a more detailed model which we may later adopt. JB: Patterning makes the cushions lay down connective tissue in three domains that force out the local endothelial lining and so the leaflets form MA:0000078 Swellings of tissue present between the endocardial and myocardial cell layers that will give rise to the interstitial cells of the cardiac valves.[TAO] TAO:0001317 The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves[GO]. Swellings of tissue present between the endocardial and myocardial cell layers that will give rise to the interstitial cells of the cardiac valves[ZFA]. UBERON:0002062 VHOG:0000932 XAO:0004189 ZFA:0001317 atrioventricular canal cushion atrioventricular cushion cardiac cushion endocardial cushion tissue endocardial cushions relationship loss: develops_from endocardial ring (TAO:0005072)[TAO] uberon dermis 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] AAO:0000128 BTO:0000294 CALOHA:TS-2076 Consider adding a layer-of-skin grouping class for all skin layers EFO:0000953 EMAPA:17527 EV:0100154 FMA:70323 GAID:1321 MA:0000152 MAT:0000153 MESH:D020405 MIAA:0000153 TAO:0001119 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]. UBERON:0002067 UMLS:C0011646 VHOG:0000108 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] XAO:0000217 ZFA:0001119 corium cutis dermal uberon vertebrate dermis hypodermis A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells. Le Guellec et al, 2004.[TAO] 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]. 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 FMA:70544 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]. TAO:0001136 UBERON:0002072 UMLS:C0278403 ZFA:0001136 hypoderm hypodermal sub-tegumental tissue subcutaneous subcutaneous tissue subcutaneus subcutis subtegumental tissue superficial fascia tela subcutanea uberon vertebrate hypodermis viscus AAO:0010386 An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO] 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 EHDAA:512 EMAPA:16245 FMA:7085 MA:0000019 MESH:D014781 Organsystem@ge RETIRED_EHDAA2:0002201 UBERON:0002075 UMLS:C0042779 XAO:0003034 general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs. splanchnic tissue uberon viscera visceral organ visceral organ system visceral tissue right cardiac atrium A cardiac atrium that is in the left side of the heart. It receives deoxygenated blood. In mammals, this comes from the superior and inferior vena cava and the coronary sinus, and pumps it into the right ventricle through the tricuspid valve. AAO:0010248 BTO:0001703 EHDAA2:0000290 EMAPA:17321 FMA:7096 MA:0000075 OpenCyc:Mx4runNcs6fqEdudWQACs5b6Bw OpenCyc:Mx8Ngh4rvgHsHZwpEbGdrcN5Y29ycB4rDJ89oqgPEdudWQACs5b6Bw Right cardiac chamber which is continuous with the superior vena cava and inferior vena cava.[FMA] The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG] UBERON:0002078 UMLS:C0225844 VHOG:0000328 XAO:0003192 atrium dextrum cardiac right atrium galen:RightAtrium heart right atrium https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern right atrium right atrium of heart right cardiac atrium uberon left cardiac atrium A cardiac atrium that is in the left side of the heart. It receives oxygenated blood from the pulmonary veins, In mammals this is pumped into the left ventricle, via the Mitral valve. AAO:0010247 BTO:0001702 EHDAA2:0000275 EMAPA:17315 FMA:7097 Left cardiac chamber which is continuous with the pulmonary venous trunk.[FMA] MA:0000074 OpenCyc:Mx4rkJN1AagEEdudWQACs5b6Bw OpenCyc:Mx8Ngh4rvgIFoJwpEbGdrcN5Y29ycB4rDJ89oqgPEdudWQACs5b6Bw The chamber of the heart that receives blood from the lungs[XAO:EJS]. The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG] UBERON:0002079 UMLS:C0225860 VHOG:0000369 XAO:0003191 atrium sinistrum cardiac left atrium galen:LeftAtrium heart left atrium https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern left atrium left atrium of heart left cardiac atrium uberon heart right ventricle A cardiac ventricle that is in the right side of the heart. BTO:0001630 CALOHA:TS-0443 EHDAA2:0000196 EMAPA:17340 FMA:7098 In mammals continuous with the pulmonary arteries MA:0000093 OpenCyc:Mx4rRMlc0KgNEdudWQACs5b6Bw OpenCyc:Mx8Ngh4rvgHsHZwpEbGdrcN5Y29ycB4rvVjj1pwpEbGdrcN5Y29ycA The muscular chamber on the right and in front of the left ventricle. It generally receives venous blood from the right atrium and conveys it into the pulmonary artery. [(1988)_Dorian_AF, Amsterdam, Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B._Anatomy, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier's_Encyclopaedic_Dictionary_of_Medicine][VHOG] UBERON:0002080 UMLS:C0225883 VHOG:0000717 cardiac right ventricle galen:RightVentricle https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern right cardiac ventricle right ventricle right ventricle of heart uberon ventriculus dexter cardiac atrium AAO:0010246 BTO:0000903 CALOHA:TS-0437 Cardiac atria Cardiac chamber in which blood enters the heart. EFO:0000277 EHDAA2:0000154 EHDAA:1265 EMAPA:16688 EV:0100019 FMA:7099 GAID:555 In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...).[well established][VHOG] MA:0000073 MAT:0000496 MESH:D006325 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] TAO:0000471 UBERON:0002081 UMLS:C0018792 VHOG:0000175 ZFA:0000471 atria atrial tissue atrium atrium of heart cardiac atria galen:Atrium heart atrium uberon cardiac ventricle A chamber of the heart that receives blood from one or more atria and pumps it by muscular contraction into the arteries.[AAO] AAO:0010249 BTO:0000862 CALOHA:TS-0444 Cardiac chamber through which blood leaves the heart. EFO:0000317 EHDAA2:0004164 EHDAA:1912 EMAPA:17331 EV:0100020 FMA:7100 GAID:568 In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...)[well established][VHOG] MA:0000091 MAT:0000497 MESH:D006352 One of four heart chambers.[TAO] OpenCyc:Mx4rvVjj1pwpEbGdrcN5Y29ycA TAO:0000009 UBERON:0002082 UMLS:C0018827 VHOG:0000435 XAO:0003193 ZFA:0000009 galen:Ventricle heart ventricle lower chamber of heart uberon ventricle ventricle of heart heart left ventricle A cardiac ventricle that is in the left side of the heart. BTO:0001629 CALOHA:TS-0439 EHDAA2:0002178 EMAPA:17337 FMA:7101 In mammals continuous with aorta MA:0000092 OpenCyc:Mx4rtW8v46gEEdudWQACs5b6Bw OpenCyc:Mx8Ngh4rvgIFoJwpEbGdrcN5Y29ycB4rvVjj1pwpEbGdrcN5Y29ycA The vertebrate heart initially forms as a tube from a population of precursor cells termed the first heart field (FHF). Cells from the adjacent second heart field (SHF) are then progressively added to the developing heart. In avian and mammalian hearts, the FHF contributes mainly to the left ventricle, whereas the SHF gives rise to the outflow tract and large portions of the right ventricle and atria. Both fields arise from common mesodermal progenitors, although the detailed lineage relationships between FHF and SHF remain uncertain.[well established][VHOG] Thick-walled muscular chamber constituting the left border and apex of the heart. It receives oxygenated blood from the left atrium through the mitral orifice and send it off into the aorta. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] UBERON:0002084 UMLS:C0225897 VHOG:0000718 cardiac left ventricle galen:LeftVentricle https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern left cardiac ventricle left ventricle left ventricle of heart uberon ventriculus sinister cordis postcranial axial skeleton AAO:0000034 EFO:0000942 EHDAA2:0000161 EHDAA:5049 EMAPA:17214 FMA:71221 MA:0002986 MAT:0000148 MIAA:0000148 Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO] TAO:0000317 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] 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 post-cranial 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]. UBERON:0002090 VHOG:0000317 VSAO:0000093 XAO:0003073 ZFA:0000317 axial skeleton http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton post-cranial axial skeleton previous some AOs had used the term 'axial skeleton' to include the skull. This is being resolved (see tracker items above). Status: MA - fixed. uberon appendicular skeleton AAO:0000747 EFO:0000951 EMAPA:32729 FMA:71222 MA:0000290 MAT:0000278 MIAA:0000278 Skeletal subdivision consisting of all the skeletal elements in the pectoral and pelvic appendage complexes.[VSAO] Skeletal system that consists of the paired fins (pectoral or pelvic fins).[TAO] Subdivision of skeleton which which consists of all the skeletal elements in in the pectoral and pelvic appendage complexes[cjm]. The pectoral and pelvic girdles, which articulate with the axial skeleton, together with their associated limbs, the forelimbs and hind limbs, form the appendicular skeleton.[AAO] UBERON:0002091 UMLS:C0222646 VHOG:0001666 VSAO:0000076 XAO:0003166 appendicular skeleton entire appendicular skeleton https://github.com/obophenotype/uberon/wiki/Appendages-and-the-appendicular-skeleton ontologies differ in whether they treat the term appendicular skeleton as being the entire set of bones in the limbs, or whether the fore and hind limbs/fins are treated as seperate appendicular skeletons. Here we follow FMA, and treat the appendicular skeleton as the sum total of skeletal elements in the organism (this is evidenced by the fact that in FMA, skeleton of left/right upper/lower limb is part_of a appendicular skeleton, and subtypes of 'subdivision of appendicular skeleton'). We have separate classes such as 'skeleton of limb', and 'skeleton of hindlimb' for the 4 parts of the appendicular skeleton. In future the ZFA/TAO classes may be moved. paired fin skeleton skeleton appendiculare uberon skin of body BTO:0001253 CALOHA:TS-0934 EFO:0000962 EHDAA2:0001844 EMAPA:17525 FMA:7163 MA uses the term skin to refer to what is called here: zone of skin MESH:D012867 MFMO:0000099 OpenCyc:Mx4rvVjX3ZwpEbGdrcN5Y29ycA The organ covering the body that consists of the dermis and epidermis. UBERON:0002097 UMLS:C1123023 XAO:0000023 consider 'integumentary system' for invertebrates entire integument entire skin galen:Skin integument integumental organ pelt skin skin organ uberon trunk AAO:0010339 BILA:0000116 BTO:0001493 CALOHA:TS-1071 EFO:0000966 EMAPA:31857 FMA:7181 MA:0000004 MAT:0000296 MIAA:0000296 OpenCyc:Mx4rvVkJjpwpEbGdrcN5Y29ycA 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 cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present. Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO] Rumpf TAO:0001115 UBERON:0002100 UMLS:C0460005 XAO:0000054 XAO:0003025 ZFA:0001115 galen:Trunk thoracolumbar region torso trunk region uberon limb A paired appendage that is evolved from a paired fin. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the girdle and its parts. AAO:0010336 AEO:0000172 CALOHA:TS-0552 EFO:0000876 EHDAA2:0003172 EHDAA:1697 EHDAA:8273 EMAPA:16405 FMA:24875 GAID:36 MA:0000007 MAT:0000090 MIAA:0000090 Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] OpenCyc:Mx4rvn1uSZwpEbGdrcN5Y29ycA Organism subdivision that has as its parts the jointed appendages used for locomotion and manipulation.[AAO] UBERON:0002101 UMLS:C0015385 VHOG:0000336 VSAO:0000121 XAO:0003027 extremities extremity flipper free limb galen:Extremity limb sensu vertebrata pentadactyl limb tetrapod limb uberon hindlimb A (free) limb that is connected to a pelvic girdle region. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the pelvic girdle and its parts. AAO:0000219 BTO:0002345 CALOHA:TS-2215 EFO:0000883 EHDAA2:0001033 EHDAA:6094 EMAPA:17458 EV:0100015 FMA:24879 GAID:1221 GAID:38 Lower limb, which connects the pes with the pelvic girdle.[AAO] MA:0000026 MAT:0000395 MESH:D006614 MIAA:0000395 Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] UBERON:0002103 UMLS:C0023216 UMLS:C1522391 VHOG:0000337 VSAO:0000150 XAO:0003031 crural free lower limb free part of lower limb galen:LowerExtremity hind limb hind-limb hindlimb inferior member lower extremity lower limb membrum inferius membrum inferius note that this corresponds to FMA:'free lower limb' (a limb segment), NOT 'lower limb'. Both MA and FMA consider shoulder (and shoulder bones) part of upper limb. Note that AAO class probably refers to skeleton pelvic appendage uberon visual system AAO:0000632 BILA:0000140 EMAPA:36003 FMA:7191 MA:0002444 OpenCyc:Mx4rvViCtpwpEbGdrcN5Y29ycA TAO:0001127 The sensory system subserving the sense of vision. The sensory system used for sight.[AAO] UBERON:0002104 UBERON:0007036 UMLS:C0587900 XAO:0003198 ZFA:0001127 photosensory system uberon visual organ system vestibulo-auditory system AAO:0000631 EMAPA:36002 FMA:78500 Sensory system responsible for the perception of spatial orientation and auditory stimuli. TAO:0001138 The sensory system used for balance and hearing.[AAO] UBERON:0002105 XAO:0003195 ZFA:0001138 auditory organ system auditory system auditory/vestibular system uberon vestibuloauditory system vestibuloauditory system liver AAO:0010111 All vertebrates possess a liver (reference 1); Later in craniate evolution, an anterior gill arch was transformed into jaws, and many new types of feeding subsequently evolved.(...) A liver evolved that, among its many functions, stores considerable energy as glycogen or lipid (reference 2).[well established][VHOG] An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO]. An organ sometimes referred to as a liver is found associated with the digestive tract of the primitive chordate Amphioxus. However, this is an enzyme secreting gland, not a metabolic organ, and it is unclear how truly homologous it is to the vertebrate liver. The zebrafish liver differs from the mammalian liver in that the hepatocytes are not clearly organized in cords or lobules and the typical portal triads are not apparent. In addition, the zebrafish liver does not have Kuppfer cells. Furthermore, a clear distinction can be made between the male and female liver in the adult zebrafish. The female hepatocytes are very basophilic (Figure 15c) as a result of the production of vitellogenin (Van der Ven et al. 2003). BTO:0000759 CALOHA:TS-0564 EFO:0000887 EHDAA2:0000997 EHDAA:2197 EMAPA:16846 EV:0100089 FMA:7197 GAID:288 MA:0000358 MAT:0000097 MESH:D008099 MIAA:0000097 Only ZFA considers this part_of immune system - we weaken this to an overlaps relation, as in general it's only a subset of cells that have clear immune function. OpenCyc:Mx4rvVimppwpEbGdrcN5Y29ycA Organ which secretes bile and participates in formation of certain blood proteins.[AAO] TAO:0000123 The liver is found in all vertebrates, and is typically the largest visceral organ. Its form varies considerably in different species, and is largely determined by the shape and arrangement of the surrounding organs. Nonetheless, in most species it is divided into right and left lobes; exceptions to this general rule include snakes, where the shape of the body necessitates a simple cigar-like form. The internal structure of the liver is broadly similar in all vertebrates. UBERON:0002107 UMLS:C0023884 VHOG:0000257 XAO:0000133 ZFA:0000123 galen:Liver hepatic iecur jecur relationship type change: differentiates_from endoderm (AAO:0000139) CHANGED TO: develops_from endoderm (UBERON:0000925)[AAO] secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO]. uberon small intestine AAO:0010397 BTO:0000651 CALOHA:TS-0942 EFO:0000841 EMAPA:32834 EV:0100072 FMA:7200 GAID:313 Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG] MA:0000337 MAT:0000047 MESH:A03.492.411.620 MIAA:0000047 OpenCyc:Mx4rvVjlIJwpEbGdrcN5Y29ycA Subdivision of digestive tract that connects the stomach to the large intestine and is where much of the digestion and absorption of food takes place (with the exception of ruminants). The mammalian small intestine is long and coiled and can be differentiated histologically into: duodenum, jejunem, ileum[WP,cjm,Kardong]. TAO:0001323 The terminal region of the mid intestine is comprised of specialized enterocytes that appear to play a role in mucosal immunity. Wallace et al, 2005.[TAO] UBERON:0002108 UMLS:C0021852 VHOG:0000055 XAO:0000130 ZFA:0001323 anterior intestine galen:SmallIntestine intestinum tenue mid intestine small bowel small intestine uberon gall bladder AAO:0010114 An organ that aids digestion and stores bile produced by the liver[WP]. BTO:0000493 CALOHA:TS-0394 EFO:0000853 EHDAA2:0000699 EHDAA:8062 EMAPA:17202 EV:0100090 FMA:7202 MA:0000356 MAT:0000072 MESH:D005704 MIAA:0000072 Membranous muscular sac in which the bile from the liver remains stored until it is required. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] OpenCyc:Mx4rvVkGr5wpEbGdrcN5Y29ycA Organ attached to the liver which stores bile and empties into the duodenum via the bile duct as needed for digestion.[AAO] Rats do not have a gallbladder, but produce bile. The bile flows directly from the liver through the (hepatic) bile duct into the small intestine (Hebel and Stromberg, 1988) TAO:0000208 The presence of a gallbladder appears to be a primitive trait. It is found in most fish and all adult reptiles and amphibians and has been well conserved in mammals, for the most part.[well established][VHOG] UBERON:0002110 UMLS:C0016976 VHOG:0000221 XAO:0000135 ZFA:0000208 galen:Gallbladder gall bladder gallbladder relationship type change: differentiates_from endoderm (AAO:0000139) CHANGED TO: develops_from endoderm (UBERON:0000925)[AAO] uberon vesica biliaris vesica fellea kidney A paired organ of the urinary tract which has the production of urine as its primary function. AAO:0000250 BTO:0000671 CALOHA:TS-0510 EFO:0000929 EMAPA:17373 EV:0100096 FMA:7203 GAID:423 MA:0000368 MAT:0000119 MESH:D007668 MIAA:0000119 One of either of a pair of structures lying on either side of the dorsal aorta in which fluid balance is regulated and waste is excreted out in the form of urine.[AAO] OpenCyc:Mx4rvVjlYpwpEbGdrcN5Y29ycA UBERON:0002113 UMLS:C0022646 XAO:0003267 galen:Kidney renal reniculate kidney uberon duodenum AAO:0010402 BTO:0000365 CALOHA:TS-0214 EFO:0000851 EMAPA:18852 EV:0100073 FMA:7206 GAID:284 In fish, the divisions of the small intestine are not as clear, and the terms anterior intestine or proximal intestine may be used instead of duodenum. In humans, the duodenum is a hollow jointed tube about 10-15 inches (25-38 centimetres) long connecting the stomach to the jejunum. It begins with the duodenal bulb and ends at the ligament of Treitz. MA:0000338 MAT:0000044 MESH:A03.492.411.620.270 MIAA:0000044 OpenCyc:Mx4rv4LJDpwpEbGdrcN5Y29ycA The first part of the small intestine. At the junction of the stomach and the duodenum the alimentary canal is inflected. The duodenum first goes anteriorly for a short distance, turns dorsally, and eventually caudally, thus it is a U-shaped structure with two horizontal sections (a ventral and a dorsal one). The fixed portion of the small intestine deeply lodged in the posterior wall of the abdomen and extending from the pylorus to the beginning of the jejunum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] UBERON:0002114 UMLS:C0013303 VHOG:0000052 XAO:0000236 duodenal galen:Duodenum proximal intestine uberon upper intestine pronephros A kidney formed of nephric tubules arising in the anterior region of the nephric ridge; forms only as a transient embryonic structure. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.748][VHOG] AAO:0011089 BTO:0001541 EFO:0000927 EHDAA2:0001570 EHDAA:1017 EMAPA:16579 FMA:72170 In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG] In mammals, the pronephros is the first of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the pronephros is the fully functional embryonic kidney and is indispensible for larval life[GO]. MAT:0000117 MIAA:0000117 Once the more complex mesonephros forms the pronephros undergoes apoptosis in amphibians. In fishes the nephron degenerates but the organ remains and becomes a component of the immune system[Wikipedia:Pronephros]. // TODO - check developmental relationships. Note that we previously include the ZFA/XAO terms under the more specific 'pronephric kidney', but these are now merged. TODO GCI: relationship: capable_of GO:0030104 Organ that serves as a transient kidney, providing osmoregulation during early developmental stages and then degenerating during metamorphosis.[AAO] TAO:0000151 The embryonic kidney, present at the level of the third somite, is composed of two glomeruli fused at the midline, two pronephric tubules, and paired bilateral pronephric ducts that modify the composition of the blood filtrate before delivering it to the cloaca for excretion.Kimmel et al, 1995.[TAO] UBERON:0002120 UBERON:0005794 UMLS:C0231048 VHOG:0000037 XAO:0002000 ZFA:0000151 archinephron embryonic kidney pronephric pronephric kidney pronephron uberon atrioventricular valve A cardial valve in the atrioventricular region that separates the atrium from the ventricle and prevent backflow from the ventricles into the atria during systole. AV valve EHDAA2:0000153 EHDAA:7421 EMAPA:35154 FMA:7233 MA:0002789 OpenCyc:Mx4rfCfdorrpEduAAAACs6hRXg TAO:0005064 The atrioventricular valve has four distinct leaflets oriented anterior, posterior, left, and right of the atrioventricular orifice. Hu et al. 2001.[TAO] The conus arteriosus is the most distal part of the primitive fish heart and forms the connection between the ventricle and the ventral aorta. At the sinoatrial, the atrioventricular, and the ventriculoconal junctions, valves developed to prevent backflow of blood during relaxation of the preceding compartment.[uncertain][VHOG] UBERON:0002133 VHOG:0001472 Valve in the heart through which blood flows from the atria to the ventricles. [TFD][VHOG] ZFA:0005064 atrio-ventricular valve galen:AtrioventricularValve in ZFA this is part of both atrium and ventricle, but we use a connecting relationship here; see also notes for left and right. uberon tricuspid valve An atrioventricular valve that is part of the outflow part of the right atrium. EHDAA2:0004029 EHDAA:7427 EMAPA:17873 FMA part_ofs changed to connects FMA:7234 GAID:567 MA:0000090 MESH:D014261 OpenCyc:Mx4rvuWAAJwpEbGdrcN5Y29ycA RETIRED_EHDAA2:0002081 The mature AV (atrioventricular) valve of the adult zebrafish 2-chambered heart is structurally similar to the mammalian AV valves with stratified ECM (extracellular matrix) and supporting chordae tendineae. Therefore, the major cellular and molecular events of valve development are largely conserved among animals with hearts composed of multiple chambers.[well established][VHOG] The three-segmented valve of the heart that keeps blood in the right ventricle from flowing back into the right atrium. [TFD][VHOG] UBERON:0002134 UMLS:C0040960 VHOG:0000816 galen:TricuspidValve right atrioventricular valve uberon valva atrioventricularis dextra valvula tricuspidalis mitral valve A valve of the heart, composed of two triangular flaps, that is located between the left atrium and left ventricle and regulates blood flow between these chambers. [TFD][VHOG] An atrioventricular valve that is part of the outflow part of the left atrium. EFO:0003933 EHDAA2:0000168 EMAPA:17871 FMA part_ofs changed to connects FMA:7235 GAID:565 MA:0000088 MESH:D008943 OpenCyc:Mx4rv4l2nJwpEbGdrcN5Y29ycA The mature AV (atrioventricular) valve of the adult zebrafish 2-chambered heart is structurally similar to the mammalian AV valves with stratified ECM (extracellular matrix) and supporting chordae tendineae. Therefore, the major cellular and molecular events of valve development are largely conserved among animals with hearts composed of multiple chambers.[well established][VHOG] UBERON:0002135 UMLS:C0026264 VHOG:0000817 bicuspid valve galen:MitralValve left atrioventricular valve uberon valva atrioventricularis sinistra valva mitralis endocardium AAO:0010408 BTO:0000387 CALOHA:TS-2075 EFO:0000821 EHDAA2:0004153 EMAPA:17868 EMAPA:32686 EV:0100021 FMA:7280 GAID:550 Layer that lines the lumen of the heart.[TAO] MA:0000076 MAT:0000455 MESH:D004699 OpenCyc:Mx4rsWA75K1cEduAAADggVaqvw Part of the heart comprised of thin serous membrane, composed of endothelial tissue, that lines the interior of the heart.[AAO] TAO:0001320 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]. 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:0002165 UBERON:0006225 UMLS:C0014124 VHOG:0000084 XAO:0000066 ZFA:0001320 endocardial lining endocardial tissue fixed in GO to reflect FMA. See email to David/Varsha June 18 2010 galen:Endocardium heart endocardial tissue heart endocardium uberon right lung EHDAA2:0001730 EHDAA:4969 EMAPA:17661 FMA:7309 Lung which consists of the right upper lobe, middle lobe and right lower lobe.[FMA] Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG] MA:0000426 OpenCyc:Mx8Ngh4rvgHsHZwpEbGdrcN5Y29ycB4rvVjKy5wpEbGdrcN5Y29ycA UBERON:0002167 UMLS:C0225706 VHOG:0000301 https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern uberon left lung EHDAA2:0000943 EHDAA:4947 EMAPA:17653 FMA:7310 Lung which consists of the left upper lobe and left lower lobe.[FMA] Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG] MA:0000425 OpenCyc:Mx8Ngh4rvgIFoJwpEbGdrcN5Y29ycB4rvVjKy5wpEbGdrcN5Y29ycA UBERON:0002168 UMLS:C0225730 VHOG:0000618 https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern uberon bronchus BTO:0001340 CALOHA:TS-1229 EFO:0000932 EMAPA:32689 EV:0100041 Each of the two primary divisions of the trachea leading respectively into the right and the left lung. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] FMA:7409 GAID:346 In humans, the main bronchus is histologically identical to trachea; 2ary and 3ary bronchi are not; epithelium becomes simple columnar, goblet cell number decreases, elastic fibers in lamina propria increases, distribution more uniform. Muscular layer between mucosa and submucosa appears. cartilage rings become discontinuous plates connected by fibrous connective tissue MA:0000436 MAT:0000133 MESH:D001980 MIAA:0000133 UBERON:0002185 UMLS:C0006255 VHOG:0000262 XAO:0000121 bronchi bronchial bronchial tissue bronchial trunk the upper conducting airways of the lung; these airways arise from the terminus of the trachea uberon bronchiole BTO:0002375 CALOHA:TS-2003 EHDAA:8171 EHDAA:8183 EHDAA:8199 EHDAA:8221 EMAPA:32697 FMA:7410 MA:0000422 OpenCyc:Mx4rvl9iDpwpEbGdrcN5Y29ycA UBERON:0002186 UMLS:C0006270 VHOG:0000675 bronchiolar bronchioli bronchiolus lacks submucosa and cartilage plates; they have 3 layers: mucosa, muscular layer and outer layer lobular bronchiole the conducting airway of the lungs found terminal to the bronchi; these structures contain neither cartilage nor mucous-secreting glands; the epithelium of the bronchioles becomes thinner with each branching uberon terminal bronchiole BTO:0003223 EMAPA:36282 FMA:7411 MA:0000424 OpenCyc:Mx4rwS7IU5wpEbGdrcN5Y29ycA UBERON:0002187 UMLS:C0225666 bronchioli terminalis bronchiolus terminalis terminal bronchiole tube the last conducting structure of non-respiratory bronchioles; after this point, the airways have alveoli in their walls uberon hemolymphoid system 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 UBERON:0002193 haemolymphoid system hematolymphoid system lymphomyeloid complex uberon integument AAO:0000239 Anatomical system that protects the body from damage, comprising the skin and its appendages.[AAO] BTO:0000634 FMA:74657 Hautsystem@de Surface structure that is the outer protective covering of the body.[VSAO] TAO:0000368 The dermis, epidermis and hypodermis. The outer protective barrier that separates the animal from its aquatic environment. Le Guellec et al, 2004.[TAO] UBERON:0002199 VSAO:0000029 ZFA:0000368 dermal system dermis plus epidermis plus hypodermis dermoid system galen:Integument 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. integumental integumentary integumentum commune skin skin and subcutaneous tissue skin plus hypodermis tegument the integument uberon vertebrate integument vasculature of head EFO:0003656 FMA:74710 TAO:0001267 UBERON:0002200 Vasculature that is part of a head [Automatically generated definition]. XAO:0004152 ZFA:0001267 adult head vascular network adult head vasculature cranial vasculature head vascular network head vasculature uberon vascular network of adult head vascular network of head vasculature of adult head vasculature of trunk A vasculature that is part of a trunk [Automatically generated definition]. FMA:74712 TAO:0005024 UBERON:0002201 ZFA:0005024 torso vascular network torso vasculature trunk vascular network trunk vasculature uberon vascular network of torso vascular network of trunk vasculature of torso vasculature of eye FMA:74743 TAO:0007057 UBERON:0002203 Vasculature that is part of the eye region. ZFA:0007057 eye vascular network eye vasculature not part of the eye in ZFA. Note this changed to a blood vessel in ZFA ocular blood vessel ocular vasculature optic vasculature uberon vascular network of eye musculoskeletal system AAO:0010546 Anatomical system that consists of the muscular and skeletal systems. Anatomical system that provides locomotion and physical support to the organism.[AAO] CALOHA:TS-1311 EMAPA:32714 EV:0100139 FMA:7482 GAID:98 MA:0002418 MESH:D009141 OpenCyc:Mx4rQRpVNgAKEdyHxgDggVfs8g 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] UBERON:0002204 UMLS:C0026860 VHOG:0001275 VSAO:0000031 XAO:0000168 musculo-skeletal system musculoskeletal uberon nerve root A continuation of the neuron projection bundle component of a nerve inside, crossing or immediately outside the central nervous system. FMA has 'central zone of nerve' which is the superclass of cranial nerve tracts, which the FMA sometimes calls roots FMA:5981 FMA:82524 The continuation of the neurite bundle and associated glia of a nerve, inside the central nervous system[FBbt:00007602, FBC:DOS]. UBERON:0002211 UMLS:C0228084 We consider cranial nerve roots to be primarily CNS structures, but model spinal nerve roots as PNS structures, due to the existence of ganglia on the roots. initial segment of nerve radix nervi uberon synovial joint AEO:0000183 CALOHA:TS-2138 EHDAA2:0003183 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] 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] MA:0000322 OpenCyc:Mx4rv2bBV5wpEbGdrcN5Y29ycA TAO:0005153 UBERON:0002217 ZFA:0005153 articulatio synoviale diarthrodial joints diarthroses diarthrosis diarthrosis joint galen:SynovialJoint uberon thoracic cavity EMAPA:36497 FMA:7565 GAID:93 In many species, the diaphragm separates thoracic and abdominal cavities MA:0000032 MESH:A01.911.800 OpenCyc:Mx4rmvyleLfEEduAAAACs6hRXg OpenCyc:Mx4rvhU_TpwpEbGdrcN5Y29ycA The part of the coelemic cavity lumen that is enclosed by the walls of the thorax. UBERON:0002224 UMLS:C0230139 cavitas thoracis cavity of chest cavity of thorax chest cavity pectoral cavity space of thoracic compartment thoracic lumen uberon spinal cord (...) 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 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 OpenCyc:Mx4rvVjjk5wpEbGdrcN5Y29ycA 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) Part of the central nervous system which descends from the hindbrain within the vertebral column.[AAO] SpC TAO:0000075 TODO - add superclass to unify with VNC? UBERON:0002240 UMLS:C0037925 VHOG:0000601 XAO:0000020 ZFA:0000075 cerebro-cerebellar fissure cerebrocerebellar fissure fissura cerebro-cerebellaris fissura cerebrocerebellaris http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=22 medulla spinalis spinal cord structure spinal medulla uberon chondrocranium AAO:0010169 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] EHDAA2:0000243 EMAPA:17681 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]. TAO:0001424 UBERON:0002241 VHOG:0000288 ZFA:0001424 calvarium chondrocranial covers the brain dorsally in chondrichthyans neurocranium uberon 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) olfactory organ AAO:0010180 An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint An organ that houses olfactory neurons and is responsible for the sense of smell. Examples include the vertebrate nose and the Drosophila dorsal organ. BTO:0001772 FBbt:00005158 FMA:77659 UBERON:0002268 VHOG:0000287 XAO:0000273 fma general anatomical term. xao has no subtypes (but Johnstons organ develops from this). An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint main olfactory organ olfactory neuroepithelium olfactory organ olfactory sense organ olfactory sensory organ organ olfactus organum olfactorium primary olfactory organ uberon telencephalic ventricle A brain ventricle that is part of a telencephalon. In mammals and species with an evaginated telencephalon, this is one of a pair of lateral structures, one in each hemisphere BAMS:LV BAMS:Tel-V BM:Tel-LV BTO:0000879 CALOHA:TS-1230 DHBA:10596 DMBA:126651562 EFO:0001961 EHDAA2:0001984 EHDAA:3502 EHDAA:6576 EMAPA:16914 EV:0100307 FMA:78448 GAID:611 HBA:9419 MA:0000192 MBA:81 MESH:D020547 OpenCyc:Mx4rvYsFdZwpEbGdrcN5Y29ycA TAO:0000696 Telencephalic ventricles 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 lateral ventricles are part of the ventricular system of the brain. Classified as part of the telencephalon, they are the largest of the ventricles. The lateral ventricles connect to the central third ventricle through the interventricular foramina of Monro[WP]. The two lateral ventricles are a cavity in each of the cerebral hemispheres derived from the cavity of the embryonic neural tube. They are separated from each other by the septum pellucidum, and each communicates with the third ventricle by the foramen of Monro, through which also the choroid plexuses of the lateral ventricles become continuous with that of the third ventricle[GO]. UBERON:0002285 UMLS:C0152279 VHOG:0000643 ZFA:0000696 forebrain ventricle lateral ventricle lateral ventricle of brain lateral ventricles modeled as space in EHDAA2 tectal ventricle telencephalic ventricle telencephalic vesicle telencephalon lateral ventricle uberon biliary system FMA:79646 GAID:279 MA:0001273 MESH:D001659 Organ system subdivision that consists of the organs and ducts that are involved in the production and transportation of bile. In most species this is the gallbladder and the bile ducts (biliary tree). UBERON:0002294 biliary apparatus biliary tract uberon brainstem '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 (ISBN10:0471888893). 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). BAMS:BS BTO:0000146 CALOHA:TS-0093 EFO:0001962 EMAPA:32678 EV:0100241 FMA:79876 MA:0000169 MBA:343 MESH:D001933 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]. 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]. TAO:0002156 UBERON:0002298 UMLS:C0006121 VHOG:0001457 ZFA:0001707 accessory medullary lamina of pallidum brain stem http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=236 lamella pallidi incompleta lamina medullaris accessoria lamina medullaris incompleta pallidi lamina pallidi incompleta 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] truncus encephali truncus encephalicus uberon choroid plexus of lateral ventricle BAMS:cplv DHBA:10601 EHDAA2:0004449 EMAPA:17769 FMA:83711 HBA:9708 MA:0000961 Part of choroid plexus contained in the lateral ventricle TAO:0001447 UBERON:0002307 UMLS:C0152289 VHOG:0001376 ZFA:0001447 chorioid plexus of cerebral hemisphere of lateral ventricle chorioid plexus of lateral ventricle choroid plexus telencephalic ventricle lateral ventricle chorioid plexus of cerebral hemisphere lateral ventricle choroid plexus uberon nucleus of brain A neural nucleus that is part of the brain. EMAPA:35185 FMA:83840 MA:0000811 UBERON:0002308 UMLS:C1706993 ZFA:0005575 brain nuclei brain nucleus uberon white matter AEO:0000139 AEO:0001011 CNS tract/commissure CNS tracts and commissures CNS white matter Cell part cluster consisting predominantly of neurites in the brain and the spinal cord[FMA:83929]. EMAPA:35927 FMA:83929 HBA:9218 MA:0001135 Multi-tissue structure comprised largely of myelinated axons.[TAO] Neural tissue consisting of myelinated axons connecting grey matter areas of the central nervous system. OpenCyc:Mx4rwOAsDZwpEbGdrcN5Y29ycA PBA:294022044 TAO:0000145 TAO:0002142 TAO:0002143 The myelination of axons by glial cells was the last major step in the evolution of cells in the vertebrate nervous system, and white-matter tracts are key to the architecture of the mammalian brain.[well established][VHOG] UBERON:0002316 UMLS:C0682708 VHOG:0001764 ZFA:0001682 neuronal white matter nlx_anat_101177 seems to have been lost in the transition from NIFGA to Neurolex substantia alba uberon white mater white matter of neuraxis white substance coelemic cavity lumen AEO:0000186 Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA]. BTO:0001707 EHDAA2:0000267 FBbt:00005060 FMA:85006 In mammals it forms the peritoneal, pleural, and pericardial cavities RETIRED_EHDAA2:0003186 TAO:0001438 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. 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]. UBERON:0000169 UBERON:0002323 UMLS:C0333343 ZFA:0001438 body cavity celom check the FMA placement here; ncit placement of body cavity here probably not correct coelom coelome coelomic cavity coelomic cavity lumen galen:BodyCavity hemocoel main body cavity space of body compartment uberon ventral body cavity notochord (...) 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] 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. AAO:0000327 Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO] BTO:0001768 CALOHA:TS-0690 EHDAA2:0001277 EHDAA:1241 EHDAA:6021 EMAPA:16191 EV:0100002 FMA:85521 GAID:1311 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. MAT:0000281 MESH:A16.254.610 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] TAO:0000135 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] UBERON:0002328 UMLS:C0028439 VHOG:0000199 VSAO:0000032 XAO:0000055 ZFA:0000135 embryonic notocord notochorda notochordal notocord relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO] uberon somite (...) 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] 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 Post-cranial axial segments which form sclerotome and dermomyotome.[AAO] 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. TAO:0000155 UBERON:0002329 UMLS:C0376449 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] VHOG:0000191 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] XAO:0000058 ZFA:0000155 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 epimere epimere mesoderm epithelial somite mesodermal cluster 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] somites somitic somitic mesoderm somitus uberon 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]. CALOHA:TS-2057 EHDAA2:0002225 EMAPA:35329 FMA:85539 MA:0002411 UBERON:0002330 UMLS:C1516995 WikipediaCategory:Exocrine_system exocrine glandular system uberon neural crest 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] 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]. 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] AAO:0010578 BTO:0001764 CALOHA:TS-0676 EHDAA2:0004419 EMAPA:32737 FMA:86666 GAID:1310 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. MAT:0000066 MESH:A16.254.600 MIAA:0000066 Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO] NC TAO:0000045 UBERON:0002342 UMLS:C0027789 VHOG:0000057 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] XAO:0000048 ZFA:0000045 consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams). crista neuralis neural crest material uberon neurectoderm (...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG] AAO:0011074 BILA:0000039 CALOHA:TS-1212 EHDAA2:0001248 EHDAA:1498 EHDAA:255 EMAPA:16073 EV:0100004 Embryonic ectoderm that gives rise to nervous tissue. FBbt:00001061 FMA:87657 MAT:0000176 MIAA:0000176 TAO:0001120 UBERON:0002346 UMLS:C1518271 VHOG:0000150 XAO:0000042 ZFA:0001120 epithelium tubi neuralis; neuroectoderma neuaral ectoderm neural ectoderm neurectodermal neuroectoderm presumptive central nervous system uberon ventral neurogenic region we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here myocardium 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 OpenCyc:Mx4ro36AFrCvEduAAAAOpmP6tw RETIRED_EHDAA2:0001220 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] TAO:0001319 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 The middle layer of the heart, consisting of cardiac muscle.[AAO] UBERON:0002349 UMLS:C0027061 VHOG:0000083 XAO:0000065 ZFA:0001319 cardiac muscle galen:Myocardium heart muscle heart myocardium muscle of heart myocardial the middle layer of the heart, comprised mainly of striated cardiac muscle fibers uberon conducting system of heart EFO:0003909 EHDAA2 divides the system from the tissue EHDAA2:0004185 EMAPA:35428 EV:0100025 FMA:9476 MA:0000094 MESH:D006329 TAO:0005063 The cardiac conduction system consists of specialized cardiomyocytes that regulate the frequency of heart beat[GO] 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] UBERON:0002350 VHOG:0001271 ZFA:0005063 cardiac conducting system cardiac conduction system cardiac impulse conducting system cardionector central conduction system complexus stimulans cordis heart conduction system impulse conducting system systema conducente cordis uberon sinoatrial node BTO:0004358 EHDAA2:0004184 EMAPA:35772 FMA:9477 GAID:561 Koch's node MA:0000097 MESH:D012849 OpenCyc:Mx4rOhejDGMcEd2AAABQjYGu0g SA nodal muscle tissue SA node TAO:0005069 The part of the cardiac conduction system that controls the timing of heart muscle contraction. It relays electrical signals to the AV node[GO]. Subdivision of conducting system of heart at the junction of the right atrium and the superior vena cava, around the sinoatrial nodal branch of right coronary artery and is continuous with the internodal tract[FMA]. UBERON:0002351 UMLS:C0037189 WP:Heart states: "The SA node is found in all amniotes but not in more primitive vertebrates. In these animals, the muscles of the heart are relatively continuous and the sinus venosus coordinates the beat which passes in a wave through the remaining chambers. Indeed, since the sinus venosus is incorporated into the right atrium in amniotes, it is likely homologous with the SA node. In teleosts, with their vestigial sinus venosus, the main centre of coordination is, instead, in the atrium.". Note however that ZFA has SA node. ZFA:0005069 cardiac pacemaker node of Keith-Flack nodus sinuatrialis nodus sinuatrialis sinoatrial node sinu-atrial node sinuatrial nodal muscle tissue sinuatrial node sinus node sinus node of Keith and Flack uberon pelvic region of trunk BTO:0001006 CALOHA:TS-2227 EFO:0002805 EMAPA:35931 EV:0100012 FMA:9578 GAID:87 MA and FMA differ in what they consider to be parts of the pelvis. MA includes ureter, urethra, urinary bladder, reproductive organs MA:0000030 MESH:A01.673 OpenCyc:Mx4rvVjiTJwpEbGdrcN5Y29ycA The lower segment of the trunk, inferioposterior to the abdomen proper, in the transition area between the trunk and the lower limbs. UBERON:0002355 UMLS:C0030797 galen:Pelvis lesser pelvis pelvic pelvic region pelvis pelvis region true pelvis uberon peritoneum A serous membrane that lines the peritoneal cavity[VHOG,modified]. AAO:0010814 An epithelium that lines the peritoneal cavity.[TAO] BTO:0001472 CALOHA:TS-2072 EV:0100087 FMA:9584 GAID:18 MA:0000449 MESH:A01.047.025.600 OpenCyc:Mx4rvjJ72ZwpEbGdrcN5Y29ycA Serous membrane that forms the lining of the abdominal cavity or the coelom. It covers most of the intra-abdominal organs, supports the abdominal organs, and serves as a conduit for their blood and lymph vessels and nerves. It is composed of a layer of mesothelium.[AAO] TAO:0005120 TODO - in ZFA is_a epithelium UBERON:0002358 UMLS:C0031153 VHOG:0001257 XAO:0000139 ZFA:0005120 galen:Peritoneum peritonaeum peritoneal todo: check MA/EMAPA. uberon meninx BTO:0000144 CALOHA:TS-1177 EFO:0000867 EMAPA:32660 EV:0100312 FMA:9589 GAID:687 In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG] MA:0001113 MAT:0000113 MESH:D008578 Membrane covering the brain and spinal cord. It is represented by a single layer in fishes, two in amphibians, reptiles and birds and three in mammals (named dura mater, arachnoid and pia mater). [TFD][VHOG] Membrane organ that surrounds the brain and the spinal cord. Not consider part of the CNS/neuraxis in FMA OpenCyc:Mx4rwDOl8JwpEbGdrcN5Y29ycA TAO:0001355 UBERON:0002360 UMLS:C0025285 VHOG:0001295 Whereas cyclostomes and fishes only have a single envelope called the primitive meninx, amphibians have two layers, consisting of an outer dura mater which is extremely dense and protective, and a pia-arachnoid or secondary meninx which is more delicate and vascular. Mammals have three meninges: pia mater (which follows all the convolutions of the brain and is the most interior), the arachnoid layer (which is delicate and sends strands to the pia mater), and the dura mater (the outer, more protective meninx). ZFA:0001355 layer of meninges meningeal meningeal layer meninx primitiva uberon 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 AEO:0000097 BTO:0000765 CALOHA:TS-2012 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 EHDAA2:0003097 EMAPA:35327 FMA:9596 GAID:34 MA:0002564 MESH:D005088 UBERON:0002365 UMLS:C0015282 ducted gland glandula exocrina uberon endocrine gland AEO:0000098 BTO:0001488 CALOHA:TS-1300 EHDAA2:0003098 EMAPA:35999 Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified]. FMA:9602 GAID:335 MA:0002563 MESH:D004702 OpenCyc:Mx4rvbkiRZwpEbGdrcN5Y29ycA UBERON:0002368 UMLS:C0014133 ductless gland ductless gland glandula endocrina glandulae endocrinae uberon adrenal gland AAO:0010551 All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] Anatomical structure which is found on the surface of the kidney and secretes various hormones including epinephrine, norephinephrine, aldosterone, corticosterone, and cortisol.[AAO] BTO:0000047 CALOHA:TS-0016 EFO:0000238 EMAPA:18426 EV:0100135 Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO]. FMA:9604 GAID:446 MA:0000116 MAT:0000071 MESH:D000311 MIAA:0000071 OpenCyc:Mx4rvXYiz5wpEbGdrcN5Y29ycA The origin of the adrenal gland is still controversial. It is thought to share the same origin as the kidney and gonads, derived from coelomic epithelium of the urogenital ridge and/or the underlying mesenchyme (Keegan and Hammer, 2002; Morohashi, 1997). We follow Kardong and state homology at the level of the cortex and medulla rather than gland as a whole UBERON:0002369 UMLS:C0001625 VHOG:0001141 XAO:0000164 adrenal adrenal capsule adrenal medulla cell atrabiliary capsule epinephric gland epinephros galen:AdrenalGland glandula adrenalis glandula suprarenalis glandula suprarenalis interrenal gland suprarenal capsule suprarenal cortex manufactures corticosteroids; suprarenal medulla manufactures epinephrine and norepinephrine; suprarenal medulla receives preganglionic sympathetic innervation from the greater thoracic splanchnic n. suprarenal gland uberon bone marrow AAO:0011007 BTO:0000141 BTO:0000829 CALOHA:TS-0087 EFO:0000868 EMAPA:32760 EV:0100046 FMA:9608 GAID:1287 In adults, marrow in large bones produces new blood cells[Wikipedia:Bone_marrow] MA:0000134 MAT:0000084 MESH:D001853 MIAA:0000084 OpenCyc:Mx4rvVm-FpwpEbGdrcN5Y29ycA TODO - create superclass for bone marrow / head kidney. both are portions of tissue in the hematopoetic system. also consider adding as subclass of zone of bone organ for consistency with FMA. See also: Leydig and epigonal organs The bone marrow is the hematopoietic organ in all vertebrates but fishes, in which hematopoiesis occurs in the kidney.[well established][VHOG] UBERON:0002371 UMLS:C0005953 VHOG:0001218 XAO:0000123 galen:BoneMarrow medulla of bone medulla ossea medulla ossium the soft tissue that fills the cavities of bones uberon tonsil BTO:0001387 CALOHA:TS-1053 EFO:0001401 EMAPA:35871 EV:0100052 FMA:9609 GAID:341 MA:0000143 MESH:A03.867.603.925 Mandel OpenCyc:Mx4rvVivrZwpEbGdrcN5Y29ycA UBERON:0002372 UMLS:C0836921 UMLS:C1519547 UMLS:C1519548 VHOG:0001139 either of the two small almond-shaped masses of lymph tissue found on either side of the oropharynx the term 'tonsil' can be ambiguous, sometimes refering specifically to the palatine tonsil, sometimes generically to include the cecal tonsils of avians. This class represents lymphoid tissue that is part of the tonsillar ring, in the mouth/throat region uberon connective tissue AAO:0000098 BTO:0000421 Bindegewebe CALOHA:TS-2009 EFO:0000952 EMAPA:35251 FMA:9640 GAID:100 MA also has set of connective tissues MA:0000011 MAT:0000301 MESH:D003238 MIAA:0000301 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] OpenCyc:Mx4rv-aBgZwpEbGdrcN5Y29ycA 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] TAO:0001641 Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance. Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO] UBERON:0002384 UMLS:C0009780 VSAO:0000017 XAO:0001017 ZFA:0001632 galen:ConnectiveTissue portion of connective tissue textus connectivus uberon muscle tissue AAO:0000306 AEO:0000122 CALOHA:TS-0642 EHDAA2:0003122 EMAPA:32715 FMA:9641 MA:0002437 MESH:D009132 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] UBERON:0002385 UMLS:C2328219 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. galen:MuscleTissue muscular tissue portion of muscle tissue textus muscularis uberon pes BTO:0000476 CALOHA:TS-0377 EFO:0003065 EHDAA2:0000546 EMAPA:17459 FMA:9664 GAID:40 MA:0000044 MESH:D005528 OpenCyc:Mx4rvVi-k5wpEbGdrcN5Y29ycA UBERON:0002387 UMLS:C0016504 VHOG:0000350 distal portion of the hind limb, including tarsal region, metatarsal region and digits. foot galen:Foot hind foot hind limb autopodium hind paw hind-paw hindfeet hindfoot hindfoot of quadruped hindlimb autopod hindlimb autopodium hindlimb distal free limb segment hindpaw pedal pes terminal segment of free lower limb uberon hematopoietic system AAO:0011002 Anatomical system that consists of the blood and blood forming tissues.[AAO] Anatomical system that is involved in the production of hematopoietic cells. BTO:0000570 Blutbildungssystem CALOHA:TS-0449 EFO:0000798 EMAPA:35402 EV:0100045 FMA:9667 GAID:1008 In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes MA:0002434 MAT:0000022 MESH:D006413 MIAA:0000022 TAO:0005023 UBERON:0002390 UMLS:C0018957 VHOG:0001624 XAO:0000122 ZFA:0005023 Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG] haematological system haematopoietic system haemopoietic system hematological system hematolymphoid system hematopoietic hemopoietic system organa haemopoietica uberon lymph BTO:0000855 CALOHA:TS-0580 EFO:0000871 ENVO:02000041 EV:0100049 FMA:9671 GAID:1186 Lymph is the fluid that is formed when interstitial fluid enters the conduits of the lymphatic system[WP]. MA:0002520 MAT:0000055 MESH:A12.207.630 MIAA:0000055 OpenCyc:Mx4rvpDOU5wpEbGdrcN5Y29ycA UBERON:0002391 UMLS:C0024202 VHOG:0001590 ZFA:0005658 galen:Lymph lympha uberon bile duct (...) the amphibian liver has characteristics in common with both fish and terrestrial vertebrates. (...) The histological structure of the liver is similar to that in other vertebrates, with hepatocytes arranged in clusters and cords separated by a meshwork of sinusoids and the presence of the traditional triad of portal venule, hepatic arteriole, and bile duct.[well established][VHOG] A duct that carries bile from the liver to the intestine. AAO:0011019 Any of the ducts that form the biliary tree, carrying bile from the liver to the small intestine. Any of the excretory ducts in the liver that convey bile between the liver and the intestine. [TFD][VHOG] BTO:0000122 CALOHA:TS-0075 EHDAA2:0000741 EMAPA:35171 EV:0100091 FMA:9706 GAID:280 MA:0000354 MESH:D001652 OpenCyc:Mx4rvdCds5wpEbGdrcN5Y29ycA TAO:0001100 UBERON:0002394 UMLS:C0005400 VHOG:0000212 XAO:0000134 ZFA:0001100 bile tube biliary duct gall duct hepatic duct uberon we place the ZFA class here as this fits its textual definition and child nodes. We may recommend a label change for ZFA parietal pleura EMAPA:16776 FMA:9733 MA:0002488 OpenCyc:Mx4rvv2Uq5wpEbGdrcN5Y29ycA The outer serous membrane of the pulmonary pleural. UBERON:0002400 UMLS:C0225777 VHOG:0001495 pleura parietalis the part of the pleura external to the visceral pleura. It lines the inner surface of the chest wall, covers the diaphragm, and is reflected over the structures occupying the middle of the thorax uberon visceral pleura EHDAA2:0002205 EMAPA:16777 Each lung is invested by an exceedingly delicate serous membrane, the pleura, which is arranged in the form of a closed invaginated sac. A portion of the serous membrane covers the surface of the lung and dips into the fissures between its lobes; it is called the pulmonary pleura (or visceral pleura). The visceral pleura is attached directly to the lungs[Wikipedia:Visceral_pleura]. FMA treats this as part of the lungs FMA:9734 MA:0002489 OpenCyc:Mx4rwNFqppwpEbGdrcN5Y29ycA The inner serous membrane of the pulmonary pleural. The visceral pleura lines the lungs. UBERON:0002401 UMLS:C0225776 VHOG:0001496 lung mesothelium lung pleura pleura pulmonalis pleura visceralis pleura visceralis (pulmonalis) pulmonary pleura pulmonary visceral pleura uberon pleural cavity BTO:0004422 EHDAA2:0001475 EMAPA:16773 EMAPA:16774 FMA:9740 GAID:95 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] MA:0000055 MESH:A01.911.800.650 OpenCyc:Mx4rwCKAppwpEbGdrcN5Y29ycA The contraction of the diaphragm creates a negative pressure within the pleural cavity which forces the lungs to expand resulting in passive exhalation and active inhalation. This breathing process can be made forceful through the contraction of the external intercostal muscles which forces the rib cage to expand and add to the negative pressure in the pleural cavity causing the lungs to fill with air. The fluid in the cavity provides lubrication and cushioning The fluid-filled cavity that lies between the visceral and parietal pleurae. UBERON:0002402 UMLS:C0178802 VHOG:0000581 cavitas pleuralis cavitum pleuralae cavitum pleurale the EHDAA2 class of the same is not equivalent. See https://github.com/obophenotype/uberon/issues/86 uberon immune system AAO:0011003 Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies. BILA:0000104 FMA:9825 GAID:328 MA:0002711 MESH:D007107 OpenCyc:Mx4rvWNkm5wpEbGdrcN5Y29ycA TAO:0001159 The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG] UBERON:0002405 UMLS:C0020962 VHOG:0001247 XAO:0003152 ZFA:0001159 uberon autonomic nervous system AAO:0000033 ANS BTO:0002507 CALOHA:TS-2001 EHDA:10095 EHDAA2:0000158 EHDAA:3767 EMAPA:16984 FMA splits this into peripheral and nervous parts; GO has ANS directly under NS; PNS is a sib FMA:65553 From comparative analyses of craniate brains, a morphotype of the brain in the earliest craniate stock can be constructed. In marked contrast to cephalochordates, the ancestral craniate morphotype had a plethora of unique features, which included a telencephalon with pallial and subpallial parts, paired olfactory bulbs with substantial projections to most or all of the telencephalic pallium, paired lateral eyes and ears, a lateral line system for both electroreception and mechanoreception, spinal cord dorsal root ganglia, and an autonomic nervous system.[well established][VHOG] GAID:706 MA:0000219 MESH:D001341 Nervous system including a portion of the central and peripheral systems and presiding over the control and coordination of the vegetative functions of the organism. It innervates smooth and cardiac muscles and glandular tissues and is responsible for many actions which are more or less automatic (e.g. secretion, vasoconstriction etc.). It consists of the sympathetic and parasympathetic nervous systems. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] Part of the peripheral nervous system which regulates involuntary functions of the body and consists of the sympathetic and parasympathetic system.[AAO] TAO:0001574 The autonomic nervous system is composed of neurons that are not under conscious control, and is comprised of two antagonistic components, the sympathetic and parasympathetic nervous systems. The autonomic nervous system regulates key functions including the activity of the cardiac (heart) muscle, smooth muscles (e.g. of the gut), and glands[GO]. UBERON:0002410 UMLS:C0004388 UMLS:C1305381 VHOG:0000396 ZFA:0001574 autonomic division of peripheral nervous system autonomic part of peripheral nervous system divisio autonomica systematis nervosi peripherici divisio autonomica systematis nervosi peripherici pars autonomica systematis nervosi peripherici peripheral autonomic nervous system uberon visceral nervous system integumental system (...) 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] AEO:0000154 BILA:0000118 CALOHA:TS-1299 CARO:0002001 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. 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 TADS:0000108 UBERON:0002416 UBERON:0007029 UMLS:C0037267 VHOG:0000403 XAO:0000176 body surface dermal system external covering of organism galen:Surface integumentary system integumentum commune organism surface surface uberon abdominal segment of trunk EMAPA:35104 FMA:259211 MA:0000021 The abdominal segment of the torso. UBERON:0002417 abdomen/pelvis/perineum lower body lower trunk lumbar region uberon cartilage tissue 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] 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 OpenCyc:Mx4rvVjeOZwpEbGdrcN5Y29ycA 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] 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] 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] Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts. Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts.[VSAO] TAO:0001501 UBERON:0002418 UMLS:C0007301 VHOG:0001207 VSAO:0000040 XAO:0000170 ZFA:0005622 cartilage cartilage tissue cartilages cartilaginous tissue chondrogenic tissue galen:Cartilage portion of cartilage tissue relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] uberon skin gland A gland that is part of a skin of body [Automatically generated definition]. EMAPA:35774 FMA:71878 MA:0000146 UBERON:0002419 check FMA, use plural for now as general class not there glandulae cutis set of skin glands skin glands skin glands set uberon hepatobiliary system AAO:0011056 CALOHA:TS-1308 EFO:0000800 EHDAA2:0000998 EHDAA:2189 EMAPA:16840 EV:0100088 MA:0000324 MAT:0000024 MIAA:0000024 System responsible for the production and movement of bile[ZFIN:curator]. TAO:0000036 The hepaticobiliary system is responsible for metabolic and catabolic processing of small molecules absorbed from the blood or gut, hormones and serum proteins, detoxification, storage of glycogen, triglycerides, metals and lipid soluble vitamins and excretion of bile. Included are the synthesis of albumin, blood coagulation factors, complement, and specific binding proteins. The parts are: liver, bile duct, gall bladder and hepatic duct [GO:0061008] The part of the digestive system that contains the liver and the biliary system UBERON:0002423 UMLS:C1711359 VHOG:0000294 XAO:0000132 ZFA:0000036 hepaticobiliary system liver and biliary system liver/biliary system uberon limb bone A bone that is part of a limb [Automatically generated definition]. EFO:0000945 MAT:0000151 MIAA:0000151 NCITA includes clavicle. MA:'limb bone' is actually a bone of limb or girdle UBERON:0002428 UMLS:C0582791 bone of extremity bone of limb free limb bone the formal definition is very inclusive, and includes sesamoids uberon endometrial gland BTO:0003433 BTO:0004518 EMAPA:29919 MA:0001726 The mucous secreting gland associated with the mucuous membrane lining the uterus. UBERON:0002451 UMLS:C1183035 endometrial gland endometrial mucuous gland endometrium gland glandulae uterinae glandulae uterinae simple or branched tubular uberon uterine gland lymphoid system EHDAA2:0001043 EHDAA:8677 FMA:74594 GAID:931 MA:0002435 MAT:0000197 MIAA:0000197 OpenCyc:Mx4rwQAKT5wpEbGdrcN5Y29ycA Part of the circulatory system which consists of a series of vessels which collect blood (exclusive of erythrocytes) which seep through capillary walls and return it to the veins.[AAO] TAO:0000385 Tetrapods have evolved distinct lymphatic systems, in which lymphatic capillaries help drain most of the tissues of the body.[well established][VHOG] The lymphatic system in vertebrates is a network of conduits that carry a clear fluid called lymph. It also includes the lymphoid tissue through which the lymph travels. Lymphoid tissue is found in many organs, particularly the lymph nodes, and in the lymphoid follicles associated with the digestive system such as the tonsils. The system also includes all the structures dedicated to the circulation and production of lymphocytes, which includes the spleen, thymus, bone marrow and the lymphoid tissue associated with the digestive system[WP]. The lymphatic system of anuran amphibians is characterized by large lymphatic sacs and two pairs of lymph hearts that return lymph into the venous circulation but no lymph vessels per se [10.1152/japplphysiol.00201.2013] The lymphatic systems of reptiles and some birds have lymph hearts, and both groups have extensive lymph vessels, but their functional role in both lymph movement and plasma volume homeostasis is almost completely unknown [10.1152/japplphysiol.00201.2013] UBERON:0002096 UBERON:0002465 UMLS:C0024235 VHOG:0000842 We follow FMA and MA in distinguishing between lymphatic system and lymphoid system, with lymhoid tissue part of the non-lymphatic component, although these terms are often used interchangeably. We assume the ZFA term lymphatic tissue actually corresponds to the broader class (e.g. ZFA lymph node in the ZFA lymphatic system). See tracker for more comments. XAO:0003199 ZFA:0000385 lymphatic circulatory system lymphatic drainage system lymphatic system lymphoid systema lymphoideum uberon autopod region BTO:0004359 EFO:0000877 EMAPA:32722 FMA:83015 MA:0002714 MAT:0000091 MIAA:0000091 Naming conventions for pod terms under discussion within phenoscape group; note that this refers to the limb segment, not just the skeleton. Terminal segment of free limb, immediately distal to the zeugopod region. The fully developed autopod consists of the autopod skeleton plus associated structures such as integument, muscle tissue, vasculature etc. The autopod is divided into mesopodial, metapodiual, and acropodial segments. Examples: human hand, mouse paw, human foot UBERON:0002470 UMLS:C0687080 autopod autopodial element autopodial limb segment autopodial segment autopodium autopodium region distal free limb segment distal segment of free limb distal segment of limb manus/pes paw paw/hand/foot/hoof pod uberon zeugopod EFO:0000878 FMA:83016 MA:0002716 MAT:0000092 MIAA:0000092 The middle free limb segment, between the autopod and stylopod segments. Includes as parts the zeugopodial skeleton. Examples: There are two types of zeugopod: forelimb zeugopod (aka forearm), hindlimb zeugopod (aka crus). There exists some controversy about which podial segments are present in some fishes, e.g. if the autopod is not newly evolved in tetrapods, there is a question as to which segments are actually present in basal vertebrate taxa.[PHENOSCAPE:curators] UBERON:0002471 epipodium middle free limb segment middle limb segment middle part of limb middle segment of free limb uberon zeugopod limb segment zeugopodial zeugopodial limb segment zeugopodium zygopod zygopodium stylopod EFO:0000879 FMA:83014 MA:0002717 MAT:0000093 MIAA:0000093 Naming conventions for pod terms under discussion within phenoscape group The proximal free limb segment. Includes as parts the stylopod skeleton. UBERON:0002472 propodium proximal free limb segment proximal part of limb proximal segment of free limb stylopodial stylopodial limb segment stylopodium uberon bone tissue CALOHA:TS-2011 EMAPA:35179 FMA:224804 MA:0002780 MESH:D001842 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. 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] UBERON:0002481 UMLS:C0391978 VSAO:0000047 XAO:0004040 ZFA:0005621 bone calcium tissue galen:BoneTissue mineralized bone tissue osseous tissue osteogenic tissue portion of bone tissue see https://github.com/obophenotype/uberon/issues/27 uberon long bone BTO:0004256 EMAPA:35503 Endochondral_ossification is an essential process during the rudimentary formation of long bones, with the exception of the clavicle[Wikipedia:Endochondral_ossification]. The medial and and lateral ends undergo EO, the mid-portion is formed by a process with features of EO & IO (the process is shared by the mandible)[ISBN:9780397517251] FMA:7474 Long bone is a limb bone that is subcylindrical and has a shaft with periosteum separating the ends of the bones. Long bones are present only in the limbs[VSAO:wd]. MA:0002802 OpenCyc:Mx4rv6axr5wpEbGdrcN5Y29ycA UBERON:0002495 UMLS:C0222647 galen:LongBone os longum uberon endochondral bone AAO:0010776 AEO:0000083 BTO:0002157 EHDAA2:0003083 FMA:24321 Replacement bone that forms within cartilage. Replacement bone that forms within cartilage.[VSAO] TAO:0001591 UBERON:0002513 VSAO:0000145 XAO:0004018 ZFA:0001591 cartilaginous bone endochondral bones https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern ossified chondrogenic bone placement in this class to be inferred some structures, e.g. in ZFA are both intramembrane and endochondral uberon elastic tissue Connective tissue composed of elastic fibers. FMA:20113 GAID:926 MA:0002853 MESH:D004547 UBERON:0002521 elastic connective tissue elastic fiber textus connectivus elasticus uberon tunica media BTO:0002011 EMAPA:36298 FMA:55590 GAID:170 MA:0002855 MESH:D017540 May be composed of smooth muscle and elastic tissue The middle layer of an artery or vein. [WP,unvetted]. UBERON:0002522 UMLS:C0162867 tunica media vasorum uberon tunica intima BTO:0002012 Bichat's tunic EMAPA:36297 FMA:55589 GAID:523 MA:0002861 MESH:D017539 The innermost layer of a blood vessel which is a lining of endothelial cells facing the lumen[Kardong]. 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] UBERON:0002523 UMLS:C0162864 intima 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 tunica intima vasorum uberon limb segment A major subdivision of a mature or developing limb, including both skeletal elements (or the mesenchyme that gives rise to the skeletal elements) and associated tissues, such as muscle, connective tissue, integument. Examples: autopod region, zeugopod region, stylopod region, metapodial region, arm region. Excludes the limb girdles. FMA has both limb segment and free limb segment, the former includes the girdles. Note that MA uses the term more generally and includes A,S,Z,S+Z(arm/leg), whereas FMA is just A,S,Z FMA:241863 MA:0002889 TODO - align this with the CARO2 class 'appendage segment'; note the FMA class does not appear to require repetition UBERON:0002529 UMLS:C1268195 extremity part free limb segment limb region region of limb segment of limb subdivision of limb uberon gland AAO:0000212 AEO:0000096 BTO:0000522 Druese 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 OpenCyc:Mx4rwP3vyJwpEbGdrcN5Y29ycA UBERON:0002530 UBERON:MIAA_0000021 UMLS:C1285092 WikipediaCategory:Glands an organ that functions as a secretory or excretory organ galen:Gland glandula glandular glandular organ uberon paired fin bud An outgrowth on the lateral trunk of the embryo that develops into a paired fin. The fin bud is divided into ectoderm and mesenchyme[cjm, modified from MP]. EFO:0003468 Embryonic surface structure that develops into a paired fin.[ZFA] MAT:0000062 MIAA:0000062 TAO:0001383 UBERON:0002531 VSAO:0000179 ZFA:0001383 fin bud fin buds uberon epiblast (generic) BTO:0004593 FMA:296704 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] 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] MAT:0000067 MIAA:0000067 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 UBERON:0002532 VHOG:0000243 blastocyst ectoblast epiblast epiblastus primitive ectoderm uberon paired fin Fin that is one of a pair located ventrally on the organism. TAO:0002278 UBERON:0002534 VSAO:0000111 ZFA:0005596 artioptérygie@fr nageoire paire@fr pelvic/pectoral fin uberon pharyngeal 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] AAO:0010359 BTO:0001785 EFO:0000959 EHDAA:571 EMAPA:16117 FMA:293015 GAID:1292 MAT:0000242 MESH:A16.254.160 MIAA:0000242 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 One of a series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO] 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. TAO:0001306 UBERON:0002539 UMLS:C0080322 VHOG:0000155 XAO:0000096 ZFA:0001306 arcus pharyngei branchial arch pharyngeal arches uberon visceral arch digit A subdivision of the autopod that has as part a series of phalanges together with associated vasculature, musculature, integument and nerves. It is continuous with the metapodial subdivision of the autopod, but does not include the metapodials. In species such as humans, fully formed digits are distinct, whereas in other species the digits may be connected by interdigital webbing, or may be completely unseparated (for example, in cetaceans). AAO:0011126 EFO:0000881 EMAPA:32725 FMA:85518 MA:0000690 MAT:0000285 MIAA:0000285 OpenCyc:Mx4rvzLD_ZwpEbGdrcN5Y29ycA Our reinterpretation of the distal fin endoskeleton of Panderichthys removes the final piece of evidence supporting the formerly popular hypothesis that tetrapod digits are wholly new structures without homologues in sarcopterygian fish fins. This hypothesis, which was based partly on the complete absence of plausible digit homologues in Panderichthys (then the closest known relative of tetrapods), has already been called into question by the discovery of digit-like radials in Tiktaalik and the fact that Hox gene expression patterns closely resembling those associated with digit formation in tetrapods occur in the distal fin skeletons of paddlefish and Australian lungfish. Our new data show that Panderichthys is not an anomaly: like Tiktaalik and other fish members of the Tetrapodomorpha, it has distal radials that can be interpreted as digit homologues.[well established][VHOG] UBERON:0002544 UMLS:C0582802 VHOG:0000944 XAO:0003032 acropodial unit digit (phalangeal portion) plus soft tissue digital galen:Digit limb digit this class represents the entire organism subdivision encompassing soft tissue as well as the underlying skeletal framework. The class represents the phalangeal part only - historically the term 'digit' has also been used to represent the unit consisting of a series of phalanges together with a metapodial bone. We may in future relabel this class to avoid confusion with this concept, but the class will continue to represent the phalangeal portion uberon cranial placode AAO:0010466 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 EFO:0001650 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. MAT:0000369 MIAA:0000369 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. UBERON:0002546 XAO:0000305 cranial placodes placode to avoid confusion, we include neurogenic placode as a subclass. Do not merge. uberon 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 MA:0002447 UBERON:0002553 cavity galen:Cavity uberon 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. FMA:55676 UBERON:0002616 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 cervical spinal cord A spinal cord segment that adjacent_to a cervical region. FMA:71166 MA:0003081 UBERON:0002726 UMLS:C0581619 UMLS:C1278837 cervical segment of spinal cord cervical segments of spinal cord [1-8] cervical spinal cord pars cervicalis medullae spinalis segmenta cervicalia medullae spinalis [1-8 uberon olfactory placode A thick plate of cells derived from the neural ectoderm in the head region of the embryo that develops into the olfactory region of the nasal cavity. AAO:0011076 EFO:0003420 EHDAA2:0001232 EHDAA:1504 EMAPA:16543 FMA:293971 Olfactory placodes are the only ectodermal placodes to produce glia, a cell type typically derived from neural crest // Note that NBK53171 classifies this as non-neurogenic TAO:0000048 UBERON:0003050 VHOG:0000186 We conclude this section by listing some of the many synapomorphies of craniates, including (...) (2) neurogenic placodes (...).[well established][VHOG] XAO:0000005 ZFA:0000048 nasal I placode nasal placode olfactory placodes placoda nasalis placoda olfactoria uberon ear vesicle AAO:0011080 BTO:0002661 EHDAA2:0001342 EMAPA:16669 Epithelial sac present beside the fifth rhombomere; forms the semicircular canals dorsally and the otolith organs ventrally, and houses the acoustico-vestibular sensory epithelia (maculae) of hair cells. Kimmel et al, 1995. (Also see Anatomical Atlas entry for ear by T. Whitfield.)[TAO] FMA:302920 OV One of the paired sacs of invaginated ectoderm that develop into the membranous labyrinth of the internal ear. [Biology_online][VHOG] TAO:0000051 The inner ear develops embryonically in all vertebrates as an invagination of the ectodermal otic placode to form an otic vesicle.[well established][VHOG] The saccular invagination of ectoderm from which the vertebrate inner ear develops[BTO]. Epithelial sac present beside the fifth rhombomere; forms the semicircular canals dorsally and the otolith organs ventrally, and houses the acoustico-vestibular sensory epithelia (maculae) of hair cells[ZFA]. epithelial sac of invaginated ectoderm formed from the otic placode that gives rise to the structures of the inner ear[MP] UBERON:0003051 UBERON:0004373 UMLS:C1518678 VHOG:0001148 XAO:0000006 ZFA:0000051 acoustic vesicle auditory vesicle otic vesicle otocyst uberon midbrain-hindbrain boundary AAO:0011064 DMBA:16810 EHDAA2:0004395 EHDAA:5789 EMAPA:32857 Lampreys also have an MHB [midbrain hindbrain boundary], expressing a similar repertoire of regulatory gene cognates as in gnathostomes.[well established][VHOG] MHB TAO:0000042 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. UBERON:0003052 VHOG:0000649 XAO:0000016 ZFA:0000042 consider adding class for organizer. Consider adding separate class for isthmus as a structure isthmic organizer territory isthmo-cerebellar region isthmus isthmus/MHB mid-hindbrain boundary mid-hindbrain junction midbrain hindbrain boundary uberon periderm 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. EHDAA2:0001846 EHDAA:6538 EVL FMA:295662 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) TAO:0001185 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] UBERON:0003055 UMLS:C1518973 VHOG:0001680 XAO:0000029 ZFA:0001185 epidermis epithelial layer epidermis outer layer epitrichium periderm relationship type change: OBO_REL:part_of ectoderm (TAO:0000016) CHANGED TO: develops_from ectoderm (UBERON:0000924)[TAO] skin periderm uberon pre-chordal neural plate (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] AAO:0011084 TAO:0007016 The portion of neural plate anterior to the mid-hindbrain junction. UBERON:0003056 VHOG:0001200 XAO:0000045 ZFA:0007016 anterior neural plate uberon chordal neural plate (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] TAO:0007017 The portion of neural plate posterior to the mid-hindbrain junction. UBERON:0003057 VHOG:0001201 XAO:0000046 ZFA:0007017 posterior neural plate uberon presomitic mesoderm AAO:0011086 EFO:0001982 EMAPA:16189 EMAPA:16752 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] PSM TAO:0000279 UBERON:0003059 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] VHOG:0000559 XAO:0000057 ZFA:0000279 presumptive somite mesoderm segmental plate somitogenic mesoderm somitomeric mesoderm uberon unsegmented mesenchyme unsegmented paraxial mesoderm pronephric duct (...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG] AAO:0011088 Duct of the embryonic kidney, present bilaterally ventral to the somites and leading to the anal region where it empties separately from, and just posterior to the anus. Kimmel et al, 1995.[TAO] In mammals, the pronephric duct is the predecessor of the Wolffian duct[WP]. TAO:0000150 The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] The pronephric duct collects the filtrate from the pronephric tubules and opens to the exterior of the pronephric kidney[GOC:mtg_kidney_jan10, http://www.ncbi.nlm.nih.gov/pubmed/15647339, XAO:0000063, ZFA:0000150] UBERON:0003060 UMLS:C1283945 VHOG:0000082 XAO:0000063 ZFA:0000150 archinephric duct ductus pronephricus pronephric ducts uberon blood island AAO:0011006 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]. EFO:0003489 EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac EHDAA:207 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] 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] TAO:0000094 TE:E5.11.2.0.0.0.4 UBERON:0003061 UMLS:C1511224 VBI VHOG:0000085 XAO:0000067 ZFA:0000094 blood islands caudal hematopoietic tissue posterior ICM posterior blood island relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO] uberon ventral blood island ventral lateral plate mesoderm prechordal plate 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 AAO:0011085 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] EHDAA2:0001493 EHDAA:181 FMA:295532 TAO:0000060 TODO - check; developmental relationship to anterior hypoblast in ZFA? 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:0003063 UBERON:0004881 VHOG:0000086 XAO:0000079 ZFA:0000060 head mesenchyme head mesoderm uberon intermediate mesoderm (...)the mesoderm of a developing vertebrate transitionally differentiates into the following sub-types: Chordamesoderm (also known as axial mesoderm) which later on gives rise to notochord in all chordates, Paraxial mesoderm, Intermediate mesoderm, Lateral plate mesoderm (reference 1); The mesoderm is present in Bilateria, therefore they are sometimes called triploblasts. Ectoderm and endoderm are usually organized as epithelial layers, while mesoderm can be epithelial or a compact, three-dimensional tissue.[well established][VHOG] AAO:0010575 EMAPA:16056 EMAPA:16178 FMA:293147 IM Mesoderm between somite and lateral plate. Traditionally thought to give rise to the urogenital system.[AAO] TAO:0001206 The intermediate mesoderm is located between the lateral mesoderm and the paraxial mesoderm. It develops into the kidney and gonads. UBERON:0003064 UMLS:C1284010 VHOG:0000087 XAO:0000085 ZFA:0001206 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'). intermediate mesenchyme intermediate plate intermediate plate mesoderm mesenchyma intermedium uberon pharyngeal arch 2 2 2nd arch 2nd pharyngeal arch 2nd visceral 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. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] AAO:0010363 EHDAA2:0000050 EHDAA:611 EMAPA:16272 FMA:293017 TAO:0001596 The second of the series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO] The second pharyngeal arch will form the hyoid apparatus. The cranial neural crest cells that populate the second pharyngeal arch emerge primarily from rhombomere 4 and will form skeletal elements. UBERON:0003066 VHOG:0000297 XAO:0000098 ZFA:0001611 arcus pharyngeus secundus branchial arch 2 hyoid arch hyoid bars in XAO, develops from visceral pouch 2 pharyngeal arch 2 pharyngeal arches 2 second branchial arch second pharyngeal arch second visceral arch uberon visceral arch 2 dorsolateral placode In summary, the collective term 'placodes' refers to some rather different structures, probably with different evolutionary origins. Some sensory placodes (at least the otic and olfactory) may have homologues in basal chordates. Even if this is so, it is apparent that they were elaborated considerably during early vertebrate evolution. Epibranchial and dorsolateral placodes appear to be new; we infer that their origin depended on the evolution of specific inductive signals.[well established][VHOG] Lateral neurogenic placodes positioned dorsal of the epibranchial placodes. TAO:0001310 The only remaining dorsolateral placode in land vertebrates is the otic/octaval placode UBERON:0003067 VHOG:0000103 XAO:0000187 ZFA:0001310 dorsolateral placodes uberon axial mesoderm AAO:0011017 EFO:0003647 TAO:0001204 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] UBERON:0003068 VHOG:0000107 XAO:0000205 ZFA:0001204 chordamesoderm uberon otic placode A cranial placode which, once specified, invaginates to form an otic cup, which eventually separates from the surface ectoderm to form the otic vesicle or otocyst, a rounded structure without appar- ent polarity. As the otic placode invaginates into a cup neuroblasts delaminate from the anterior ventral aspect of the otic epithelium to give rise to neurons of the vestibulocochlear (statoacoustic) ganglion of cranial nerve VIII[NBK] AAO:0011079 EFO:0003429 EHDAA2:0001339 EHDAA:506 EMAPA:16195 FMA:293973 Primordium of the ear epithelium before it hollows into the otic vesicle, present beside the hindbrain rudiment in the midsegmentation period. Kimmel et al, 1995. (Also see Anatomical Atlas entry for ear by T. Whitfield.)[TAO] TAO:0000138 UBERON:0003069 UMLS:C1518677 VHOG:0000235 We conclude this section by listing some of the many synapomorphies of craniates, including (...) (2) neurogenic placodes (...).[well established][VHOG] With the exception of the pigment cells of the stria vascularis and the secretory epithelium of the cochlea, which are of neural crest origin, all compo- nents of the inner ear derive from the otic placode. In most species the thickening of the ectoderm into a placode occurs in a region adjacent to rhombomere 5 (reviewed in Ohyama et al., 2007), while in amphibians the otic placode is centered onto rhombomere 4 (Ruiz i Altaba and Jessell, 1991). XAO:0000223 ZFA:0000138 auditory placode ear placode ear/otic placode octaval VIII placode octaval placode placoda otica uberon eye primordium AAO:0011038 EFO:0003541 EHDAA2:0004431 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. TAO: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. UBERON:0003071 UBERON:0005060 XAO:0000227 XAO:0004090 ZFA:0000570 eye anlage eye field eye placode occular primordium ocular primordium optic field optic placode optic placode of camera-type eye optic placodes optic primordium uberon optic cup (...) 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 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]. TAO:0001202 UBERON:0003072 UMLS:C0231109 VHOG:0000167 ZFA:0001202 eye cup eyecup ocular cup ophtalmic cup uberon lens placode (...) 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] A thickened portion of ectoderm which serves as the precursor to the lens. SOX2 and Pou2f1 are involved in its development[WP]. AAO:0011055 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) EFO:0003494 EHDAA2:0000982 EHDAA:2908 EMAPA:16672 Ectodermal primordium of the lens of the eye. Kimmel et al, 1995.[TAO] FMA:296767 TAO:0000122 UBERON:0003073 UMLS:C1517770 VHOG:0000166 XAO:0000240 ZFA:0000122 lens placodes placoda lentis uberon mesonephric duct (...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG] AAO:0000637 Anatomical structure consisting of either of a pair of longitudinal ducts which carry urine and in males, sperm, to the cloaca.[AAO] Consider adding subclasses for male and female specific variants EHDAA2:0001243 EHDAA:1590 EMAPA:16577 GAID:1315 In the male the Wolffian duct persists, and forms for example the epididymis, the ductus deferens, the ejaculatory duct, seminal vesicle and efferent ducts. Leydig's duct MESH:A16.254.940 Paired organ that connects the primitive kidney Wolffian body (or mesonephros) to the cloaca and serves as the anlage for certain male reproductive organs. the Wolffian duct is what remains of the pronephric duct after the atrophy of the pronephros[WP]. In Zebrafish: Duct of the adult kidney (mesonephros), present bilaterally ventral to the somites and leading to the cloacal chamber[ZFA]. TAO:0000546 TODO - mesonephric portion of the nephric duct The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] UBERON:0003074 UMLS:C0043204 VHOG:0000082 Wolffian duct XAO:0000242 ZFA:0000546 archinephric duct ductus mesonephricus; ductus Wolffi renal duct uberon neural plate (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] 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] AAO:0011072 BTO:0001765 DHBA:10153 DMBA:15565 EHDAA:346 EHDAA:902 EMAPA:35593 FMA:293879 RETIRED_EHDAA2:0001252 TAO:0000132 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] UBERON:0003075 UMLS:C0920623 VHOG:0000068 XAO:0000249 ZFA:0000132 lamina neuralis presumptive central nervous system uberon posterior 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] AAO:0011082 TAO:0007037 UBERON:0003076 VHOG:0001383 XAO:0000250 ZFA:0007037 uberon paraxial mesoderm AAO:0010568 EFO:0003515 EMAPA:16183 EMAPA:16751 FMA:293145 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] TAO:0000255 The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO] UBERON:0003077 UMLS:C1284009 VHOG:0000114 XAO:0000259 ZFA:0000255 mesoderma paraxiale 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) paraxial mesenchyme somitic mesoderm uberon epibranchial placode AAO:0011036 EFO:0003455 Epibranchial placodes-derived neurons innervate internal organs to transmit information such as heart rate, blood pressure, and visceral distension from the periphery to the central nervous system (Baker and Bronner-Fraser, 2001). From rostral to caudal the epibranchial placodes comprise the geniculate, petrosal, and nodose placodes, each associated in sequence with the first, second and third branchial clefts. Each placode contributes sensory neurons to cranial nerves VII (facial nerve), IX (glossopharyngeal nerve), and X (vagal nerve), respectively FMA:293968 Focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches and that produce the neuroblasts that migrate and condense to form the distal cranial ganglia. Focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches and that produce the neuroblasts that migrate and condense to form the distal cranial ganglia. [Graham_A, The_development_and_evolution_of_the_pharyngeal_arches._J_Anat_(2001)_199:_133-141][VHOG] TAO:0001294 These (the epibranchial placodes) are focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches in all vertebrates, and they produce the neuroblasts which migrate and condense to form the distal cranial ganglia: the geniculate, petrosal and nodose ganglia. (...) The one substantial difference between the vertebrate pharyngeal arches and those of the protochordates is the presence of the epibranchial placodes but the evolution of these structures was undoubtedly driven by the endoderm.[well established][VHOG] UBERON:0003078 VHOG:0000117 XAO:0000284 ZFA:0001294 epibranchial placodes in XAO this develops_from dorsolateral placode, but in NBK53175, this is a separate group uberon ventrolateral placode anterior 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] AAO:0011012 TAO:0007038 TODO - add grouping class for the anterior end of the neural tube at all stages UBERON:0003080 VHOG:0001384 XAO:0000307 ZFA:0007038 uberon lateral plate mesoderm 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] AAO:0010574 EHDAA2:0000919 EHDAA:379 EMAPA:16179 FMA:293149 LPM Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO] 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]. TAO:0000121 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] UBERON:0003081 UBERON:0006258 UMLS:C1517749 VHOG:0000118 XAO:0000311 ZFA:0000121 lateral mesoderm lateral plate lateral plate mesenchyme mesoderma laminae lateralis subclass of mesoderm in ZFA. uberon myotome A transitional population of migrating mesenchymal cells that derive from somites and that will become muscle cells. AAO:0011067 AEO:0001018 BTO:0000742 EHDAA2_RETIRED:0003431 EHDAA:1721 EHDAA:1727 EHDAA:1733 EHDAA:1739 EMAPA:32841 FMA:295658 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] Portion of the somites giving rise to body wall muscle masses. Kimmel et al, 1995.[TAO] TAO:0001056 The term 'myotome' is also used to describe the muscles served by a single nerve root / spinal segment - consider adding new class, myomere. UBERON:0003082 UMLS:C1513802 VHOG:0001244 XAO:0000315 ZFA:0001056 muscle plate myomere myomeres myotome region myotomes myotomus uberon heart primordium AAO:0011044 BTO:0001887 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] 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. TAO:0000028 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] UBERON:0003084 UMLS:C1514450 XAO:0000336 ZFA:0000028 cardiac field fused heart primordium relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO] should probably be merged with heart rudiment. uberon sclerotome AAO:0010571 AEO:0000212 EHDAA2:0003439 EMAPA:31159 FMA:295652 Skeletogenic portion of somites.[AAO] TAO:0001080 The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG] UBERON:0003089 UMLS:C0183176 VHOG:0000680 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]. XAO:0000397 ZFA:0001080 part_of somite in XAO sclerotomes sclerotomus uberon thyroid primordium AAO:0011106 BTO:0004709 EHDAA2:0002033 EHDAA:952 EMAPA:16361 In all vertebrates the thyroid arises from the ventral aspect of the second pouch Note that we follow EHDAA2 in dividing this into endoderm and mesenchyme. In this ontology we place the broad developmental relationship at this level, and include specific relationships to the pharyngeal endoderm at the level of the endoderm Portion of tissue part of the pharyngeal endoderm that is fated to become thyroid follicle[ZFIN:curator]. TAO:0001081 The initial thyroid precursor, the thyroid primordium, starts as a simple midline thickening and develops to form the thyroid diverticulum. This structure is initially hollow, although it later solidifies and becomes bilobed. The 2 lobes are located on either side of the midline and are connected via an isthmus. UBERON:0003091 UMLS:C1519512 XAO:0000444 ZFA:0001081 thyroid primordia uberon cranial neural crest AAO:0010580 Anterior most portion of the neural crest. Migrates in three highly conserved streams: mandibular, hyoid and branchial.[AAO] CNC EFO:0003645 EHDAA2:0004420 EMAPA:16091 Neural crest that is part of the head.[TAO] TAO:0001194 UBERON:0003099 VHOG:0000063 We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] XAO:0001001 ZFA:0001194 cephalic neural crest cranial NCC population crista neuralis cranialis head NCC population head crest head 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. uberon female organism AAO:0010030 BILA:0000028 CARO:0000028 FBbt:00007011 FMA:67812 Gonochoristic organism that can produce female gametes. HAO:0000028 TAO:0000303 TGMA:0001839 UBERON:0003100 XAO:0003005 ZFA:0000303 female female human body uberon male organism AAO:0010033 BILA:0000027 CARO:0000027 FBbt:00007004 FMA:67811 Gonochoristic organism that can produce male gametes. HAO:0000027 TAO:0000242 TGMA:0001838 UBERON:0003101 WBbt:0007850 XAO:0003006 ZFA:0000242 male male human body uberon surface structure AAO:0010337 AEO_RETIRED:0000010 Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism. EHDAA2_RETIRED:0003010 Organism subdivision which is the collection of anatomical structures on the body surface.[ZFA] TAO:0000292 UBERON:0003102 VSAO:0000001 XAO:0003028 ZFA:0000292 anatomical surface feature galen:SurfaceRegion surface feature surface region surface structures uberon compound organ AAO:0010015 AEO:0000024 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. BILA:0000024 CARO:0000024 EHDAA2:0003024 HAO:0000024 TADS:0000598 TAO:0000496 TGMA:0001837 UBERON:0003103 VHOG:0001723 XAO:0003041 ZFA:0000496 organ 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 uberon mesenchyme A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO] AAO:0010427 AEO:0000145 BTO:0001393 CALOHA:TS-0620 EHDAA2:0003145 EV:0100007 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] Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage[XAO]. A mesh-like cell arrangement, less compact than an epithelium[ZFA]. The part of the embryonic mesoderm, consisting of loosely packed, unspecialized cells set in a gelatinous ground substance, from which connective tissue, bone, cartilage, and the circulatory and lymphatic systems develop[BTO]. TAO:0000393 UBERON:0003104 UMLS:C0162415 VHOG:0000170 XAO:0003046 ZFA:0000393 mesenchyma mesenchymal mesenchymal tissue mesenchyme tissue portion of mesenchymal tissue portion of mesenchyme tissue the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense uberon otic region AAO:0010208 Anatomical cluster that is a posterolateral part of the cranium and structurally supports the vestibuloauditory system.[TAO] Anatomical cluster that is a posterolateral part of the neurocranium and structurally supports the vestibuloauditory system.[AAO] TAO:0000189 UBERON:0003110 UBERONREF:0000007 has this as a syn for otic capsule XAO:0003175 ZFA:0000189 cranial vault relationship loss: overlaps hyomandibular-otic region joint (TAO:0001947)[TAO] uberon pharyngeal arch 3 3 3rd arch 3rd pharyngeal arch 3rd visceral 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. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] AAO:0010365 EHDAA2:0000069 EHDAA:1080 EMAPA:16399 FMA:293029 TAO:0001598 The most anterior, or first, pharygeal/branchial arch, composed of the mandibular process, forming the posterior border of the stomodeum, and the maxillary process anterior to the stomodeum, contains the first aortic arch.[AAO] The third branchial arch contributes to the development of the hyoid bone, stylopharyngeus muscle, inferior parathyroid gland, and thymus. UBERON:0003114 VHOG:0000298 XAO:0000447 ZFA:0001606 branchial arch 1 first branchial arch first gill arch gill arch 1 in XAO, called branchial arch 1 and df VP3 third pharyngeal arch third visceral arch uberon visceral arch 3 pharyngeal arch 6 6 6th arch 6th pharyngeal arch 6th visceral 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. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] AAO:0010368 EHDAA2:0004075 EMAPA:32766 FMA:293047 TAO:0001601 The 6th pharyngeal arch. contributes to the development of the sternocleidomastoid and trapezius muscles The forth in a series of paired bars in the wall of the pharynx, within which are formed the forth aortic arch and the cartilage bar of the visceral skeleton, forms and supports the gills.[AAO] UBERON:0003117 UBERON:0004349 VHOG:0001205 XAO:0000453 ZFA:0001609 branchial arch 4 fourth branchial arch gill arch 4 sixth branchial arch sixth pharyngeal arch sixth visceral arch uberon visceral arch 6 trachea AAO:0010140 An elongated tube which carries air to and from the lungs.[AAO] BTO:0001388 CALOHA:TS-1060 EFO:0000935 EHDAA2:0002066 EHDAA:3078 EMAPA:16853 EV:0100040 FMA:7394 GAID:361 In birds, the trachea runs from the pharynx to the syrinx, from which the primary bronchi diverge. Swans have an unusually elongated trachea, part of which is coiled beneath the sternum; this may act as a resonator to amplify sound. In some birds, the cartilagenous rings are complete, and may even be ossified. In amphibians, the trachea is normally extremely short, and leads directly into the lungs, without clear primary bronchi. A longer trachea is, however found in some long-necked salamanders, and in caecilians. While there are irregular cartilagenous nodules on the amphibian trachea, these do not form the rings found in amniotes. The only vertebrate to have lungs, but no trachea, is Polypterus, in which the lungs arise directly from the pharynx. In primitive fishes and most tetrapods, the lungs of adults are usually paired. They lie ventral to the digestive tract and are connected to the outside environment through the trachea.[well established][VHOG] MA:0000441 MAT:0000137 MESH:D014132 MIAA:0000137 OpenCyc:Mx4rvViOX5wpEbGdrcN5Y29ycA The respiratory tube between the larynx and the bronchi. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] The trachea is the portion of the airway that attaches to the bronchi as it branches [GO:dph]. UBERON:0003126 UMLS:C0040578 VHOG:0000371 XAO:0000118 cartilaginous trachea in mouse 15-18 C-rings, 15-20 in human. tracheal tracheal tubule uberon vertebrate trachea windpipe cranium BTO:0001328 EFO:0000831 EHDAA:6029 EMAPA:17680 FMA:71325 MA:0000316 MAT:0000340 MIAA:0000340 OpenCyc:Mx4rvVlEyJwpEbGdrcN5Y29ycA The term cranium can be ambiguous, in that it can refer to the neurocranium, or the neurocranium and the Facial skeleton UBERON:0003128 Upper portion of the skull that excludes the mandible (when present in the organism). VHOG:0000334 bones of cranium calvarium cranial epicranial plate ossa cranii set of bones of cranium skeletal system of head skull minus mandible 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 uberon upper part of skull skull 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 Anatomical structure that is part of the head consisting entirely of cranium and mandible[WP]. BTO:0001295 CALOHA:TS-2344 EHDAA2:0000325 EMAPA:17680 FMA:46565 GAID:82 MESH:D012886 OpenCyc:Mx4rvVjOsZwpEbGdrcN5Y29ycA UBERON:0003129 UMLS:C0037303 WikipediaCategory:Skull cranial skeleton galen:Skull 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 skeletal system of head uberon reproductive organ An organ involved in reproduction EMAPA:17381 GO uses genitalia for the singular organ MA:0001752 MESH:D005835 OpenCyc:Mx4rwO39aJwpEbGdrcN5Y29ycA TGMA:0000591 UBERON:0003133 UMLS:C0017420 WBbt:0008422 genital organ genitalia reproductive system organ sex organ uberon female reproductive organ A female organ involved in reproduction EMAPA:28540 MA:0000544 UBERON:0003134 female organism reproductive organ female organism reproductive structure female organism reproductive system organ female organism sex organ female reproductive gland/organ female reproductive system organ female sex organ reproductive organ of female organism reproductive structure of female organism reproductive system organ of female organism sex organ of female organism uberon metanephric mesenchyme A mass of intermediate mesodermal cells around the distal end of the ureteric bud that gives rise to nephrons in the metanephric kidney. [TFD][VHOG] EHDAA2:0004062 EHDAA:4041 EHDAA:5021 EHDAA:5915 EMAPA:17208 EMAPA:17375 EMAPA:29990 Genes: The positional specification of the metanephrogenic mesenchyme is negatively regulated by Foxc1 and Foxc2. Next the permanent kidney forming metanephrogenic mesenchyme is specified by Hox11 genes. The competence to respond to ureteric bud inducers is regulated by WT1. GDNF secretion restricted to posterior region by Robo2 and Sprouty1. The receptors for GDNF are synthesized in the nephric ducts and later in ureteric buds [ISBN:9780878932504 "Developmental Biology"] UBERON:0003220 VHOG:0000540 When the ureteric buds emerge from the nephric duct, they enter the metanephrogenic mesenchyme. The ureteric buds induce this mesenchymal tissue to condense around them and differentiate into the nephrons of the mammalian kidney. As this mesenchyme differentiates, it tells the ureteric bud to branch and grow.[well established][VHOG] metanephric blastema metanephric mesoderm metanephrogenic mesenchyme metanephros associated mesenchyme one of the two embryological structures that give rise to the kidney (the other is the ureteric bud). The metanephric blastema mostly develops into nephrons, but can also form parts of the collecting duct system.[WP]. Metanephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the metanephros[GO] uberon phalanx CALOHA:TS-2211 EMAPA:32614 Endochondral bones that are often elongate and arranged in rows of articulating elements, and form the visible part of the digits. FMA:321661 In primates such as humans and monkeys, the thumb and big toe have two phalanges, while the other fingers and toes consist of three MA:0000304 OpenCyc:Mx4rvolPZpwpEbGdrcN5Y29ycA UBERON:0003221 UMLS:C0222682 VSAO:0000199 digit long bone galen:Phalanx long bone of digit phalange phalangeal phalanges phalanx bone uberon amniotic ectoderm BTO:0000897 EHDAA2:0000117 EHDAA:138 EMAPA:16110 UBERON:0003254 UBERON:0008359 VHOG:0000621 amnion ectoderm amnion epithelium amnionic ectoderm uberon we make the germ layer relationship develops_from, as currently the germ layers are declared to be purely embryonic. TODO - check. WP:Amnion - In the human embryo the earliest stages of the formation of the amnion have not been observed; in the youngest embryo which has been studied the amnion was already present as a closed sac, and appears in the inner cell-mass as a cavity. This cavity is roofed in by a single stratum of flattened, ectodermal cells, the amniotic ectoderm, and its floor consists of the prismatic ectoderm of the embryonic disk-the continuity between the roof and floor being established at the margin of the embryonic disk. Outside the amniotic ectoderm is a thin layer of mesoderm, which is continuous with that of the somatopleure and is connected by the body-stalk with the mesodermal lining of the chorion. endoderm of foregut An endoderm that is part of a foregut [Automatically generated definition]. EHDAA2:0004568 EHDAA:524 TODO - check UBERON:0003258 foregut endoderm uberon amniotic mesoderm A mesenchyme that is part of a amnion. EHDAA2:0000118 EHDAA:140 EMAPA:16111 EMAPA:16265 UBERON:0003262 UBERON:0003411 VHOG:0000622 amnion mesenchyme amnion mesoderm amnionic mesenchyme amnionic mesoderm mesenchyme of amnion uberon we make the germ layer relationship develops_from, as currently the germ layers are declared to be purely embryonic. TODO - check. WP:Amnion - In the human embryo the earliest stages of the formation of the amnion have not been observed; in the youngest embryo which has been studied the amnion was already present as a closed sac, and appears in the inner cell-mass as a cavity. This cavity is roofed in by a single stratum of flattened, ectodermal cells, the amniotic ectoderm, and its floor consists of the prismatic ectoderm of the embryonic disk-the continuity between the roof and floor being established at the margin of the embryonic disk. Outside the amniotic ectoderm is a thin layer of mesoderm, which is continuous with that of the somatopleure and is connected by the body-stalk with the mesodermal lining of the chorion. skeleton of lower jaw 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. AAO:0000274 EHDAA2:0004606 EHDAA:8005 EMAPA:17906 EMAPA:17910 FMA:54398 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 MA:0001906 TAO:0001273 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] The ventral portion of the first pharyngeal arch, comprising the lower jaw.[TAO] UBERON:0003278 VHOG:0000428 XAO:0003084 ZFA:0001273 lower jaw lower jaw skeleton mandible mandibles mandibular series uberon gland of foregut A gland that is part of a foregut [Automatically generated definition]. EHDAA2:0000567 EHDAA:950 EMAPA:16557 UBERON:0003294 VHOG:0000650 foregut gland uberon gland of integumental system A gland that is part of a integumental system [Automatically generated definition]. EHDAA2:0000837 EHDAA:6522 EMAPA:17758 MA:0000144 UBERON:0003297 VHOG:0000654 integumental gland integumental system gland integumentary gland uberon eye mesenchyme EHDAA2:0000485 EHDAA:2910 EMAPA:16673 Mesenchyme that is part of a developing camera-type eye. TODO - change mesenchyme relationships to precursor_of UBERON:0003314 VHOG:0001084 mesenchyme of eye uberon epithelium of mucosa A layer of epithelial cells on the surface of the mucosa. BTO:0003752 UBERON:0003350 lamina epithelialis mucosa lamina epithelialis mucosae lies on top of lamina propria uberon epithelium of hindgut An epithelium that is part of a hindgut [Automatically generated definition]. EHDAA2:0000782 EMAPA:16717 MA:0003206 UBERON:0003353 epithelial tissue of hindgut hindgut epithelial tissue hindgut epithelium uberon smooth muscle of eye EMAPA:18807 MA:0001268 Not clear if we need this and intra-ocular muscle. See issue #331. MA includes ciliary and iris smooth muscle UBERON:0003386 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 ocular smooth muscle uberon gland of gut A gland that is part of a digestive tract [Automatically generated definition]. EMAPA:18815 MA:0003202 UBERON:0003408 digestive tract gland gland of digestive tract gland of lower gastrointestinal tract gut gland lower gastrointestinal tract gland uberon pelvic appendage bud mesenchyme EHDAA2:0001035 EMAPA:16781 Mesenchyme that is part of a pelvic appendage bud. Mesoderm part of pelvic fin bud.[TAO] TAO:0001386 UBERON:0003412 ZFA:0001386 hindlimb bud mesenchyme leg mesenchyme lower limb bud mesenchyme mesoderm pelvic fin bud pelvic fin bud mesenchyme uberon thoracic cavity nerve A nerve that is located in a thoracic cavity [Automatically generated definition]. MA:0000556 UBERON:0003443 cavity of chest nerve cavity of thorax nerve chest cavity nerve consider merging with thoracic nerve. In MA the only subclass is the phrenic nerve, which arises from a cervical nerve nerve of cavity of chest nerve of cavity of thorax nerve of chest cavity nerve of pectoral cavity nerve of thoracic cavity pectoral cavity nerve uberon thoracic cavity vein A vein that is part of a thoracic cavity [Automatically generated definition]. MA:0001903 UBERON:0003479 cavity of chest vein cavity of thorax vein chest cavity vein pectoral cavity vein uberon vein of cavity of chest vein of cavity of thorax vein of chest cavity vein of pectoral cavity vein of thoracic cavity heart blood vessel A blood vessel that is part of a heart [Automatically generated definition]. EMAPA:35397 MA:0002483 UBERON:0003498 blood vessel of heart cardiac blood vessel uberon neck blood vessel A blood vessel that is part of a neck [Automatically generated definition]. MA:0000583 UBERON:0003502 blood vessel of neck blood vessel of neck (volume) neck (volume) blood vessel uberon arterial blood vessel A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta. EMAPA:35144 MA:0000061 UBERON:0003509 only in MA - supertype of artery, arteriole, aorta. uberon trunk blood vessel A blood vessel that is part of a trunk [Automatically generated definition]. MA:0000511 UBERON:0003513 blood vessel of torso blood vessel of trunk torso blood vessel uberon thoracic cavity blood vessel A blood vessel that is part of a thoracic cavity [Automatically generated definition]. MA:0000554 UBERON:0003519 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 brain gray matter A gray matter that is part of a brain [Automatically generated definition]. EMAPA:35184 MA:0000810 UBERON:0003528 UMLS:C1707348 brain grey matter brain grey substance gray matter of brain grey matter of brain grey substance of brain uberon hindlimb skin A zone of skin that is part of a hindlimb [Automatically generated definition]. EMAPA:32620 FMA:23102 MA:0000665 TODO - check free limb vs pelvic complex UBERON:0003532 UMLS:C0222268 hind limb skin inferior member skin lower extremity skin lower limb skin skin of hind limb skin of hindlimb skin of inferior member skin of lower extremity skin of lower limb uberon brain white matter EMAPA:35187 HBA:9218 MA:0000820 The regions of the brain that are largely or entirely composed of myelinated nerve cell axons and contain few or no neural cell bodies or dendrites. UBERON:0003544 UMLS:C1706995 brain white matter of neuraxis brain white substance uberon white matter of brain white matter of neuraxis of brain white substance of brain respiratory system connective tissue A portion of connective tissue that is part of a respiratory system [Automatically generated definition]. EMAPA:35968 EMAPA:35977 MA:0001814 UBERON:0003570 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 lower respiratory tract connective tissue A portion of connective tissue that is part of a lower respiratory tract [Automatically generated definition]. MA:0002409 UBERON:0003580 connective tissue of lower respiratory tract lower respiratory tract portion of connective tissue lower respiratory tract textus connectivus portion of connective tissue of lower respiratory tract textus connectivus of lower respiratory tract uberon trunk connective tissue A portion of connective tissue that is part of a trunk [Automatically generated definition]. MA:0000513 UBERON:0003586 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 limb long bone A long bone that is part of a limb [Automatically generated definition]. EMAPA:35495 MA:0000298 UBERON:0003606 long bone of limb uberon limb joint Any joint that is part of a (free) limb. EMAPA:36501 FMA:321558 MA:0000691 Most limb joints are synovial, but a few such as the tibiofibular joints are syndesmoses UBERON:0003657 galen:LimbJoint joint of limb joint of limb skeletal system skeletal limb joint uberon abdominal cavity EFO:0000213 EMAPA:36505 FMA:12266 GAID:17 MA:0003057 MESH:A01.047.025 OpenCyc:Mx4rvZR1TJwpEbGdrcN5Y29ycA The part of the ventral body cavity that is within the abdomen proper (excluding the pelvic cavity). UBERON:0003684 UMLS:C0230168 cavitas abdominis cavity of abdominal compartment cavity of compartment of abdomen galen:AbdominalCavity in FMA this contains the pelvic cavity, but this is inconsistent with the concept of abdominopelvic cavity space of abdominal compartment uberon abdominal wall FMA:10429 FMA:259054 GAID:26 MESH:A01.047.050 The tissues that surround the organs that are present within the abdominal cavity. The abdominal wall tissue is composed of layers of fat, parietal peritoneum, fascia, and muscles. UBERON:0003697 UMLS:C0836916 abdominal wall proper layers of the abdominal wall paries abdominalis paries abdominalis uberon wall of abdomen wall of abdomen proper extrahepatic bile duct FMA:14678 GAID:281 MA:0002659 MESH:D017734 Passages external to the liver for the conveyance of bile. These include the common bile duct and the common hepatic duct. UBERON:0003703 UMLS:C0206187 bile duct extrahepatic part extrahepatic biliary system includes all the cystic duct, all the common bile duct and the extrahapetic part of the hepatic duct uberon intrahepatic bile duct Duct that collects bile from the bile ductules and connects to the extrahepatic bile duct.[TAO] FMA:15766 GAID:287 MA:0001630 MESH:D001653 Passages within the liver for the conveyance of bile. Includes right and left hepatic ducts even though these may join outside the liver to form the common hepatic duct. TAO:0005169 UBERON:0003704 UMLS:C0005401 ZFA:0005169 bile duct intrahepatic part includes the hepatic duct of the caudate lobe, and the intra- and inter- lobar bile ducts intrahepatic biliary system uberon neural tissue AAO:0000325 AEO:0000123 EHDAA2:0003123 FMA definition includes vasculature FMA:9642 GAID:609 MESH:D009417 One of the four types of tissue in traditional classifications. Cells forming the brain, spinal cord and peripheral nervous system.[AAO] OpenCyc:Mx4rVmfYCsQ_QdeM_bFAeS8NRQ Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature. UBERON:0003714 UMLS:C0027757 nerve tissue nervous tissue portion of neural tissue uberon recurrent laryngeal nerve A branch of the vagus nerve that supplies motor function and sensation to the larynx (voice box). It travels within the endoneurium. It is the nerve of the 6th Branchial Arch. AAO:0010754 Branch of the vagus nerve that separates from the vagus well postcranially, then continues anteriorly to innervate the larynx[AAO:0010754]. FMA:6246 GAID:804 MESH:D012009 UBERON:0003716 VHOG:0001347 inferior laryngeal nerve nervus laryngeus recurrens ramus recurrens recurrent laryngeal nerve from vagus nerve recurrent nerve uberon vagus X nerve recurrent laryngeal branch intercostal nerve EMAPA:18227 FMA:6028 GAID:858 MESH:D007367 The intercostal nerves are the anterior divisions (rami anteriores; ventral divisions) of the thoracic spinal nerves from T1 to T11. Each nerve is connected with the adjoining ganglion of the sympathetic trunk by a gray and a white ramus communicans. The intercostal nerves are distributed chiefly to the thoracic pleura and abdominal peritoneum and differ from the anterior divisions of the other spinal nerves in that each pursues an independent course without plexus formation. The first two nerves supply fibers to the upper limb in addition to their thoracic branches; the next four are limited in their distribution to the parietes of the thorax; the lower five supply the parietes of the thorax and abdomen. The 7th intercostal nerve terminates at the xyphoid process, at the lower end of the sternum. The 10th intercostal nerve terminates at the umbilicus. The twelfth thoracic is distributed to the abdominal wall and groin. [WP,unvetted]. UBERON:0003727 UMLS:C1285089 anterior ramus of thoracic nerve anterior ramus of thoracic spinal nerve nervi intercostales ramus anterior, nervus thoracicus thoracic anterior ramus uberon ventral ramus of thoracic spinal nerve prostate bud A region of the fetal urogenital sinus epithelium destined to become the prostate[GO]. AR activation releases instructive signals from UGM that acts on UGS epithelium (UGE) to stimulate cell proliferation, form prostate ductal progenitors (prostatic buds), and regulate cell adhesion dynamics to permit prostatic bud outgrowth. There are three phases of prostatic budding: (1) the specification phase, when instructive developmental cues define where buds will form in the UGS, (2) the initiation phase, when prostatic buds begin to form, and (3) the elongation phase, when proliferation, cell adhesion, and cell migration coordinate outgrowth of prostatic buds into UGM. Timing of prostatic bud formation and the quantity and pattern of buds that are formed in the UGS are strictly regulated [3, 4]. The position of prostatic buds as they emerge from the UGS in utero determines the arrangement of prostate ducts in adulthood.[PMID:18977204] EMAPA:36141 UBERON:0003820 prostate ductal progenitor prostate gland bud prostate primordium prostatic bud uberon metapodium bone A bone of the metapodial skeleton MA:0000301 UBERON:0003821 metacarpal or metatarsal bone metacarpal/metatarsal metacarpal/metatarsal bone metapodi bone metapodial bone metapodium bone uberon thoracic segment muscle Any muscle organ that is part of a thorax [Automatically generated definition]. MA:0000561 UBERON:0003830 muscle organ of thorax thorax muscle organ uberon upper body muscle respiratory system muscle Any muscle organ that is part of a respiratory system [Automatically generated definition]. EMAPA:35733 MA:0001828 UBERON:0003831 apparatus respiratorius muscle organ muscle organ of apparatus respiratorius muscle organ of respiratory system respiratory system muscle organ uberon thoracic segment blood vessel A blood vessel that is part of a thorax [Automatically generated definition]. MA:0000558 UBERON:0003834 blood vessel of thorax thorax blood vessel uberon upper body blood vessel thoracic segment connective tissue A portion of connective tissue that is part of a thorax [Automatically generated definition]. MA:0000560 UBERON:0003837 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 autopod joint A limb joint that is part of an autopod [Automatically generated definition]. EMAPA:35160 MA:0002715 UBERON:0003841 autopod joint of limb autopod limb joint distal free limb segment joint of limb distal free limb segment limb joint joint of limb of autopod joint of limb of distal free limb segment limb joint of autopod limb joint of distal free limb segment paw joint uberon neural tube lumen (...) 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:0011073 An anatomical space that surrounded_by a neural tube. EHDAA2:0001269 EHDAA:2889 EHDAA:914 EMAPA:16167 EMAPA:16533 UBERON:0003842 UBERON:0005713 VHOG:0001119 XAO:0000252 cavity of neural tube central lumen lumen of neural tube neural lumen neural tube neural lumen neurocoel prosencoel uberon mesencephalic neural crest A neural crest that has_potential_to_developmentally_contribute_to a midbrain. EFO:0003591 EHDAA2:0001101 EHDAA:360 TAO:0000935 UBERON:0003849 VHOG:0000796 We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] ZFA:0000935 mesencephalic neural crest neural crest midbrain uberon telencephalon neural crest A neural crest that has_potential_to_developmentally_contribute_to a telencephalon. Cranial neural crest that is part of the telencephalon.[TAO] EFO:0003574 RETIRED_EHDAA2:0001991 TAO:0000812 UBERON:0003850 VHOG:0000799 We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] ZFA:0000812 neural crest telencephalon uberon rhombencephalon neural crest A neural crest that has_potential_to_developmentally_contribute_to a hindbrain. Cranial neural crest that is part of the hindbrain.[TAO] EHDAA2:0001628 EHDAA:362 EMAPA:35747 TAO:0007063 UBERON:0003852 VHOG:0001210 We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] ZFA:0007063 neural crest hindbrain rhombencephalic neural crest rhombomere neural crest uberon spinal cord neural crest A neural crest that has_potential_to_developmentally_contribute_to a spinal cord. EHDAA:696 EMAPA:16163 EMAPA:16529 EMAPA:16881 UBERON:0003853 VHOG:0001006 We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)[well established][VHOG] neural crest spinal cord spinal neural crest uberon presumptive ganglion A presumptive structure that has the potential to develop into a ganglion. UBERON:0003869 uberon future coelemic cavity lumen An anatomical cavity that has the potential to develop into a coelemic cavity lumen. UBERON:0003886 body cavity precursor uberon intraembryonic coelom (...) 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 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 UBERON:0003887 UMLS:C1512940 VHOG:0000316 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 somatic coelom uberon fallopian tube CALOHA:TS-0732 EHDAA2:0000504 EMAPA:18984 EMAPA:35660 EV:0100112 FMA:18245 GAID:365 Homologous to appendix testis Initial section of the oviduct through which the ova pass from the ovary to the uterus MA:0000385 MESH:D005187 OpenCyc:Mx4rvViVeZwpEbGdrcN5Y29ycA UBERON:0003889 UMLS:C0015560 fallopian tubes female paramesonephric duct galen:FallopianTube mammalian oviduct paramesonephric duct of female salpinges salpinx tuba uterina uberon uterine tube (sensu Mammalia) Mullerian duct AAO:0010141 EHDAA2:0004048 EMAPA:27665 Either of the paired embryonic ducts developing into the uterine tubes, uterus, and vagina in the female and becoming largely obliterated in the male. [TFD][VHOG] GAID:1309 In females, the archinephric (mesonephric) ducts tend to function only within the urinary systems. The muellerian duct arises embryologically next to the archinephric (wolffian) duct. In males, the muellerian duct regresses if it appears at all, but in females, the muellerian ducts become the oviducts of the reproductive system.[well established][VHOG] MESH:A16.254.570 Muellerian duct Müllerian duct RETIRED_EHDAA2:0001399 Sertoli cells secrete anti-Mullerian hormone (AMH) inducing the demise of this duct Transient developmental organ which gives rise to oviducts in female (documented to persist in some male frogs).[AAO] UBERON:0003890 UBERON:0005318 UMLS:C0026732 VHOG:0001199 XAO:0000330 ductus paramesonephricus early paramesonephric duct paired ducts of the embryo that run down the lateral sides of the urogenital ridge and terminate at the mullerian eminence in the primitive urogenital sinus. In the female, they will develop to form the fallopian tubes, uterus, and the upper portion of the vagina; in the male, they are lost. These ducts are made of tissue of mesodermal origin[WP]. develops either by lengthwise splitting of the archinephric duct (in chondrichthyans and some amphibians) or by a elongated invagination of the coelomic epithelium (other vertebrates) In males, the oviducts regress. The cranial end of the oviduct maintains an opening into the coelom (which primitively may have been the anteriormost coelomic funnels connecting the nephrocoel with the coelom). This opening is the ostium tubae[USM]. paramesonephric duct uberon liver primordium A small endodermal thickening in the foregut adjacent to the transverse septum. Invaginates forming the hepatic diverticulum. AAO:0011058 BTO:0003391 EFO:0002577 EFO:0003428 EHDAA2:0000744 EHDAA:973 EMAPA:16847 TAO:0000124 UBERON:0003894 UMLS:C0734013 UMLS:C1514451 XAO:0003266 ZFA:0000124 consider adding further subdivisions of the endoderm, e.g. ventral foregut. Note we place two EFO classes here, it's not clear how they differ embryological hepatic plate hepatic plate liver bud liver endoderm primordium of the liver uberon retinal neural layer (...) 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 TAO:0000046 The part of the retina that contains neurons and photoreceptor cells[GO]. UBERON:0003902 UMLS:C1518263 VHOG:0000535 XAO:0003216 ZFA:0000046 neural layer of retina neural retina neural retinal epithelium neuroretina stratum nervosum (retina) stratum nervosum retinae uberon epithelial tube AEO:0000114 EHDAA2:0003114 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. FBbt:00007474 UBERON:0003914 contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers epithelial or endothelial tube uberon endothelial tube Any endothelium that has the quality of being cylindrical [Automatically generated definition]. UBERON:0003915 uberon kidney mesenchyme Kidney mesenchyme is the tissue made up of loosely connected mesenchymal cells in the kidney[GO]. UBERON:0003918 check this mesenchyme of kidney uberon venous blood vessel A blood vessel that carries blood from the capillaries toward the heart Compare to: vein EMAPA:35932 FMA:86188 MA:0000066 UBERON:0003920 segment of venous tree organ uberon venous tree organ segment pancreas primordium EFO:0002579 EFO:0003434 EHDAA2:0001382 EHDAA:2163 EMAPA:17066 FMA:79792 TAO:0000254 UBERON:0003921 XAO:0001101 ZFA:0000254 embryonic structure that develops into pancreatic bud. in EHDAA2 this has dorsal and ventral primordia as parts. the buds are part of the primordium, with the ducts developing from the buds; only parenchyma and ducts have contribution from buds pancreatic anlage pancreatic endoderm pancreatic primordium primordial pancreas revisit after standardizing terms 'primordium', 'anlagen', 'bud' uberon pancreatic epithelial bud EFO:0003470 EMAPA:35645 TAO:0001390 The embryonic pancreas develops from two separate anlagen in the foregut epithelium, one dorsal and two ventral pancreatic buds[PMID]. UBERON:0003922 UMLS:C1283285 ZFA:0001390 pancreas epithelium pancreatic anlage pancreatic bud pancreatic buds uberon dorsal pancreatic bud AAO:0011031 EFO:0003465 EHDAA2:0001385 EMAPA:17067 In chick, Xenopus laevis, and the teleost fish Medaka, the pancreas develops from three buds that emerge from the gut tube, two from its ventral aspect, and one from its dorsal aspect. In mouse, although there are initially three buds that arise from the gut tube at the point of contact between the endoderm and the vasculature, the pancreas develops from only two of these buds, one dorsal and one ventral. (...) In this study, we use a transgenic zebrafish line (...). We provide evidence for the existence of two distinct pancreatic anlagen - a ventral anterior bud and a dorsal posterior bud - that join to form the definitive pancreas (reference 1); The pancreas develops from the fusion of distinct endoderm-derived dorsal and ventral diverticula. In humans, by day 35 of development, the ventral pancreatic bud begins to migrate backwards and comes into contact and eventually fuses with the dorsal pancreatic bud during the sixth week of development (reference 2).[well established][VHOG] TAO:0001370 The pancreatic bud that gives rise to the accessory pancreatic duct.[AAO] UBERON:0003923 VHOG:0001428 XAO:0000467 ZFA:0001370 dorsal pancreas anlage dorsal pancreatic anlage pancreas dorsal primordium duct bud pancreas primordium dorsal bud pancreatic bud that gives rise to the accessory pancreatic duct. posterior pancreatic anlage posterior pancreatic bud primary pancreatic bud uberon ventral pancreatic bud AAO:0011111 EFO:0003464 EHDAA2:0001389 EMAPA:17256 In chick, Xenopus laevis, and the teleost fish Medaka, the pancreas develops from three buds that emerge from the gut tube, two from its ventral aspect, and one from its dorsal aspect. In mouse, although there are initially three buds that arise from the gut tube at the point of contact between the endoderm and the vasculature, the pancreas develops from only two of these buds, one dorsal and one ventral. (...) In this study, we use a transgenic zebrafish line (...). We provide evidence for the existence of two distinct pancreatic anlagen - a ventral anterior bud and a dorsal posterior bud - that join to form the definitive pancreas (reference 1); The pancreas develops from the fusion of distinct endoderm-derived dorsal and ventral diverticula. In humans, by day 35 of development, the ventral pancreatic bud begins to migrate backwards and comes into contact and eventually fuses with the dorsal pancreatic bud during the sixth week of development (reference 2).[well established][VHOG] TAO:0001369 The ventral pancreatic bud becomes the head and uncinate process, and comes from the hepatic diverticulum[WP] UBERON:0003924 VHOG:0001429 XAO:0001103 ZFA:0001369 anterior pancreatic anlage anterior pancreatic bud pancreas primordium ventral bud pancreas ventral primordium duct bud pancreatic bud that gives rise to the major pancreatic duct. the ventral pancreas and liver are derived from a common precursor cell population[PMID:16417468]. TODO - add this relationship. uberon ventral pancreas anlage ventral pancreatic anlage digestive system duct A duct that is part of a digestive system [Automatically generated definition]. TAO:0005162 UBERON:0003928 ZFA:0005162 duct of digestive system duct of gastrointestinal system gastrointestinal system duct uberon digestive tract epithelium An epithelium that lines the lumen of the digestive tract. BTO:0000956 EHDAA2:0004567 EMAPA:32928 Epithelium lining the lumen of the gut.[TAO] MA:0003201 TAO:0005123 UBERON:0003929 UMLS:C0836205 XAO:0003200 ZFA:0005123 alimentary tract epithelium 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 sex gland Any of the organized aggregations of cells that function as secretory or excretory organs and are associated with reproduction. MA:0001751 UBERON:0003937 genitalia gland gland of genitalia gland of reproductive system reproductive gland reproductive system gland uberon brain ventricle/choroid plexus TODO - check relationship between CP and BV. If this is part of then this class should be obsoleted The brain ventricles or their associated choroid plexuses UBERON:0003947 uberon internal female genitalia BTO:0003099 FMA:45654 TODO: Relabel. Make distinct organ class. See https://github.com/obophenotype/uberon/issues/547 The internal feminine genital organs, including the ovaries, uterine tubes, uterus, uterine cervix, and vagina. UBERON:0003975 female internal genitalia internal female genital organ internal genitalia of female reproductive system organa genitalia feminina interna uberon valve EHDAA2:0004046 EHDAA:1892 EHDAA:4406 FMA:67611 OpenCyc:Mx4rvqiwE5wpEbGdrcN5Y29ycA UBERON:0003978 anatomical valve galen:Valve uberon valvular uterine tube infundibulum EMAPA:29897 FMA:18307 The funnel-like expansion of the abdominal extremity of the uterine tube[MP] The third part of the uterine tube is the infundibulum. It terminates with the ostium of Fallopian tube, surrounded by fimbriae, one of which is attached to the ovary[Wikipedia:Infundibulum_of_uterine_tube]. UBERON:0003984 infundibulum infundibulum of fallopian tube infundibulum of oviduct infundibulum of uterine tube infundibulum tubae uterinae uberon dermatome A transitional population of migrating mesenchymal cells that derive from somites and that will become dermal cells. AAO:0011028 AEO:0001017 EHDAA2_RETIRED:0003428 EHDAA:1719 EHDAA:1725 EHDAA:1731 EHDAA:1737 EMAPA:32838 FMA:295656 Not to be confused with 'dermatome segment of skin'. UBERON:0004016 UMLS:C0180383 XAO:0000220 cutis plate dermatomal mesenchyme epimere mesoderm mesenchyma dermatomiale uberon germinal neuroepithelium 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] The single layer of epithelial cells that lines the early neural tube and develops into the nervous system and into the neural crest cells UBERON:0004022 germinal neuroepithelial layer germinal neuroepithelium original neural tube uberon biliary ductule BTO:0002840 In ZFA, Digestive system duct that collects bile from the canaliculus and transports bile through the liver -- (check if the same) // The smallest and the most peripheral branches of the biliary tree consist of a portal part (portal ductule) and an intralobular part (intralobular ductule) One of the fine terminal elements of the bile duct system, leaving the portal canal, and pursuing a course at the periphery of a lobule of the liver[BTO]. the excretory ducts of the liver that connect the interlobular ductules to the right or left hepatic duct[MP] TAO:0005164 UBERON:0004058 ZFA:0005164 bile capillary bile ductule biliary ductule biliary ductule cholangiole ductuli biliferi terminal cholangiole uberon neural tube ventricular layer EMAPA:17152 EMAPA:35362 EMAPA_RETIRED:16783 MA:0003193 The layer of undifferentiated, proliferating cells that line the neural tube lumen The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium UBERON:0004060 consider merging with 'ventricular zone'; note that the MA class probably does not belong here, as this is an embryonic structure ependymal layer neural tube ependymal layer neural tube ependymal zone neural tube ventricular germinal zone neural tube ventricular zone uberon neural tube mantle layer EMAPA:17148 EMAPA:35360 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. UBERON:0004061 future brain marginal layer neural tube intermediate zone uberon neural tube marginal layer EMAPA:17151 The outermost layer of the neural tube that consists of axons from the developing mantle layer and will form the white matter UBERON:0004062 brain marginal zone neural tube marginal zone uberon neural tube basal plate AAO:0010561 EFO:0001904 The region of the mantle layer of the neural tube that lies ventral to the sulcus limitans and contains primarily motor neurons and interneurons. UBERON:0004064 UMLS:C1511061 basal plate basal plate of neural tube motor part of neural tube spinal cord basal plate uberon ventral part of neural tube brain ventricle BTO:0001442 EFO:0001914 EMAPA:32674 EMAPA:32675 FMA draws the distinction between e.g. 'fourth ventricle' and 'cavity of fourth ventricle'. The latter is a cavity, and part of the former, which is a region. The superclass of 'fourth ventricle' is_a 'region of ventricular system of the brain'. We place this class here, although it is not equivalent to ventricles, as it includes ventricle bodies. FMA:78447 HBA:9418 MA:0000818 MESH:D002552 OpenCyc:Mx4rvmTY65wpEbGdrcN5Y29ycA Organ cavity of the brain which consists of the lateral ventricles, the third and fourth ventricles and the cerebral aqueduct[NIFSTD:birnlex_1356]. UBERON:0004086 UMLS:C0007799 brain ventricles cerebral ventricle one of the system of communicating cavities in the brain that are continuous with the central canal of the spinal cord, that like it are derived from the medullary canal of the embryo, that are lined with an epithelial ependyma, and that contain a serous fluid region of ventricular system of brain uberon vena cava AAO:0010215 Any of the veins that carries deoxygenated blood from a part of the body into the right atrium of the heart. BTO:0001438 EMAPA:18415 FMA:321896 GAID:547 MA:0000068 MESH:D014684 OpenCyc:Mx4rkJQ4U6gEEdudWQACs5b6Bw UBERON:0004087 UMLS:C0042460 caval vein uberon venae cavae orbital region FMA:260119 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 UBERON:0004088 content of orbital part of eye eye region in HP covers eyelid, eyebrow. 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 ocular and peri-ocular region ocular region orbital content orbital part of eye orbital part of face uberon midface EMAPA:32806 FMA:285406 MA:0001910 The middle of the face including the nose and its associated bony structures[MW]. UBERON:0004089 lower face midface/lower face midfacial snout this class is currently a union of the snout (e.g. in mouse), the midface and the lower face. Note that in MA, snout includes the whole jaw and should thus be more alike the lower face than the midface, so its placement here is not strictly accurate. In future we might introduce specific classes for each of these, and include the full parthood relationships. if this is done, then care should be taken to preserve inferences such as an abnormality of the lower face being an abnormality of the midface. uberon anatomical conduit 2 2 AEO:0000080 Any tube, opening or passage that connects two distinct anatomical spaces. EHDAA2:0003080 FMA has both conduit and conduit space. In EHDAA2 this is a surface feature FMA:242873 UBERON:0004111 foramen foramina opening ostia ostium uberon pharyngeal pouch 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] AAO:0011113 An internal pocketing of pharyngeal endoderm that contacts a region of ectoderm (a pharyngeal cleft) and interdigitates in the anterior and posterior directions with the pharyngeal arches. EFO:0003627 EHDAA:1086 EHDAA:1669 EHDAA:579 EHDAA:617 EMAPA also includes a distinct pouch endoderm EMAPA:32752 FMA:293063 Outpocketings of pharyngeal endoderm that interdigitate with the neural crest derived pharyngeal arches. The pouches later fuse with the surface ectoderm to form the gill slits. Crump et al, 2004.[TAO] TAO:0001106 The pouches are polarized structures. For example, whereas the rostral half of each pouch expresses Bmp-7, the caudal half expresses FGF-8 and the dorsal aspect of each pouch is marked via its expression of Pax-1. each pouch has an individual sense of identity. Shh expression is a prominent early feature of the caudal endoderm of the second arch, and individual pouches mark the anterior limits of expression of Hox genes within the pharyngeal endoderm; Hox-a2 has a rostral boundary at the second pouch, Hox-a3 at the third pouch and Hox-a4 at the most caudal pouch[PMID:16313389] UBERON:0004117 UMLS:C0231067 VHOG:0001203 XAO:0000282 ZFA:0001106 branchial pouch pharyngeal pouches uberon visceral pouch visceral pouches endoderm-derived structure An anatomical structure that develops (entirely or partially) from the endoderm. Grouping term for query purposes UBERON:0004119 uberon mesoderm-derived structure An anatomical structure that develops (entirely or partially) from the mesoderm. Grouping term for query purposes UBERON:0004120 uberon ectoderm-derived structure An anatomical structure that develops (entirely or partially) from the ectoderm. Grouping term for query purposes UBERON:0004121 uberon genitourinary system AAO:0000624 Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction. Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.[AAO] BILA:0000122 BTO:0003091 EFO:0003864 EHDAA:1013 EMAPA:16367 EV:0100094 FMA:280610 GAID:362 GU tract Kidneys and gonads (of vertebrates) develop from adjacent tissues, and after the excretory or urinary ducts have developed, the reproductive system usually taps into them or their derivatives.[well established][VHOG] MESH:D014566 OpenCyc:Mx4rQRpVMgAKEdyHxgDggVfs8g UBERON:0004122 UG tract UMLS:C0042066 Urogenitalsystem VHOG:0000286 XAO:0000140 galen:GenitoUrinarySystem genito-urinary system genitourinary genitourinary tract relationship type change: differentiates_from intermediate mesoderm (AAO:0010575) CHANGED TO: develops_from intermediate mesoderm (UBERON:0003064)[AAO] uberon urogenital urogenital system urogenital tract optic 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.[well established][VHOG] AAO:0011039 EHDAA2:0001320 EMAPA:16540 FMA:293357 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] TAO:0000050 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]. UBERON:0004128 UMLS:C0231106 VHOG:0000165 XAO:0000228 ZFA:0000050 evagination eye vesicle ocular vesicle optic vesicles uberon cardiogenic plate (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 TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO The first recognizable structure derived from the heart field UBERON:0004139 VHOG:0000975 cardiac crescent cardiogenic crescent heart rudiment myocardial plate uberon primary heart field 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. FHF PHF UBERON:0004140 XAO:0004185 first heart field heart field primary heart field 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] uberon heart tube AAO:0010411 An epithelial tube that will give rise to the mature heart. EFO:0003526 EMAPA:32685 TAO:0000360 UBERON:0004141 XAO:0000337 ZFA:0000360 embryonic heart tube endocardial heart tube endocardial tube 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. uberon outflow tract Depending on the species, attached at the cardiac outflow are described the conus arteriosus, the truncus arteriosus and, or the bulbus arteriosus. At the distal limit of these outflow structures, but lying outside the pericardial cavity, is the ventral aorta[PMID:20735616] EHDAA2:0001351 EHDAA:464 EHDAA:798 EMAPA:16229 EMAPA:16346 MA:0000100 The outflow tract is the portion of the heart through which blood flows into the arteries UBERON:0004145 VHOG:0000670 XAO:0004139 arterial (outflow) pole cardiac outflow tract heart outflow tract uberon cardiac chamber A cardiac chamber surrounds an enclosed cavity within the heart FMA:7095 OpenCyc:Mx4rmexpjPdAEduAAAAOpmP6tw UBERON:0004151 chamber of heart 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 heart chamber uberon septum transversum A thick plate of mesodermal tissue that occupies the space between the thoracic cavity and yolk stalk in the early embryo, forming a transverse partition partially separating the coelomic cavity into thoracic and abdominal portions. It gives rise to the central tendon of the diaphragm. [TFD][VHOG] 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]. EHDAA2:0001829 EHDAA:736 EMAPA:16318 FMA:295593 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. UBERON:0004161 UMLS:C0231004 VHOG:0000019 in EHDAA2 this is divided into mesenchymal portion and hepatic diverticulum transverse septum uberon internal genitalia FMA:45652 TODO: make a subdivision of reproductive system. Relabel. See https://github.com/obophenotype/uberon/issues/547 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 UBERON:0004175 internal genitalia internal genitals internal reproductive organ internal sex organ uberon external genitalia FMA:45643 TODO: make a subdivision of reproductive system. Relabel. See https://github.com/obophenotype/uberon/issues/547 The external genitalia are the outer sex organs, such as the penis or vulva in mammals UBERON:0004176 external genitalia external reproductive organ external sex organ uberon endodermal part of digestive tract A portions of the gut that is derived from endoderm. EMAPA:32930 UBERON:0004185 endodermal gut gut endoderm uberon comma-shaped body CSB EMAPA:27681 EMAPA:27835 The comma-shaped body is the precursor structure to the S-shaped body that contributes to the morphogenesis of the nephron UBERON:0004198 ZFA:0005588 uberon S-shaped body EMAPA:27756 EMAPA:27853 SSB TODO The S-shaped body is the successor of the comma-shaped body that contributes to the morphogenesis of the nephron UBERON:0004199 ZFA:0005589 stage II nephron uberon nephrogenic mesenchyme Nephrogenic mesenchyme is the tissue made up of loosely connected mesenchymal cells in the nephron The detailed events associated with the differentiation of the nephrogenic mesenchyme are somewhat complex. It has been suggested that each terminal branch of the ureteric bud stimulates the associated cap mesenchyme tissue to form a renal vesicle (the most primitive stage of nephron development: a stage I nephron). This then elongates, becomes a comma-shaped and then an S-shaped body (stage II nephron), and makes contact with and fuses with the distal component of the ureteric bud. The latter then forms the collecting duct. One fold of the S-shaped body gives rise to Bowman's capsule (also termed the glomerular capsule). Soon afterwards, endothelial cells invade to make a capillary knot-like outgrowth, the glomerular tuft, which goes on to form the glomerulus. The inner epithelial layer of the Bowman's capsule (also called the visceral epithelium, or podocyte layer because it consists of podocytes) is closely apposed to the endothelial glomerulus. Together, the Bowman's capsule and the glomerulus comprise the definitive renal corpuscle. The rest of the nephron elongates to form components of the proximal tubule, the loop of Henle and the distal tubule. The distal pole of the developing nephron connects to the ureteric bud that induced it at an early stage of nephron/ collecting duct development, before differentiation of the proximal tubule, the loop of Henle and the distal tubule are complete. This connection allows the excretory products produced by the kidney to be removed and subsequently transferred, via the ureter, into the bladder where they are stored until it is appropriate to empty the bladder. [http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron] UBERON:0004208 mesenchyme of nephron nephron mesenchyme uberon renal vesicle The renal vesicle is the primordial structure of the nephron epithelium, and is formed by the condensation of mesenchymal cells. UBERON:0004209 note that this class includes both metanephric and mesonephric vesicles - ZFA and EHDAA2 associations are placed with these classes. TODO - make a more specific develops_from relationship - see UBERON:0005107 ! metanephric cap stage I nephron uberon nephron epithelium The nephron epithelium is a tissue that covers the surface of a nephron UBERON:0004211 epithelial tissue of nephron epithelium of nephron nephron epithelial tissue uberon blood vessel smooth muscle BTO:0001431 CALOHA:TS-1107 EMAPA:35177 MA:0000710 MESH:D009131 TAO:0005321 UBERON:0004237 UBERON:0010508 UMLS:C1519956 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. 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 found within, and composing the majority of the wall of blood vessels. smooth muscle of blood vessel smooth muscle tissue of blood vessel uberon vascular smooth muscle vascular smooth muscle tissue eye muscle A muscle that is part of the eye region. AAO:0000156 EMAPA:35335 MA:0000271 OpenCyc:Mx8Ngx4rwKSh9pwpEbGdrcN5Y29ycB4rvViTvpwpEbGdrcN5Y29ycB4rvYA8cJwpEbGdrcN5Y29ycA UBERON:0004277 uberon skeleton AEO:0000168 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] EHDAA2:0001843 EHDAA:5047 EMAPA:17213 FMA:23875 GAID:177 MA:0003006 MAT:0000032 MESH:D012863 MIAA:0000032 OpenCyc:Mx4rvVi1rpwpEbGdrcN5Y29ycA UBERON:0004288 VSAO:0000026 XAO:0004053 galen:Skeleton https://github.com/obophenotype/uberon/wiki/The-skeletal-system set of all bones set of bones of body skeletal uberon dermomyotome AAO:0010572 AEO:0000214 EHDAA2:0003259 EMAPA:31109 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] FMA:295654 Portion of somites that gives rise to dermis and muscles.[AAO] TAO:0001513 The bilaminar epithelium formed from the myotome and dermatome. 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] UBERON:0004290 UMLS:C1511786 VHOG:0000676 ZFA:0001513 all but the sclerotome of a mesodermal somite; the primordium of skeletal muscle and, perhaps, of the dermis. dermamyotome dermomyotomes uberon 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. TAO:0000115 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] UBERON:0004291 ZFA:0000115 heart cone rudimentary heart uberon cardiac skeleton Dense connective tissue that separates the atria from the ventricles and provides physical support for the heart. EMAPA:36645 FMA:9496 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] UBERON:0004292 anulus fibrosus dexter cordis anulus fibrosus sinister cordis cardiac fibrous skeleton fibrous skeleton of heart heart fibrous skeleton skeleton of heart trigona fibrosa trigonum fibrosum dextrum cordis trigonum fibrosum sinistrum cordis uberon distal phalanx AAO:0010676 Distal-most phalanx within a digit. EMAPA:35287 In human anatomy, the distal phalanges of the four fingers and toes articulate proximally with the intermediate phalanges at the distal interphalangeal joints (DIP); in the thumb and big toe, with only two phalanges, the distal phalanges articulate proximally with the proximal phalanges. The distal phalanges carry and shape nails and claws and are therefore occasionally referred to as the ungual phalanges. The distal phalanges are cone-shaped in most mammals, including most primates, but relatively wide and flat in humans. MA:0002914 UBERON:0004300 phalanx distalis phalanx distalis terminal phalanx uberon ungual phalanx middle phalanx A phalanx located between proximal and distal phalanges. AAO:0010677 EMAPA:35572 Intermediate phalanges are bones found in the limbs of most vertebrates. In humans, they are the bones of the finger and toe which lie in the middle, between the two wrinkly joints. The thumb and big toe do not have intermediate phalanges. In most other vertebrates, they have a corresponding place in their limbs, whether they be paw, wing, hoof or fin MA:0002915 UBERON:0004301 consider using numbering system, and axioms to the effect that there is a single middle phalanx per finger in humans. This should perhaps be renamed 'intermediate phalanx', leaving the term middle phalanx open for the specific intermediate phalanx of a 3-phalanx digit in some groups such as whales, there are multiple intermediate phalanges intermediate phalanx medial phalanx penultimate phalanx phalanx 2 phalanx II uberon proximal phalanx 1 AAO:0010680 EMAPA:35716 MA:0002916 Proximal phalanges are bones found in the limbs of most vertebrates. In humans, they are the bones at the base of a toe or finger, the prominent, knobby ends of which are often called the knuckles. In other vertebrates, proximal phalanges have a similar placement in the corresponding limbs, be they paw, wing or fin. In many species, they are the longest and thickest phalanx ('finger' bone) Proximal-most phalanx within a digit. UBERON:0004302 phalanx 1 phalanx I proximal-most phalanx uberon primitive streak (...) the blastopore equivalent of chordates (germ ring in fish, marginal zone/blastopore lip in frog and node/primitive streak in chick and mouse) (...) (reference 1); Indeed, the primitive streak has been considered the homologue of the blastopore since the 1870s (reference 2).[well established][VHOG] EHDAA2:0001525 EHDAA:185 EMAPA:16072 FMA:293110 The primitive streak is a structure that forms during the early stages of avian, reptilian and mammalian embryonic development[WP]. the midline ridge of the embryonic epiblast that later develops into mesoderm and endoderm[MP] UBERON:0004341 UMLS:C0033153 VHOG includes a very broad grouping here based on http://www.ncbi.nlm.nih.gov/pubmed/9609826 VHOG:0001202 primitive streak - blastopore - germ ring uberon trophectoderm (...) the trophoblast develops rapidly so that contact may be made with the maternal uterine tissues when conditions are appropriate. We have here an excellent example of an embryonic adaptation, the development of a structure never present in either adult or embryo of 'lower' vertebrates.[well established][VHOG] BTO has this has part of the trophoblast BTO:0001840 EHDAA2:0002091 EHDAA:56 EMAPA:16046 The outer cellular layer of the mammalian blastocyst. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.750, see_Kardong_KV][VHOG] UBERON:0004345 VHOG:0000979 distinction between trophectoderm and trophoblast unclear/inconsistent in many sources outermost layer of cells in the blastodermic vesicle, which will develop into the trophoblast layer and then contact the endometrium and take part in establishing the embryo's means of nutrition trophectodermal uberon limb bud AAO:0010375 An outgrowth on the lateral trunk of the embryo that develops into a limb. The limb bud is divided into ectoderm and mesenchyme[cjm, modified from MP]. BTO:0001640 EMAPA:35944 Early outgrowth of presumptive limb.[AAO] FMA:296780 GAID:1307 MESH:A16.254.462 UBERON:0004347 UMLS:C0282505 XAO:0003161 developmentally_induced_by Fgf10, capable of initiating limb forming interactions between endoderm and mesoderm gemmae membrorum limb buds limbbud uberon optic eminence EHDAA:938 EMAPA:16322 RETIRED_EHDAA2:0001308 The embryonic structure that gives rise to the corneal ectoderm UBERON:0004348 VHOG:0001296 uberon apical ectodermal ridge AAO:0010760 AER Distal ectodermal thickening which forms along the anterior-posterior limb axis. Signaling from this region influences proximal-distal patterning of the limb. Structure is missing in some lineages (salamanders, Eleutherodactylus coqui) however morphologically their indistinct distal ectoderm may still be involved in signaling.[AAO] EMAPA:32744 Proliferative region that is part of the developing fin fold or fin.[TAO] TAO:0002146 The AER of tetrapods regresses after specification of skeletal progenitors, the AER of teleosts form an elongating fin fold UBERON:0004356 UMLS:C1516037 XAO:0004121 ZFA:0001702 apical epidermal ridge crista ectodermalis apicalis maintaining mesenchyme in plastic proliferating state; maintaining expression of A-P axis genes; interacting with D-V proteins. Genes: AER induced by Fgf10 in mesenchyme. AER secretes Fgf8, which stimulates mitosis in the mesenchyme causing Fgf10 production - positive feedback loop multilayered ectodermal region at the distal tip of a limb or fin bud necessary for the proper development of the underlying mesenchyme[MP,modified]. Along with the zone of polarizing activity, it is a crucial organizing region during limb development[WP]. note that media, dorsal fins etc have AERs. relationship loss: subclass proliferative region (TAO:0000098)[TAO] uberon paired limb/fin bud An outgrowth on the lateral trunk of the embryo that develops into a limb or paired fin. The limb/fin bud is divided into ectoderm and mesenchyme[cjm, modified from MP]. Genes: In limb buds of chick and mouse, Shh expression is activated as soon as there is a morphological bud, whereas in S. canicula fin buds, consistent with reported data in other cartilaginous fishes, Shh is transcribed late in fin development[PMID:17187056] The tetrapod limb is derived from a posterior part of the fin endoskeleton of elasmobranchs and basal bony fish, the so-called metapterygium, a series of endoskeletal elements that is the first to form in the developing paired fins. (...) In addition, there is an independent endoskeletal element called the protopterygium that develops anterior to the metapterygium in many basal fishes (e.g., the bichir and sturgeon). Teleosts have lost the metapterygium whereas the sarcopterygians, on the other hand, have lost the protopterygium. Sarcopterygians thus develop all their endoskeletal structures from the metapterygium and consequently the tetrapod limb skeleton is derived from the metapterygium.[uncertain][VHOG] UBERON:0004357 VHOG:0001258 limb - fin bud paired appendage bud paired limb/fin bud uberon pharyngeal arch 1 1 1st arch 1st pharyngeal arch 1st visceral 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. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG] AAO:0010364 CALOHA:TS-2089 EHDAA2:0000006 EHDAA:573 EMAPA:16118 FMA:293019 MFMO:0000095 TAO:0001595 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 of the series of pharyngeal arches that develop into jaw bones or their homologs, and their associated nerves and arteries UBERON:0004362 UMLS:C1517197 VHOG:0000296 XAO:0000097 ZFA:0001612 arcus pharyngeus primus branchial arch 1 first branchial arch first pharyngeal arch first visceral arch mandibular arch the first arch which contributes to development of mastication muscles, maxilla, mandible, incus, malleus, Meckel's cartilage, trigeminal nerve, and maxillary artery uberon visceral arch 1 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. Acellular anatomical structure that is the zone of collagen fibers adjacent the basement membrane of the corneal epithelium.[TAO] Bowman's anterior elastic lamina Bowman's layer Bowman's membrane 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 Reichert's membrane TAO:0002155 UBERON:0004370 UMLS:C0229127 ZFA:0001684 anterior elastic lamina anterior limiting lamina anterior limiting lamina of cornea anterior limiting membrane lamina limitans anterior (cornea) lamina limitans anterior corneae uberon bone of free limb or fin A bone that is part of an appendage [Automatically generated definition]. UBERON:0004375 appendage bone bone of appendage bone of free segment of appendicular skeleton uberon skeleton of limb EHDAA2 considers hip and shoulder joints part of limb skeleton. EHDAA2:0002221 EMAPA:32702 Skeletal subdivision that is part of the limb.[VSAO] The collection of all skeletal elements in an individual limb. UBERON:0004381 VSAO:0000300 free limb skeleton limb skeleton set of bones of limb uberon entire sense organ system FMA:78499 Sum of all sensory systems in an organism. UBERON:0004456 note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs sense organ system uberon musculature of thorax 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 FMA:71293 UBERON:0004464 muscle group of thorax muscles of thorax musculi thoracis set of muscles of thorax thoracic musculature uberon musculature of trunk AAO:0011572 Any collection of muscles that is part of a trunk [Automatically generated definition]. EFO:0003531 FMA:50187 UBERON:0004479 currently defined by location rather than attachment muscle group of trunk muscular system of trunk set of muscles of trunk uberon cardiac muscle tissue of myocardium A portion of cardiac muscle tissue that is part of a myocardium [Automatically generated definition]. EMAPA:32688 FMA:261726 MA:0002441 Note placement of MA class based on parthood relationship UBERON:0004493 uberon anatomical projection A projection or outgrowth of tissue from a larger body or organ. AAO:0010278 Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, or tissue.[AAO] Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, tissue, fin, scale, etc.[TAO] Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, tissue, fin, scale, etc.[VSAO] FMA:67601 HAO:0000822 TAO:0001834 UBERON:0004529 VSAO:0000180 XAO:0004020 anatomical process anatomical protrusion flange flanges galen:Ridge lamella lamellae lamina laminae organ process papilla process process of organ processes processus projection projection projections protrusion ridge ridges shelf shelves should be declared disjoint from organ, but in some ontologies (e.g. ZFA), structures such as neural spines are classified as bones (and hence organs) spine uberon cardiovascular system AAO:0011001 Anatomical system that has as its parts the heart and blood vessels. BILA:0000016 BTO:0000088 CALOHA:TS-1297 CV system EFO:0000791 EHDAA2:0000216 EHDAA:394 EMAPA:16104 EMAPA:16370 EV:0100017 FMA:7161 GAID:467 Herz und Gefaesssystem MA:0000010 MAT:0000016 MESH:D002319 MIAA:0000016 OpenCyc:Mx4rvVjzG5wpEbGdrcN5Y29ycA TAO:0000010 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] UBERON:0004535 UMLS:C0007226 VHOG:0000302 WikipediaCategory:Cardiovascular_system XAO:0000100 XAO:0001010 ZFA:0000010 uberon we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph. lymph vasculature A network of blunt ended vessels lacking direct connection to the blood vascular system. These vessels collect and drain fluids and macromolecules from interstitial spaces throughout the animal. They derive from a subpopulation of endothelial cells and have walls that are much thinner than the blood carrying vessels. Lymphatic vessels are usually classified as either superficial or deep. A network of blunt ended vessels lacking direct connection to the blood vascular system. These vessels collect and drain fluids and macromolecules from interstitial spaces throughout the animal. They derive from a subpopulation of endothelial cells and have walls that are much thinner than the blood carrying vessels. Lymphatic vessels are usually classified as either superficial or deep.[TAO] FMA:63815 TAO:0005105 UBERON:0004536 ZFA:0005105 consider merging with parent lymph vessels lymphatic trunks and ducts lymphatic vasculature lymphatic vessel network lymphatic vessels set set of lymphatic vessels trunci et ductus lymphatici uberon blood vasculature A vascular network consisting of blood vessels. TAO:0001079 UBERON:0004537 ZFA:0001079 blood system blood vascular network blood vessel system blood vessels set of blood vessels uberon systemic arterial system FMA:45623 The part of the arterial system which carries oxygenated blood away from the heart to the body, and returns deoxygenated blood back to the heart. UBERON:0004571 systemic arterial circulatory system uberon arterial system BTO:0004690 EHDAA2:0000143 EHDAA:396 EMAPA:16201 EMAPA:16371 MA:0002719 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] The part of the cardiovascular system consisting of all arteries. UBERON:0004572 VHOG:0000273 uberon systemic artery An artery of the systemic circulation, which is the part of the cardiovascular system which carries oxygenated blood away from the heart, to the body, and returns deoxygenated blood back to the heart. FMA:66464 UBERON:0004573 systemic arterial subtree uberon systemic venous system FMA:45626 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] The part of the venous system that drains the general body tissues[Kardong] UBERON:0004581 systemic venous circulatory system uberon venous system BTO:0004692 EHDAA2:0002171 EHDAA:486 EMAPA:16240 MA:0002720 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] 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. UBERON:0004582 UMLS:C1267406 VHOG:0000277 uberon vein system sphincter muscle A structure, usually a circular muscle, that normally maintains constriction of a natural body passage or orifice and which relaxes as required by normal physiological functioning. FMA class is not a subtype of muscle FMA:75004 UBERON:0004590 UMLS:C1409894 circular muscle sphincter uberon otic capsule AAO:0010143 Otic capsules develop around the parts of the ear that lie within the chondrocranium. This part of the ear, known as the inner ear, is composed of the semicircular ducts and associated sacs that contain the receptive cells for equilibrium and hearing (reference 1); (...) considerations have led to our rethinking issues related to the origin of several aspects of vertebrate hearing, and to the view that many basic auditory functions evolved very early in vertebrate history, and that the functions observed in more `advanced' vertebrates, such as birds and mammals, are frequently modifications of themes first encountered in fishes, and perhaps even more ancestral animals.[well established][VHOG] Skeletal elements surrounding the membranous labyrinth of the inner ear. Sensory capsules anterolateral to and confluent with occipital arch.[AAO] The capsule surrounding the inner ear mechanism. The cartilage capsule surrounding the inner ear mechanism; in the embryos of higher vertebrates, it is cartilaginous at first but later becomes bony. [Biology_online][VHOG] UBERON:0004637 VHOG:0000854 auditory capsule developmental relationships need to be checked in elasmobranchs, it remains cartilaginous in the adult; in the embryos of higher vertebrates, it is cartilaginous at first but later becomes bony (at approximately 23 weeks in humans) otic capsule otic capsule element otic capsule endochondral element otic capsule skeletal element otic region periotic periotic capsule relationship loss: part_of occipito-petrosal (AAO:0010831)[AAO] relationship loss: part_of otic and occipital (AAO:0000993)[AAO] uberon blood vessel endothelium An endothelium that lines the blood vasculature. Other endothelia may line lymph vessels, the heart BTO:0000766 CALOHA:TS-2155 EMAPA:35176 MA:0000709 TAO:0005257 UBERON:0004638 UMLS:C1706972 ZFA:0005257 uberon liver lobule EMAPA:35499 FMA:14471 MA:0002494 UBERON:0004647 UMLS:C0227518 hepatic lobule lobules of liver lobuli hepatici lobuli hepatis lobulus hepaticus should not be confused with the anatomic lobes of the liver (caudate lobe, quadrate lobe, left lobe, and right lobe), or any of the functional lobe classification systems.[WP] the polygonal structure of the liver that consists of hepatocytes radiating outward from a hepatic vein uberon arterial system endothelium An endothelium that is part of an arterial system [Automatically generated definition]. EMAPA:35145 MA:0000703 UBERON:0004700 UMLS:C1706849 uberon bulbus cordis A pear shaped chamber that functions as a capacitor, maintaining continuous blood flow into the gill arches. The bulbus arteriosus has three distinct layers. Hu et al. 2000.[TAO] EHDAA2:0000197 EHDAA:438 EHDAA:768 EMAPA:16216 EMAPA:16333 FMA:70300 TODO - check relationship to bulbus arteriosus UBERON:0004706 UMLS:C1284055 a transient fetal dilation of the distal (or cranial) heart tube located where the arterial trunk joins the ventral roots of the aortic arches primitive right ventricle endocardium uberon paired limb/fin An appendage that is part of a appendage girdle complex. UBERON:0004708 UBERON:0009872 VSAO:0000067 girdle-associated appendage jointed paired lateral appendage limb or fin limb/fin paired appendage pectoral or pelvic appendage pelvic/pectoral appendage this class is the union of the classes limb, pectoral fin and pelvic fin. uberon pelvic appendage Paired appendage that consists of the posterior appendicular skeleton and associated soft and hard tissues, but excludes the pelvic girdle and its associated soft and hard tissues. UBERON:0004709 UBERON:0009876 VSAO:0000126 hindlimb/pelvic fin pelvic appendage pelvic limb/fin posterior appendage posterior limb/fin posterior paired appendage uberon jugular vein BTO:0001744 CALOHA:TS-0497 EMAPA:18638 GAID:536 MA:0002154 MESH:D007601 The jugular veins are veins that bring deoxygenated blood from the head back to the heart via the superior vena cava. UBERON:0004711 UMLS:C0022427 jugular uberon vena jugularis conceptus AEO:0000194 BTO:0003834 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 EHDAA2:0000001 EHDAA2:0003235 EMAPA:36040 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]. UBERON:0004716 UMLS:C1516779 embryo plus adnexa uberon segmental subdivision of nervous system Any segmental subdivision of a nervous system. Includes metameric developmental segments, such as vertebrates neuromeres. FBbt:00005140 UBERON:0004732 neuromere 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) uberon segmental subdivision of hindbrain An organ subunit that is part of a hindbrain [Automatically generated definition]. FMA:61998 UBERON:0004733 hindbrain segment segment of hindbrain uberon gastrula BILA:0000060 BTO:0001403 FBbt:00005317 FMA:293108 GAID:1302 MESH:A16.254.412 MIAA:0000179 Organism at the gastrula stage. UBERON:0004734 UBERON:0007012 UMLS:C0017199 UMLS:C1284022 We explicitly merge the NCITA terms here blastocystis trilaminaris gastrula embryo tri-laminar disc tri-laminar disk trilaminar blastocyst trilaminar blastoderm trilaminar disc trilaminar disk trilaminar germ uberon skeletal tissue 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] 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 MA:0003047 UBERON:0004755 VSAO:0000015 XAO:0004038 ZFA:0005619 uberon cartilaginous neurocranium AAO:0000094 AAO:0010153 EHDAA:6031 FMA:76621 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]. UBERON:0004761 UMLS:C1516496 XAO:0003059 cartilaginous chondocranium cartilaginous skull cartiligionous skeletal structure of skull chondocranium embryonic chondocranium 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) neurocranium uberon skeletal element AAO:0011129 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] TAO:0001890 UBERON:0004765 VSAO:0000128 XAO:0004012 ZFA:0005494 galen:SkeletalStructure uberon articular system Anatomical system that consists of all the joints of the body. EMAPA:35150 FMA:23878 MA:0003007 UBERON:0004770 VSAO:0000181 joint system set of all joints set of all joints of body set of joints of body uberon gastrointestinal system mucosa A mucosa that is part of a gastrointestinal system. BTO:0000546 BTO:0005568 EMAPA:36591 MA:0001521 The gut mucosa of amphioxus has insulin-secreting cells. http://www.ncbi.nlm.nih.gov/pubmed/16417468 UBERON:0004786 digestive tract mucosa gut mucosa gut mucuous membrane mucosa of gut uberon blood vessel layer Any of the tissue layers that comprise a blood vessel. Examples: tunica media, tunica adventitia. EMAPA:36296 MA:0002854 UBERON:0004797 uberon respiratory tract epithelium BTO:0000419 CALOHA:TS-0023 EMAPA:32827 MA:0001480 UBERON:0004802 VHOG:0000981 airway epithelium epithelial tissue of respiratory tract epithelium of respiratory tract respiratory epithelium respiratory tract epithelial tissue the pseudostratified ciliated epithelium that lines much of the conducting portion of the airway, including part of the nasal cavity and larynx, the trachea, and bronchi uberon oviduct epithelium An epithelium that is part of a oviduct [Automatically generated definition]. BTO:0002402 CALOHA:TS-1316 EMAPA:29043 MA:0001718 UBERON:0004804 columnar epithelium of the Fallopian tube columnar epithelium of the oviduct epithelial tissue of oviduct epithelium of fallopian tube epithelium of oviduct epithelium of uterine tube fallopian tube epithelium in FMA, epithelium of uterine tube is a subclass of ciliated columnar epithelium. MA introduces subtypes: ciliated columnar and cuboidal. We map the FMA type according to its relationships, not its label oviduct epithelial tissue uberon respiratory system epithelium An epithelium that is part of a respiratory system [Automatically generated definition]. CALOHA:TS-0023 EMAPA:32826 MA:0001823 UBERON:0004807 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 gastrointestinal system epithelium An epithelium that is part of a digestive system [Automatically generated definition]. EMAPA:32683 MA:0001520 UBERON:0004808 digestive system epithelial tissue digestive system epithelium epithelial tissue of digestive system epithelial tissue of gastrointestinal system epithelium of digestive system epithelium of gastrointestinal system gastrointestinal system epithelial tissue uberon endometrium epithelium An epithelium that is part of an endometrium [Automatically generated definition]. EMAPA:35307 In rodents and primates, the uterine epithelium (the endometrium) is eroded away so that maternal blood comes into direct contact with the trophoblast surface (called haemochorial) MA:0002731 UBERON:0004811 endometrium epithelial tissue epithelial tissue of endometrium epithelium of endometrium epithelium of tunica mucosa of endometrium uberon uterine epithelium upper respiratory tract epithelium An epithelium that is part of a upper respiratory tract [Automatically generated definition]. EMAPA:35894 MA:0001912 UBERON:0004814 epithelial tissue of upper respiratory tract epithelium of upper respiratory tract uberon upper respiratory tract epithelial tissue kidney epithelium BTO:0000059 CALOHA:TS-0505 EMAPA:35457 MA:0002846 UBERON:0004819 epithelial tissue of kidney epithelium of kidney kidney epithelial tissue renal epithelium the cellular avascular layer of the kidney luminar surfaces uberon cardiovascular system endothelium An endothelium that is part of the cardiovascular system. BTO:0001853 EMAPA:35201 GAID:519 MA:0000717 MESH:D004730 TAO:0002171 UBERON:0004852 UMLS:C0014261 VHOG:0001217 Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] XAO:0000356 ZFA:0001639 consider merging with 'endothelium' endothelia uberon vascular endothelia somatic layer of lateral plate mesoderm AAO:0011100 BILA:0000047 FMA:295570 Layer of lateral plate mesoderm that forms the future body wall - underlies the ectoderm[WP]. UBERON:0004871 XAO:0000271 check BILA outer layer of lateral plate mesoderm parietal mesoderm somatic mesoderm uberon splanchnic layer of lateral plate mesoderm AAO:0011102 BILA:0000044 FMA:295568 Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP]. UBERON:0004872 We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors XAO:0000276 inner layer of lateral plate mesoderm splanchnic mesoderm uberon visceral mesoderm somatopleure A structure created during embryogenesis when the lateral mesoderm splits into two layers - the outer (or somatic) layer becomes applied to the inner surface of the ectoderm, and with it forms the somatopleure.[WP]. EHDAA2:0001847 EHDAA:381 EMAPA:16180 FMA:295566 Gives rise to the paired appendages in jawed vertebrates. a persistent somatopleure through the redistribution and expansion of the lateral plate mesoderm is a synapomorphy for gnathostomes and a critical step in generating a novel developmental module with dramatic evolutionary potentia (Tulenko et al. 2012) http://burkelab.research.wesleyan.edu/current-projects/lamprey/ UBERON:0004874 UMLS:C1519423 VHOG:0000557 sources differ as to whether this is part-of or develops-from the LPM uberon nephrogenic cord A portion of the urogenital ridge which is the source of much of the urinary system[WP]. FMA:72168 UBERON:0004875 UMLS:C1283944 chorda nephrogenica part_of or develops_from urogenital ridge? uberon urogenital fold EHDAA2:0004022 EMAPA:30888 FMA:321919 Less commonly, urogenital fold refers to the fold in the mesonephros which is the precursor of e.g. the suspensory ligament of the ovary. This is the case in older versions of Gray's anatomy[WP] One of of the pair of folds derived from the cloacal folds which give rise to a portion of the external genitalia; in male embryos they close over the urethral plate and fuse to form the spongy (penile) urethra and ventral aspect of the penis, not including the glans; failure of fusion of the urethral folds leads to hypospadias; in female embryos they fuse only anterior to the anus and form the labia minora[MP]. UBERON:0004876 uberon urethral fold urogenital fold urogenital ridge chordamesoderm AAO:0000478 EFO:0003426 Notochord rudiment[ZFIN:ZDB-PUB-961014-576]. TAO:0000091 The central region of trunk mesoderm. This tissue forms the notochord UBERON:0004880 WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord. ZFA:0000091 axial chorda mesoderm chorda mesoderm dorsal mesoderm presumptive notochord uberon lung mesenchyme EMAPA:32866 The mass of tissue made up of mesenchymal cells in the lung. UBERON:0004883 lung-associated mesenchyme mesenchyme of lung pulmonary mesenchyme uberon urogenital sinus epithelium EHDAA2:0004061 EMAPA:31509 EMAPA:31520 The fetal urogenital sinus (from which the prostate derives) is a simple cylinder of stratified basal epithelium, surrounded by mesenchyme and positioned between the embryonic bladder and pelvic urethra UBERON:0004902 UGE epithelium of urogenital sinus uberon we follow EHDAA2 in dividing the UGS into epithelium and lumen articulation Anatomical cluster that connects two or more adjacent skeletal elements or hardened body parts. FBbt:00005811 UBERON:0004905 joint uberon lower digestive tract FMA:49179 MA class was moved from here. See https://github.com/obophenotype/uberon/issues/509 The region of the digestive tract extending from the beginning of the intestines to the anus[GO - gut definition]. UBERON:0004907 UMLS:C0226875 WP: small intestine, large intestine, anus. Anal canal not part of LGIT according to FMA, but anus is considered part of LGIT according to WP. Duodenum overlaps both U/L galen:LowerGastrointestinalTract gut lower GI tract lower gastrointestinal tract uberon upper digestive tract FMA:49177 The region of the digestive tract extending from the mouth cavity through pharynx esophagus stomach and duodenum. UBERON:0004908 UMLS:C0226874 WP: small intestine, large intestine, anus. Anal canal not part of LGIT according to FMA, but anus is considered part of LGIT according to WP. Duodenum overlaps both U/L. In Galen, entire GI tract excludes esophagus galen:UpperGastrointestinalTract uberon upper GI tract upper gastrointestinal tract biliary bud EHDAA2:0000171 EMAPA:16561 EMAPA_RETIRED:16565 UBERON:0004912 VHOG:0001351 hepatic diverticulum uberon hepatopancreatic ampulla A dilation of the duodenal papilla that is the opening of the juncture of the common bile duct and the main pancreatic duct. Ampulla formed by the union of the pancreatic duct and the common bile duct where they enter the intestine.[TAO] CALOHA:TS-2348 FMA:15076 GAID:283 MESH:A03.159.183.079.300.900 TAO:0005167 UBERON:0004913 UMLS:C0042425 Vater's ampulla ZFA:0005167 ampulla Vaterii ampulla biliaropancreatica ampulla hepatopancreatica ampulla of Vater ampulla of bile duct biliaropancreatic ampulla galen:AmpullaOfVater papilla Vateri papilla duodeni major uberon duodenal papilla EMAPA:18662 FMA:15953 MA:0003107 One of the two small elevations on the mucosa of the duodenum, the major at the entrance of the conjoined pancreatic and common bile ducts and the minor at the entrance of the accessory pancreatic duct. UBERON:0004914 papilla duodenalis papilla duodeni papilla of duodenum uberon subdivision of digestive tract A proximal-distal subdivision of the digestive tract. FBbt:00100315 FMA:71131 UBERON:0004921 alimentary system subdivision intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct. intestinal tract segment of intestinal tract subdivision of alimentary system uberon organ component layer A part of a wall of an organ that forms a layer. FMA:82485 UBERON:0004923 uberon mucosa of pylorus A mucosa that is part of a pylorus [Automatically generated definition]. BTO:0004110 EMAPA:27199 FMA:17461 UBERON:0004998 antropyloric mucosa mucosa of organ of pyloric part of stomach mucosa of organ of pylorus mucosa of organ of stomach pyloric region mucosa of pyloric part of stomach mucosa of stomach pyloric region mucous membrane of pyloric part of stomach mucous membrane of pylorus mucous membrane of stomach pyloric region organ mucosa of pyloric part of stomach organ mucosa of pylorus organ mucosa of stomach pyloric region pyloric part of stomach mucosa pyloric part of stomach mucosa of organ pyloric part of stomach mucous membrane pyloric part of stomach organ mucosa pylorus mucosa pylorus mucosa of organ pylorus mucous membrane pylorus organ mucosa stomach pyloric region mucosa stomach pyloric region mucosa of organ stomach pyloric region mucous membrane stomach pyloric region organ mucosa uberon neural groove AAO:0011071 EMAPA:35594 FMA:295624 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]. UBERON:0005061 UMLS:C0814992 XAO:0000248 uberon neural fold EHDAA2:0001249 EMAPA:16142 EMAPA:16146 EMAPA:16151 EMAPA:16155 EMAPA:16159 EMAPA:16162 EMAPA:16288 EMAPA:16292 EMAPA:16295 EMAPA:16299 EMAPA:16303 EMAPA:16307 EMAPA:16528 FMA:295618 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]. One of the two elevated edges of the neural groove[GO,MP]. UBERON:0005062 UMLS:C0814993 XAO:0004087 medullary fold uberon 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]. 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 UBERON:0005068 ZFA:0000133 neural tube rod uberon metanephric ureteric bud The portion of the ureteric bud tube that contributes to the morphogenesis of the metanephros[GO]. UBERON:0005080 uberon ureter ureteric bud The portion of the ureteric bud that contributes to the morphogenesis of the ureter. The ureter ureteric bud is the initial structure that forms the ureter[GO]. UBERON:0005081 uberon ectodermal placode AEO:0000218 An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm[GO] FMA:293966 UBERON:0005085 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. consder adding placodal ectoderm as a distinct class? Also place placodal ectoderm as develops_from ectoderm; need to check taxon-appropriateness epithelial placode in GO, covers optic, otic, olfactory, mammary, hair, tooth, sebaceous. uberon muscle structure EMAPA:32715 FBbt:00005073 FMA:30316 Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO]. UBERON:0005090 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 muscle muscle element musculus uberon kidney rudiment . UBERON:0005095 class added for consistency with GO - consider merging with kidney mesenchyme. kidney anlage uberon mesonephric epithelium An epithelium that is part of a mesonephros [Automatically generated definition]. UBERON:0005103 uberon epithelial bud A bud is a protrusion that forms from an epithelial sheet by localized folding. BTO:0001639 UBERON:0005153 uberon reproductive structure Any anatomical structure that is part of the reproductive system. UBERON:0005156 reproductive system element reproductive system structure uberon epithelial fold An epithelial sheet bent on a linear axis. UBERON:0005157 uberon multi cell part structure A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part. AAO:0011000 CARO:0001000 FBbt:00007060 FMA:83115 UBERON:0005162 cell part cluster multi-cell-component structure multi-cell-part structure uberon 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.' hepatic duct A duct that carries bile from the liver to the small intestine.[TAO] A duct that carries bile from the liver to the small intestine[ZFA]. Any portion of the ducts that carry bile from the liver to the common bile duct. This may include both intrahapetic components (parts of left and right hepatic ducts) and extrahapetic components (common hepatic duct, plus hilar portion). EHDAA2:0000741 EHDAA:3049 EMAPA:16843 FMA:71891 MA:0000357 OpenCyc:Mx4rvWo8WJwpEbGdrcN5Y29ycA TODO - MA distinguishes between bile duct, hepatic duct, common bile duct and common hepatic duct. in FMA hepatic duct and common hepatic duct are the same The excretory duct of the liver or one of its branches in the lobes of the liver. [TFD][VHOG] The hepatic duct is the duct that leads from the liver to the bile duct[GO]. UBERON:0005171 UMLS:C0917710 VHOG:0000219 galen:HepaticDuct uberon abdomen element An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland. MA:0000522 UBERON:0005172 abdomen organ uberon abdominal segment element An organ or element that is part of the adbominal segment of the organism. This region can be further subdivided into the abdominal cavity and the pelvic region. MA:0000529 UBERON:0005173 abdominal segment organ uberon dorsal region element An organ or element that part of the dorsum of the organism. Examples: spinal cord, vertebrae, muscles of back. MA:0001901 UBERON:0005174 back organ dorsal region organ uberon 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. MA:0000516 UBERON:0005177 trunk organ uberon thoracic cavity element An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli. MA:0000557 UBERON:0005178 thoracic cavity organ uberon pelvic region element An organ or element that is part of the pelvic region. Examples: reproductive organs (in some organisms), urinary bladder, bones of the pelvis. MA:0000543 UBERON:0005179 pelvic element pelvis organ pelvis region organ uberon thoracic segment organ An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions. MA:0000563 UBERON:0005181 uberon upper body organ right atrium valve A valve that is part of a right atrium [Automatically generated definition]. EHDAA2:0000302 EMAPA:17327 MA:0001871 UBERON:0005208 right atrium valves superior vena cava valve uberon valve of right atrium basal plate metencephalon EHDAA2:0001154 EMAPA:17078 The ventral half of the developing neural tube that is the metencephalon. [Chordate_evolution_and_the_origin_of_craniates:_An_old_brain_in_a_new_head._AnaT_Rec_(New_Anat)_(2000)_261(3):_111-125, See_Butler_AB][VHOG] UBERON:0005239 VHOG:0000320 metencephalon basal plate uberon head mesenchyme EFO:0003492 EHDAA2:0000732 EHDAA:179 EMAPA:16098 EMAPA_RETIRED:16269 FMA:76622 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] 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. TAO:0000113 UBERON:0005253 VHOG:0000332 ZFA:0000113 cephalic mesenchyme cranial mesenchyme desmocranium uberon trunk mesenchyme EFO:0003485 EHDAA2:0002092 EHDAA:377 EMAPA:16177 Mesenchyme that is part of a developing trunk. TAO:0000081 UBERON:0005256 VHOG:0000281 ZFA:0000081 trunk and cervical mesenchyme uberon ventricular system of central nervous system A set of structures containing cerebrospinal fluid in the brain. It is continuous with the central canal of the spinal cord[WP]. CNS ventricular system EFO:0003650 EHDAA2:0004362 EV:0100306 FMA:242675 MBA:73 TAO:0001261 TODO - resolve space vs structure conflation. We follow FMA in making this and the various ventricles a structure - it follows from this that strutures such as the tela choroidea and choroid plexuses can be part of the ventricles and ventricular system. Note: see also the class 'neuraxis cavity' UBERON:0005281 ZFA:0001261 uberon ventricle system ventricular system ventricular system of neuraxis ventriculi cerebri ventricular system of brain CALOHA:TS-1295 FMA:242787 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] UBERON:0005282 VHOG:0000005 brain ventricular system uberon tela choroidea A structure found in the walls of the ventricles of the brain, consisting of part of the meninges (pia mater in mammals) plus ependyma[cjm]. FMA:242849 Note that the structure in ZFA may be different Portion of tissue that is part of the primitive meninx which forms a fold, roofing a ventricle of the brain and supporting the choroid plexus[ZFA:0000447]. TAO:0000447 UBERON:0005283 Vascularized tela choroidea is choroid plexus. ZFA:0000447 tela chorioidea uberon myelencephalon BTO:0000758 CALOHA:TS-0607 CALOHA:TS-2365 DHBA:10662 EHDAA2:0001207 EHDAA:5526 EMAPA:17082 HBA:9512 MA:0000205 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 posterior of the two brain vesicles formed by specialization of the rhombencephalon in the developing embryo, it comprises the medulla oblongata. [TFD][VHOG] 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]. UBERON:0005290 VHOG:0000456 myelencephalon (medulla oblongata) 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 uberon embryonic tissue A portion of tissue that is part of an embryo. CALOHA:TS-2100 UBERON:0005291 developing tissue portion of embryonic tissue uberon extraembryonic tissue BTO:0003360 CALOHA:TS-2119 EFO:0001406 MAT:0000061 MIAA:0000061 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. UBERON:0005292 extra-embryonic tissue uberon ventricle of nervous system A layer in the central nervous system that lines system of communicating cavities in the brain and spinal cord. EMAPA:35209 FMA:242770 UBERON:0005358 region of wall of ventricular system of neuraxis uberon ventricular layer photoreceptor array An array of photoreceptors and any supporting cells found in an eye. FBbt:00004200 UBERON:0005388 light-sensitive tissue uberon 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. UBERON:0005389 directing or focusing light onto light receptors lens uberon female reproductive gland A sex gland that is part of a female reproductive system. BTO:0000254 MA:0000383 UBERON:0005398 uberon male reproductive gland A sex gland that is part of a male reproductive system. BTO:0000080 EMAPA:19285 MA:0000399 UBERON:0005399 accessory sex gland uberon alimentary part of gastrointestinal system All metazoans (with degenerate exceptions) have some sort of digestive cavity with a means of entrance to and exit from it.[well established][VHOG] BTO:0000058 CALOHA:TS-0407 EHDAA2:0000110 EHDAA:514 EMAPA:16246 EV:0100056 FMA:71132 GAID:294 GI tract MA:0000323 MESH:A03.492 The part of the digestive system that excludes the hepatobiliary system. The system that includes the esophagus, stomach, small and large intestine, anus, liver, biliary tract, and pancreas[ncithesaurus:Gastrointestinal_System]. UBERON:0005409 UMLS:C0012240 VHOG:0000412 alimentary system alimentary tract galen:GastrointestinalTract gastro-intestinal system gastrointestinal (GI) tract gastrointestinal system gastrointestinal tract that many anatomy ontologies consider this synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class. We have one entity that is part of both gastrointestinal and hepatobiliary systems: hepatopancreatic ampulla. the decision to split digestive and gastrointestinal in this way may be revisited. As it currently stands, this class more closely aligns what MA calls the alimentary system uberon hindlimb bud A limb bud that develops into a hindlimb. AAO:0010382 EHDAA:2358 EMAPA:16779 Genes: Tbx4 specifies hindlimbs. Wnt8c restricts Fgf10 in chick. MIAA:0000256 RETIRED_EHDAA2:0003197 The bilateral thickening of the ectoderm in the region of the first noticeable at NF stage 47, and innervated by NF stage 51. The hind limb buds develop before the forelimb buds.[AAO] UBERON:0005418 XAO:0003066 hind limb bud leg bud limb bud - hindlimb posterior limb bud uberon pelvic appendage bud A limb bud that develops into a hindlimb or pelvic fin. EFO:0003469 Fin bud that develops into the pelvic fin.[TAO] Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG] TAO:0001384 UBERON:0005420 VHOG:0001260 ZFA:0001384 at this time we have no need to name a more specific 'pelvic fin bud' class, but we may in future hindlimb/pelvic fin bud pelvic fin bud pelvic fin buds uberon developing anatomical structure AEO:0000125 CALOHA:TS-2122 EHDAA2:0003125 FBbt:00007006 FMA:292313 MIAA:0000019 UBERON:0005423 developing structure developmental structure developmental tissue uberon presumptive 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 Portion of tissue that is the inner layer of the optic cup and will become the neural retina. TAO:0001071 UBERON:0005425 VHOG:0000490 ZFA:0001071 future NR future neural epithelium future neural layer future neural retina future retinal neural layer inner layer optic cup optic cup inner layer presumptive retina presumptive retinas uberon 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] A vesicle formed from the lens pit of the embryo, developing into the crystalline lens. [TFD][VHOG] EHDAA2:0000983 EHDAA:4737 EMAPA:17163 Portion of tissue that gives rise to the lens. TAO:0002205 UBERON:0005426 VHOG:0001163 ZFA:0001679 hollow lens vesicle immature lens lens mass presumptive lens solid lens vesicle 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 uberon corneal primordium Portion of tissue that is part of the eye and gives rise to the mature, fully layered cornea. TAO:0002188 UBERON:0005427 ZFA:0001688 uberon cervical region FMA:24219 UBERON:0005434 cervical region neck subdivision region of neck subdivision of neck uberon sulcus limitans of neural tube A longitudinal groove in the neural tube wall that divides the neural tube into dorsal (alar) and ventral (basal) halves (dorsal receives input from sensory neurons, ventral effects motor functions); stretches from the mesencephalon caudad[TMD]. BAMS:slim BAMS:slm UBERON:0005478 neural tube lateral wall sulcus limitans sulcus limitans uberon tricuspid valve leaflet A valve leaflet that is part of a tricuspid valve. EMAPA:18630 FMA:7237 Leaf of caridac valve which has as its parts the anterior, posterior and septal leaflets that is is attached to the chorda tendinea of the right ventricle and the fibrous ring of tricuspid valve. MA:0003180 RETIRED_EHDAA2:0002082 The mature AV (atrioventricular) valve of the adult zebrafish 2-chambered heart is structurally similar to the mammalian AV valves with stratified ECM (extracellular matrix) and supporting chordae tendineae. Therefore, the major cellular and molecular events of valve development are largely conserved among animals with hearts composed of multiple chambers.[uncertain][VHOG] UBERON:0005484 VHOG:0000821 leaflet of tricuspid valve tricuspid valve leaflet tricuspid valve leaflets tricuspid valvular leaflet uberon neural tube lateral wall EHDAA2:0001257 EHDAA:2873 EHDAA:912 EMAPA:16532 Portion of tissue on the side of the lumen of the neural tube. TAO:0001435 UBERON:0005496 VHOG:0000513 ZFA:0001435 lateral wall neural tube uberon non-neural ectoderm After gastrulation, neural crest cells are specified at the border of the neural plate and the non-neural ectoderm. EFO:0003643 EHDAA:257 EMAPA:16074 Gene notes: One of the first genes to be expressed in nonneural ectoderm in amphioxus is BMP2/4 (Panopoulou et al. 1998). BMP2/4 homologues appear to have a very ancient role in distinguishing neural from nonneural ectoderm; in Drosophila as well as in amphioxus and vertebrates, BMP2/4 homologues are expressed in nonneural ectoderm and function in distinguishing neural from nonneural ectoderm (Francois & Bier, 1995 ; Sasai et al. 1995 ; Wilson & Hemmati-Brivanlou, 1995; Panopoulou et al. 1998). A change in level of BMP2/4 from very high in nonneural ectoderm to low in neural ectoderm appears to be a key factor in development of neural crest (Baker & Bronner-Fraser,1997a,1997b;Erickson&Reedy,1998;Marchantet al.1998 ;Selleck et al. 1998). Editor note: todo - epidermis? todo - track down EHDAA2 class in new release In the early gastrula of vertebrates, factors from the organizer (e.g. noggin, chordin, and follistatin in Xenopus) antagonize the epidermalizing factor bone morphogenetic protein 4 (BMP4), thus dividing the epiblast into neuroectoderm. In Drosophila, decapentaplegic, the homologue of BMP4, interacts similarly with the protein short gastrulation, the homologue of chordin. Thus, a comparable molecular mechanism for distinguishing non-neural ectoderm from neural ectoderm was probably present in the common ancestor of all bilaterally symmetrical animals.[well established][VHOG] RETIRED_EHDAA2:0001273 TAO:0001178 UBERON:0005497 VHOG:0001372 XAO:0004091 ZFA:0001178 epidermal ectoderm epithelial ectoderm non neural ectoderm surface ectoderm uberon ventral ectoderm primitive heart tube EHDAA2:0001512 EHDAA:424 EHDAA:436 EMAPA:16208 EMAPA:16215 FMA:321916 Multi-tissue structure that arises from the heart rudiment and will become the heart tube. TAO:0000149 UBERON:0005498 ZFA:0000149 early primitive heart tube primitive heart tube uberon gonad primordium EFO:0003651 EHDAA:5927 EMAPA:17204 Immature reproductive tissue that has not undergone final maturation into either testis or ovary.[TAO] Portion of tissue that gives rise to the immature gonad. RETIRED_EHDAA2:0002148 TAO:0001262 UBERON:0005564 WBbt:0008366 ZFA:0001262 future gonad gonadal primordium immature gonad primitive gonad this is a very broad grouping class uberon undifferentiated gonad head somite EHDAA2 has both 'head somite' and 'head somite group', with part_of and develops_from for latter EHDAA2:0003437 EMAPA:16172 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) UBERON:0005594 XAO:0000313 cranial somite in humans this includes somites 1-4 occipital somite uberon lung primordium A pair of lateral diverticula just over the liver rudiment representing the primordia of the lungs, formed by the floor of the foregut just anterior to the liver diverticulum. AAO:0011059 EFO:0002578 EMAPA:36007 UBERON:0005597 UBERON:3010717 XAO:0001002 lateral diverticula lung diverticulum lung endoderm uberon extrahepatic part of hepatic duct EMAPA:16844 MA:0001636 UBERON:0005604 VHOG:0000215 extrahepatic part of the hepatic duct hepatic duct extrahepatic part uberon left dorsal aorta A study of embryos shows that in all vertebrates six arterial arches link the ventral aorta with a pair of lateral dorsal aortae on each side of the body. The latter unite posteriorly to form a single median dorsal aorta wich takes blood to the body.[well established][VHOG] Contributes to the arch of aorta in humans EHDAA2:0000936 EHDAA:404 EMAPA:16205 MA:0000478 UBERON:0005613 VHOG:0000484 uberon right dorsal aorta A study of embryos shows that in all vertebrates six arterial arches link the ventral aorta with a pair of lateral dorsal aortae on each side of the body. The latter unite posteriorly to form a single median dorsal aorta wich takes blood to the body.[well established][VHOG] EHDAA2:0001720 EHDAA:406 EMAPA:16206 MA:0000479 Normally regresses in humans UBERON:0005622 VHOG:0000485 uberon vascular plexus A vascular network formed by frequent anastomoses between the blood vessels (arteries or veins) of a part. AEO:0000219 EHDAA2:0004112 EMAPA:35904 FMA:5900 In a vascular plexus, the contents of the vessels mix. A plexus allows blood to flow via multiple routes. If one branch of the plexus is obstructed, the blood may flow via the open branches[Wikipedia:Plexus#Circulatory_system]. UBERON:0005629 XAO:0004143 plexus vasculosus uberon extraembryonic membrane EHDAA2 is a mereological sum. EHDAA2:0004714 FMA:305915 Intrinsic membrane that arises from embryonic germ layers and grow to surround the developing embryo. UBERON:0005631 https://github.com/obophenotype/uberon/wiki/Modeling-extraembryonic-membranes stuctures homologous to the four extraembryonic membranes appear in mammals [ISBN10:0073040584 (Vertebrates, Kardong)] uberon otocyst epithelium An epithelium that is part of a ear vesicle. EHDAA2:0001344 EMAPA:16671 EMAPA:16996 EMAPA:16999 UBERON:0005641 VHOG:0000986 uberon pronephric mesoderm A mesoderm that has the potential to develop into a pronephros. AAO:0011090 EFO:0003479 Portion of tissue that consists of the mesenchymal precursor to the pronephric kidney and that begins to separate from the intermediate mesoderm at NF stage 21 and epithelializes by NF stage 30.[AAO] TAO:0000067 UBERON:0005721 VHOG:0001239 XAO:0000264 ZFA:0000067 pronephric anlage pronephric bulge pronephric mesenchyme pronephric primordium the intermediate mesoderm of the chick embryo acquires its ability to form kidneys through its interactions with the paraxial mesoderm [ISBN:9780878932504 "Developmental Biology", http://www.ncbi.nlm.nih.gov/pubmed/10720431 "Signals from trunk paraxial mesoderm induce pronephros formation in chick intermediate mesoderm"]. These interactions induce the expression of TFs including Lim1, Pax2 and Pax6 that cause the intermediate mesoderm to form the kidney uberon olfactory system A sensory system that is capable of olfacttion (the sensory perception of smell). AAO:0000334 AAO:0000978 BILA:0000144 EFO:0001973 EMAPA:36004 FMA:7190 In mammals, the main olfactory system detects odorants that are inhaled through the nose, where they contact the main olfactory epithelium, which contains various olfactory receptors. These olfactory receptors are membrane proteins of bipolar olfactory receptor neurons in the olfactory epithelium. Rather than binding specific ligands like most receptors, olfactory receptors display affinity for a range of odor molecules. Olfactory neurons transduce receptor activation into electrical signals in neurons. The signals travel along the olfactory nerve, which belongs to the peripheral nervous system. This nerve terminates in the olfactory bulb, which belongs to the central nervous system. The complex set of olfactory receptors on different olfactory neurons can distinguish a new odor from the background environmental odors and determine the concentration of the odor[WP]. MA:0002445 OpenCyc:Mx4rvViw75wpEbGdrcN5Y29ycA TAO:0001149 The olfactory system is the sensory system used for olfaction, or the sense of smell. Most mammals and reptiles have two distinct parts to their olfactory system: a main olfactory system and an accessory olfactory system. The main olfactory system detects volatile, airborne substances, while the accessory olfactory system senses fluid-phase stimuli. Behavioral evidence indicates that most often, the stimuli detected by the accessory olfactory system are pheromones. The olfactory system is often spoken of along with the gustatory system as the chemosensory senses because both transduce chemical signals into perception[WP][Wikipedia:Olfactory_system]. The sensory system used for olfaction (the sense of smell).[AAO] UBERON:0005725 UMLS:C0228065 XAO:0003196 ZFA:0001149 consider splitting into main and accessory. See also: vomeronasal organ uberon we make the relationship to nervous system 'overlaps', as the olfactory system includes e.g. apertures in the cranium that are not part of the nervous system chemosensory system BILA:0000139 UBERON:0005726 uberon extraembryonic mesoderm . EHDAA2:0000474 EMAPA:31862 EMAPA:31863 FMA:296719 UBERON:0005728 VHOG:0000616 extra-embryonic mesoderm extraembryonic mesenchyme uberon pelvic appendage field A limb/fin field that has the potential to develop into a pelvic appendage bud mesenchyme. Embryonic region that develops into the pelvic fin bud.[TAO] TAO:0001454 UBERON:0005730 ZFA:0001454 pelvic appendage field of lateral plate mesoderm pelvic fin field uberon fin field A limb/fin field that has_potential_to_developmentally_contribute_to a paired fin bud. UBERON:0005731 fin field of lateral plate mesoderm uberon paired limb/fin field A ring of cells capable of forming a limb or paired fin[Gilbert,modified]. UBERON:0005732 limb/fin field of lateral plate mesoderm paired limb/fin field uberon we represent the field as being a part of the LPM (consistent with ZFA, Gilbert). As a consequence, the relationship between limb bud (with is ectoderm+mesenchyme) stands in a weaker has_developmental_contribution_from relation to the field - TODO implement this. limb field A ring of cells capable of forming a limb. UBERON:0005733 limb field of lateral plate mesoderm the central portion of the limb field gives rise to the limb proper. mesenchyme cells proliferate from from the somatic layer of limb field lateral plate mesoderm (limb skeletal precursors) and from the somites (limb muscle precursors) . these mesenchymal cells accumulate under the ectedermal tissue to make a limb bud. // The lateral plate mesoderm in the limb field is also special in that it will induce myoblasts to migrate out from the somites and enter the limb bud. No other region of the lateral plate mesoderm will do that (Hayashi and Ozawa 1995) uberon tunica adventitia of blood vessel EMAPA:36299 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, composed mainly of fibrous tissue. 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_%28vessels%29]. UBERON:0005734 UMLS:C0225342 adventitia externa external coat tunica adventitia tunica adventitia of vessel tunica adventitia vasorum tunica externa vasorum uberon adventitia An outermost connective tissue covering of an organ, vessel, or other structure[WP]. FMA:45635 UBERON:0005742 tunica advetitia tunica externa uberon glomerular tuft ...Soon afterwards, endothelial cells invade to make a capillary knot-like outgrowth, the glomerular tuft, which goes on to form the glomerulus EMAPA:28239 The capillary loops of the kidney that normally function as a filtration unit[MP]. UBERON:0005749 glomerular capillary tuft glomerulus uberon caudal part of nephrogenic cord The metanephros develops from the most caudal part of the nephrogenic cord that is itself derived from the intermediate plate mesoderm. UBERON:0005753 caudal portion of nephrogenic cord caudal region of nephrogenic cord rear part of nephrogenic cord rear portion of nephrogenic cord uberon rostral part of nephrogenic cord The initial renal anlage that develops from the most rostral part of the nephrogenic cord is termed the pronephros. UBERON:0005754 uberon acellular membrane A acellular anatomical structure that is the bounding layer of a anatomical structure. FMA:63871 UBERON:0005764 uberon basement membrane of epithelium AAO:0010596 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. FMA:63872 GAID:915 UBERON:0005769 UMLS:C0004799 basement membrane basement membrane of connective tissue membrana basalis 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. uberon nephric ridge EHDAA2:0001242 EHDAA:1015 EMAPA:16368 Nephric tubules (nephrons) form embryonically along the nephric ridge. The ridge comprises three regions; anterior, middle and posterior. The functional kidney uses nephrons from only one or two regions of the ridge. A pronephric kidney uses only the nephrons from the anterior region of the ridge. A mesonephric kidney uses only the middle region, a metanephric kidney uses only the posterior region and an opisthonephric kidney uses the middle and posterior regions. TODO - check ridge vs cord vs nephrogenic cord vs blastema UBERON:0005792 VHOG:0001240 nephric cord uberon embryonic uterus FMA:72173 UBERON:0005795 fetal uterus uberon section of aorta Any portion of the aorta including the ascending and descending aorta, and aortic arch or a portion of the aortic orifice of the left ventricle. FMA:13087 UBERON:0005800 UMLS:C0506947 aortic section aortic segment portion of aorta segment of aorta uberon dorsal aorta AAO:0011029 BTO:0004673 DA EHDAA:402 EMAPA:18606 Each primitive aorta receives anteriorly a vein 'the vitelline vein' from the yolk-sac, and is prolonged backward on the lateral aspect of the notochord under the name of the dorsal aorta. The dorsal aortae give branches to the yolk-sac, and are continued backward through the body-stalk as the umbilical arteries to the villi of the chorion. The two dorsal aortae combine to become the descending aorta in later development[WP]. Principal unpaired, median artery of the trunk, leading from the paired roots (radices) of the dorsal aorta to the caudal artery. Kimmel et al, 1995.[TAO] TAO:0000014 The artery in vertebrate embryos that transports blood from the aortic arches to the trunk and limbs. In adult fish it is a major artery that carries oxygenated blood from the efferent branchial arteries to branches that supply the body organ. In adult tetrapods it arises from the systemic arch The dorsal aorta is a blood vessel in a single-pass circulatory system that carries oxygenated blood from the gills to the rest of the body. In a single-pass circulatory system blood passes once through the heart to supply the body once. UBERON:0005805 VHOG:0000264 When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG] XAO:0000051 ZFA:0000014 aorta dorsalis aortae dorsales dorsal aorta root dorsal aortae dorsal aortic root dorsal aortæ relationship loss: part_of axial vasculature (TAO:0001073)[TAO] uberon portal system FMA:45628 In the circulatory system of animals, a portal venous system occurs when a capillary bed drains into another capillary bed through veins, without first going through the heart. Both capillary beds and the blood vessels that connect them are considered part of the portal venous system. They are relatively uncommon as the majority of capillary beds drain into veins which then drain into the heart, not into another capillary bed. Portal venous systems are considered venous because the blood vessels that join the two capillary beds are either veins or venules. Examples of such systems include the hepatic portal system and the hypophyseal portal system. Unqualified, 'portal venous system' often refers to the hepatic portal system. For this reason, 'portal vein' most commonly refers to the hepatic portal vein[WP]. MESH:D011168 UBERON:0005806 UMLS:C0226727 portal venous system uberon spinal cord segment FMA:62420 MA:0003080 This is currently used loosely to refer to cervical, lumbar, etc as well as the metamerically repeated segments, which may correspond more closely with the ZFA neuromere term UBERON:0005844 axial part of spinal cord axial regional part of spinal cord segment of spinal cord spinal neuromeres uberon developing mesenchymal condensation A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 EHDAA2_RETIRED:0003148 EHDAA:8979 UBERON:0005856 mesenchyme condensation uberon cartilaginous condensation AEO:0000147 Cell condensation that is an aggregation of mesenchymal cells that are committed to differentiate into chondroblasts and chondrocytes. EHDAA2_RETIRED:0003147 EMAPA:32731 UBERON:0005863 VSAO:0000092 XAO:0004022 cartilage condensation cartilagenous condensation chondrogenic condensation isa cell condensation in VSAO; has_part chondroblast in AEO uberon pre-cartilage condensation A closely packed aggregation of mesenchymal cells just prior to their differentiation into embryonic cartilage. A delimited region of dense mesenchyme within looser mesenchyme whose cells are committed to become chondroblasts. AEO:0000150 EHDAA2:0003150 EMAPA:32736 UBERON:0005866 pre-chondrogenic condensation precartilage condensation precartilagenous condensation prechondrogenic condensation uberon mandibular prominence EHDAA2:0001061 EHDAA:5871 EMAPA:17355 FMA:293051 UBERON:0005867 UMLS:C1512982 check develops_from mandibular process mandibular swelling prominentia mandibularis 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 uberon autopodial extension A subdivision of the autopod that corresponds to one or more bones arranged in series branching from the main limb axis. UBERON:0005881 digit or predigit encompasses digits and prepollex. requires review limb outgrowth uberon serous sac EMAPA:16060 FMA:9689 MA:0000005 Organ with organ cavity, which has as parts a serous membrane and a serous cavity . Examples: pleural sac, pericardial sac, tendon sheath, bursa.[FMA] See notes for serous membrane UBERON:0005906 uberon endo-epithelium Epithelium that derives from the endoderm. Examples: urothelium, transitional epithelium of ureter, epithelium of prostatic gland.[FMA] FMA:69065 UBERON:0005911 endoderm-derived epithelium endoepithelium uberon axial skeleton plus cranial skeleton AAO:0000963 EMAPA:17214 EMAPA:18043 MA:0000308 Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO] Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified]. UBERON:0005944 UMLS:C0222645 VSAO:0000056 XAO:0004011 http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton skeleton axiale uberon outflow tract of atrium An outflow tract that is part of a cardiac atrium. FMA:14141 UBERON:0005946 outflow part of atrium uberon outflow part of right atrium FMA:9550 Outflow part of atrium which consists of wall and cavity of the outflow part of right atrium and the tricuspid valve.[FMA] UBERON:0005965 main part of right atrium outflow tract of right atrium uberon outflow part of left atrium An outflow tract of atrium that is part of a left atrium. FMA:9551 UBERON:0005966 main part of left atrium outflow tract of left atrium uberon amniotic fold A sheet of somatopleure that grows upward over the embryo and eventually meets in the midline enclosing the embryo, eventually giving rise to the amnion and chorion[Kardong]. EMAPA:16076 UBERON:0005971 uberon heart layer The laminar structure of the heart UBERON:0005983 uberon coronary vessel Any of the arteries or veins that supply blood to the heart or return blood from the heart muscles to the circulation MESH:D003331 TODO - change relation from part_of UBERON:0005985 uberon chorda tendineae FMA:12225 GAID:564 MESH:D002815 The tendinous strands that connect the papillary muscles on the wall of the ventricles to the leaflets of the atrioventricular valves; the chordae tendineae serve to prevent the AV valves from prolapsing back into the atria UBERON:0005994 UMLS:C0008484 chordae tendinea chordae tendineae cordis uberon mitral valve anulus FMA:9498 The fibrous ring of the mitral valve that attaches the cusps of mitral valve to the heart, and which consists of portions of the fibrous scallops of the anterior and posterior cusps UBERON:0005995 anulus of mitral valve fibrous ring of mitral valve mitral annulus mitral anulus mitral valvar anulus uberon mitral valve cusp The two fibrous components and associated flaps of the mitral valve UBERON:0005996 uberon 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. UBERON:0006003 add subclasses based on resolution of CARO tracker item. Also check: adnexal gland. Note that MP implicitly includes hypodermis. adnexae cutis body hair or bristle skin adnexa skin adnexal structure skin appendage 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] uberon fibrous ring of heart A ring of ribrous tissue that surrounds the atrioventricular and arterial orifices BTO:0003628 FMA:9497 Lower's ring TODO - compare with ZFA atrioventricular ring, part of the conduction system UBERON:0006008 annulus fibrosus cordis anulus fibrosus cordis anulus fibrosus of heart aortic annulus atrioventricular ring coronary tendon fibrous ring of heart uberon cusp of cardiac valve FMA:7232 The part of the heart valves that serves to seal the heart valves when closed. There are three cusps for each valve except for the mitral valve, which has only two (hence its alternate name, 'bicuspid valve'). 'Nodules' are located at the tip of the valve, to form a tighter seal[WP]. UBERON:0006009 UMLS:C0225923 cardiac valve cusp cardiac valvular cusp cardiac valvule cardial valve cusp semilunar valvule uberon multi-limb segment region A collection of two or more connected limb segments. Examples: arm (comprising stylopod and zeugopod regions). UBERON:0006058 uberon nerve fiber A threadlike extension of a nerve cell and consists of an axon and myelin sheath (if it is myelinated) in the nervous system. There are nerve fibers in the central nervous system and peripheral nervous system. A nerve fiber may be myelinated and/or unmyelinated. In the central nervous system (CNS), myelin by oligodendroglia cells is formed. Schwann cells form myelin in the peripheral nervous system (PNS). Schwann cells also make a thin covering in an axon without myelin (in the PNS). A peripheral nerve fiber contains an axon, myelin sheath, schwann cells and its endoneurium. There are no endoneurium and schwann cells in the central nervous system. BAMS:nfi FMA:5914 MESH:A08.663.542 UBERON:0006134 nerve fibers nerve fibre neurofibra neurofibra neurofibrous neurofibrum uberon myelinated nerve fiber Axons of neurons encased in a lipoproteinaceous material called myelin. (MeSH) FMA:5915 GAID:745 MESH:A08.663.542.512 UBERON:0006135 UMLS:C0027750 consider adding link to UBERON:0002316 ! white matter of neuraxis http://www1.pbrc.hawaii.edu/~danh/MyelinEvolution/evolution.html, http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=6134604, http://en.wikipedia.org/wiki/Myelin#Invertebrate_myelin uberon unmyelinated nerve fiber FMA:5916 GAID:767 MESH:A08.663.542.756 UBERON:0006136 UMLS:C0501409 non-myelinated nerve fiber uberon rhombic lip DHBA:10664 EHDAA2:0000231 EMAPA:17074 TAO:0001440 The interface between the dorsal neuroepithelium and the roofplate of the fourth ventricle. The source of a number of migratory neuron populations of the hindbrain.[TAO] UBERON:0006215 UBERON:0013163 XAO:0004135 ZFA:0001440 cerebellar anlage cerebellar primordium cerebellum primordium dorsal part of alar plate of metencephalon future cerebellum presumptive cerebellum rostral rhombic lip the posterior section of the developing metencephalon recognized transiently within the vertebrate embryo; the rhombic lip extends posteriorly from the roof of the fourth ventricle to dorsal neuroepithelial cell and can be divided into eight structural units based on rhombomeres 1-8 (r1-r8), recognized at early stages of hindbrain development; producing granule cells and five brainstem nuclei, the rhombic lip plays an important role in developing a complex cerebellar neural system uberon cloacal membrane A membrane that separates the proctodeum and the hindgut in the early embryo. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.497, see_Kardong_KV][VHOG] EHDAA2:0000257 EHDAA:214 EHDAA:2933 EMAPA:16832 FMA:295525 In mammals, the cloaca exists as an embryonic structure that undergoes septation to become distinct urethral, anal, and genital orifices.[well established][VHOG] The membrane that covers the embryonic cloaca, formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm; the urorectal septum joins the cloacal membrane and divides it into an anal membrane and a urogenital membrane; the point where the urorectal septum intersects the cloacal membrane is the future site of the perineal body; proliferation of mesoderm and ectoderm around the cloacal membrane produces primordial tissues of the external genitalia in both sexes: the genital tubercle, genital folds, and genital swellings. UBERON:0006217 UMLS:C0231056 VHOG:0001198 embryonic cloacal membrane membrana cloacalis uberon foregut-midgut junction Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[well established][VHOG] An anatomical junctions that overlaps the foregut and midgut. EHDAA2:0000569 EHDAA:526 EMAPA:16363 UBERON:0006235 VHOG:0000291 uberon future brain BAMS:Enc BTO:0004726 EFO:0003431 EHDAA:300 EHDAA:830 EMAPA:16089 EMAPA:16471 FMA:312967 RETIRED_EHDAA2:0000591 TAO:0000146 The embryonic precursor of the brain and the set of mature brain structures that derive from it (CUMBO) The embryonic precursor of the brain. UBERON:0006238 ZFA:0000146 brain rudiment embryonic brain encephalon presumptive brain uberon future forebrain A presumptive structure that has the potential to develop into a forebrain. BAMS:Pros EFO:0003423 EHDAA2:0000661 EHDAA:2643 EMAPA:16640 TAO:0000062 TODO. Add relationships to neural plate (both ZFA and EMAPA time this with the neural plate) UBERON:0006240 ZFA:0000062 future prosencephalon presumptive forebrain presumptive prosencephalon prosencephalon uberon future spinal cord EFO:0003438 EHDAA2:0000674 EHDAA:898 EMAPA:16092 EMAPA:16525 EMAPA:16755 TAO:0000417 UBERON:0006241 ZFA:0000417 presumptive spinal cord presumptive spinal cord neural keel presumptive spinal cord neural plate presumptive spinal cord neural rod uberon gall bladder primordium A sac-like cavity ventral to the liver, lying in the sub-mesodermal space and closed by a thin sheet of ectodermal cells, from which the future gall bladder develops. EHDAA2:0000700 EHDAA:3047 EMAPA:16713 UBERON:0006242 XAO:0004205 uberon lingual swellings EHDAA2:0000996 EMAPA:17186 Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle.[well established][VHOG] Primordium of the tongue; the median swelling and the distal and proximal swellings arise from the ventral aspect of the stomodeum. [TFD][VHOG] UBERON:0006260 VHOG:0000449 lingual swelling the collection consisting of the two lateral swellings and the medial swelling uberon notochordal plate EHDAA2:0001278 EHDAA:264 EMAPA:16101 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. 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] UBERON:0006267 UMLS:C1518429 VHOG:0001212 uberon notochordal process A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot EHDAA2:0001279 EHDAA:224 EMAPA:16102 FMA:293135 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. UBERON:0006268 UMLS:C1518430 VHOG:0001213 chordamesoderm presumptive notochord uberon otic pit A depression appearing in each otic placode, marking the beginnning of embryonic development of the internal ear. [TFD][VHOG] EHDAA2:0001336 EHDAA:929 EMAPA:16536 FMA:302911 UBERON:0006273 UBERON:0009123 VHOG:0001147 otic cup the pair of depressions of thickened otic placode epithelium, that further develops into the otic vesicles uberon future cardiac ventricle EHDAA2:0001531 EMAPA:16233 EMAPA:16350 FMA:71006 Multi-tissue structure that is part of the heart tube and will become the cardiac ventricle. TAO:0002231 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] UBERON:0006283 UBERON:0010226 ZFA:0001719 early heart ventricle embryonic heart ventricle embryonic ventricle future heart ventricle presumptive cardiac ventricle heart tube primitive ventricle primitive ventricle of heart primordial cardiac ventricle primordial ventricle uberon early prosencephalic vesicle DHBA:10595 EHDAA2:0001571 EHDAA:1356 EMAPA:16521 TAO:0001259 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] UBERON:0006284 VHOG:0000644 ZFA:0001259 forebrain ventricle forebrain vesicle future brain vesicle that gives rise to telencephalic ventricle/lateral ventricles and 3rd ventricle preevaginated forebrain vesicle prosencephalic ventricle prosencephalic vesicle uberon bodily fluid FMA:280556 GAID:266 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:D001826 UBERON:0006314 body fluid fluid galen:BodyFluid uberon annulus fibrosus A ring of fibrous or fibrocartilaginous tissue (as of an intervertebral disk or surrounding an orifice of the heart). BTO:0003627 EMAPA:32670 FMA:76704 UBERON:0006444 anulus anulus fibrosus fibrocartilaginous ring fibrous ring uberon renal duct A tube in the kidney that collect and transport urine. TAO:0005289 UBERON:0006553 ZFA:0005289 in ZFA this is defined as part of mesonephros uberon obsolete urinary system structure 1 Obsoleted because this ontology discusses part-wise grouping classes UBERON:0006554 uberon excretory tube A tube that is part of a excretory system. UBERON:0006555 uberon lymphatic part of lymphoid system AAO:0010522 An organ system subdivision that is a network of vessels capable of removing accumulating protein and fluid from the interstitial space and returning it to the vascular space. In some species, this network is connected to the immune system via lymph nodes and lymphocyte-producing organs, with the whole being the lymphoid system. CALOHA:TS-2024 EFO:0000870 EMAPA:18248 FMA:7162 MA:0002961 MESH:D008208 Part of the circulatory system which consists of a series of vessels which collect blood (exclusive of erythrocytes) which seep through capillary walls and return it to the veins.[AAO] UBERON:0006558 VHOG:0001761 consider merging with lymph vasculature in FMA this is part of the cardiovascular system, but here we treat the CV system as a separate component of the circulatory system from the lymphatic system lymphatic system lymphatic tree system lymporeticular lymporeticular system uberon pharynx FBbt:00005380 MAT:0000049 MIAA:0000049 The pharynx is the part of the digestive system immediately posterior to the mouth[GO]. UBERON:0006562 anterior part of foregut branchial currently this is an extremely generic class, encompassing both protostomes and deuterostomes. pharyngeal pharyngeal tube uberon presumptive endoderm AAO:0000471 EFO:0003437 Presumptive structure of the blastula that will develop into endoderm. TAO:0000416 UBERON:0006595 ZFA:0000416 uberon presumptive blood AAO:0000468 EFO:0003439 TAO:0000568 UBERON:0006596 ZFA:0000568 future blood uberon presumptive structure AAO:0000479 Consider merging with anlage Portion of embryonic tissue determined by fate mapping to become a structure. TAO:0001116 UBERON:0006598 ZFA:0001116 future structure presumptive structures uberon presumptive ectoderm AAO:0000470 EFO:0003466 Presumptive structure of the blastula that will develop into ectoderm. TAO:0001376 UBERON:0006601 XAO:0004132 ZFA:0001376 presumptive epidermis uberon presumptive mesoderm AAO:0000476 EFO:0003467 Presumptive structure of the blastula that will develop into mesoderm. TAO:0001377 UBERON:0006603 ZFA:0001377 uberon interphalangeal joint 2 2 A joint that connects one phalanx to another along a proximodistal axis. FMA:42765 Hinge joints between the phalanges of the hand or foot[ncithesaurus:Interphalangeal_Joint]. UBERON:0006658 galen:InterphalangealJoint inter-phalangeal joint inter-phalanx joint uberon mesopodium region Naming conventions for pod terms under discussion within phenoscape group The third segment of the limb, including either the wrist segment (carpus) or the ankle segment (tarsus) UBERON:0006716 carpus/tarsus mesopod mesopodial limb segment mesopodial segment uberon autopodial skeleton Distal section of the limb skeleton, consisting of the anterior autopodium or posterior autopodium.[VSAO] Naming conventions for pod terms under discussion within phenoscape group The collection of all skeletal elements in an autopodium region. UBERON:0006717 VSAO:0005019 autopod skeleton autopodial skeleton autopodium skeletal parts of autopod skeleton of autopod uberon median lingual swelling During the third week of embryological development there appears, immediately behind the ventral ends of the two halves of the mandibular arch, a rounded swelling named the tuberculum impar, which was described by His as undergoing enlargement to form the buccal part of the tongue. More recent researches, however, show that this part of the tongue is mainly, if not entirely, developed from a pair of lateral swellings which rise from the inner surface of the mandibular arch and meet in the middle line. The site of their meeting remains post-embryonically as the median sulcus of the tongue. The tuberculum impar is said to form the central part of the tongue immediately in front of the foramen cecum, but Hammar insists that it is purely a transitory structure and forms no part of the adult tongue[WP, Gray's]. EHDAA2:0001081 EMAPA:17187 FMA:312476 Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle.[well established][VHOG] The thyroid initially develops caudal to the tuberculum impar . This embryonic swelling arises from the first pharyngeal arch and occurs midline on the floor of the developing pharynx, eventually helping form the tongue as the 2 lateral lingual swellings overgrow it. [http://emedicine.medscape.com/article/845125-overview] UBERON:0006756 VHOG:0000730 median lingual swelling median tongue bud tuberculum impar tuberculum linguale mediale uberon lateral lingual swelling During the third week there appears, immediately behind the ventral ends of the two halves of the mandibular arch, a rounded swelling named the tuberculum impar, which was described by His as undergoing enlargement to form the buccal part of the tongue. More recent researches, however, show that this part of the tongue is mainly, if not entirely, developed from a pair of lateral swellings (or distal tongue bud) which rise from the inner surface of the mandibular arch and meet in the middle line. EHDAA2:0000911 EMAPA:17189 FMA:313628 Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle.[well established][VHOG] UBERON:0006757 VHOG:0000731 lateral lingual prominence lateral swellings paired tuberculum laterale tuberculum linguale laterale uberon glandular epithelium An epithelium that is composed primarily of secretory cells. BTO:0002991 UBERON:0006799 UMLS:C0682578 UMLS:C1708242 consider splitting epithelium from epithelial tissue uberon surface groove A furrow or an incomplete tube. AEO:0000161 EHDAA2_RETIRED:0003161 UBERON:0006846 groove uberon adrenal/interrenal gland All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG] This gland can either be a discrete structure located bilaterally above each kidney, or a cluster of cells in the head kidney that perform the functions of the adrenal gland. In either case, this organ consists of two cells types, aminergic chromaffin cells and steroidogenic cortical cells[GO] UBERON:0006858 VHOG:0001141 adrenal - interrenal gland adrenal gland - interrenal gland adrenal gland/interrenal tissue keep this grouping class so long as it is required for GO suprarenal gland - interrenal gland uberon terminal part of digestive tract FBbt:00005756 The distalmost portion of the digestive tract, derived from the hindgut, and terminating with the anus. UBERON:0006866 WBbt:0005773 rectal part of digestive tract rectum terminal section of digestive tract this class is the superclass of 'rectum', which is currently reserved for the vertebrate structure. May be merged in future. uberon footplate EHDAA2 does not have a single class for footplate, but includes epithelium, mesenchyme and AER EHDAA:5143 EHDAA:6096 EMAPA:17249 FMA:296800 UBERON:0004343 UBERON:0006871 UMLS:C1517291 distal part of hindlimb bud foot disk foot plate the distal elements of the developing limb of vertebrates that will give rise to the pedal appendages (e.g. hand, foot, paw) uberon vasculature of organ A vasculature that is part of a organ. FMA:74612 UBERON:0006876 organ vasculature set of blood vessels of organ uberon head mesenchyme from mesoderm A head mesenchyme that develops_from a mesoderm. AAO:0011051 EFO:0003337 EFO:0003603 EHDAA2:0001118 EHDAA:655 EMAPA:16099 EMAPA_RETIRED:16270 FMA:293859 TAO:0000998 UBERON:0006904 VHOG:0000185 XAO:0000053 ZFA:0000998 cranial mesoderm head mesenchyme derived from mesoderm head mesenchyme from head mesoderm head mesenchyme from mesoderm head 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 mesenchyme derived from head mesoderm mesenchyme from head mesoderm uberon lumen of digestive tract An anatomical space that surrounded_by a digestive tract. BTO:0000349 EMAPA:32908 FMA:45677 UBERON:0006909 digestive tract lumen gut cavity gut lumen lumen of alimentary tract lumen of digestive tract lumen of gut uberon squamous epithelium An epithelium characterised by its most superficial layer consisting of squamous epithelial cells. BTO:0002072 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 UBERON:0006914 UMLS:C0221909 uberon stomach glandular epithelium A glandular epithelium that lines the stomach. The stomach's glandular epithelium is characterized by the presence of gastric glands. EMAPA:17623 EMAPA:35814 FMA:63458 MA:0002784 UBERON:0006924 epithelium of gastric gland gastric gland epithelium uberon we follow Kardong in treating the glandular epithelium as a distinct entity, and thus as an epithelium which has glands; FMA has 'epithelium of gastric gland', which is part of the gastric gland. digestive gland A gland, such as the liver or pancreas, that secretes into the alimentary canal substances necessary for digestion. AAO:0000130 BTO:0000345 UBERON:0006925 digestive system gland uberon glandular columnar epithelium FMA:64800 Simple columnar epithelium that constitutes the secretory part of a gland. Examples: epithelium of stomach, luminal epithelium of lactiferous duct.[FMA] UBERON:0006929 UMLS:C0225337 uberon stomach glandular region mucosa EMAPA:27167 MA:0001614 UBERON:0006931 stomach glandular region glandular mucous membrane stomach mucosa that is lined with glandular epithelium and part of a stomach glandular region. uberon uterine epithelium An epithelium that is part of a uterus. BTO:0003082 UBERON:0006955 uberon uterus epithelium vascular cord EFO:0003709 TAO:0005077 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]. UBERON:0006965 ZFA:0005077 uberon anatomical surface 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 AAO:0010270 BILA:0000010 CARO:0001002 EHDAA2:0003192 FMA:24137 ID:0000000 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. UBERON:0006984 UMLS:C1515977 ZFA:0005594 uberon cardiac mesoderm AAO:0011021 BILA:0000051 EFO:0000315 EHDAA2:0000214 EHDAA:385 FMA:293143 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]. UBERON:0007005 VHOG:0001641 XAO:0000235 cardiogenic mesoderm cardiogenic region consider FBbt:00005541 ! cardiogenic mesoderm heart primordia review EHDAA2 placement uberon cleaving embryo BILA:0000058 Organism at the cleavage stage. UBERON:0007010 uberon presumptive gut BILA:0000084 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 UBERON:0007026 UMLS:C1514442 embryonic digestive tube future digestive tract future digestive tube future gut primitive gut primordial digestive tube primordial gut uberon primary circulatory organ A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified]. FBbt:00003154 Gene notes: Bmp, Nkx, Gata SPD:0000130 TADS:0000147 UBERON:0007100 adult heart dorsal tube heart 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 uberon pharyngeal pouch 2 2nd arch branchial pouch 2nd arch branchial pouch endoderm 2nd arch pouch endoderm 2nd branchial pouch 2nd pharyngeal pouch endoderm 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] A pharyngeal puch that is between the pharyngeal arches 2 and 3. A pouch that is situated between the 2nd and 3rd pharyngeal arch. [ISBN10:0124020607][VHOG] AAO:0011115 Contributes to the middle ear, epithelial lining of Crypts (spaces) of the palatine tonsils, supplied by the facial nerve EFO:0003633 EHDAA2:0000058 EMAPA:16275 EMAPA:16276 FMA:295676 RETIRED_EHDAA2:0000060 Second of the pharyngeal (endodermal) evaginations between the visceral arches from which the Eustachian tube is derived; pouches 2-4 open as gill slits.[AAO] TAO:0001130 UBERON:0005715 UBERON:0007123 UMLS:C0231069 VHOG:0000561 VHOG:0000967 XAO:0000247 ZFA:0001130 pharyngeal pouches 2 second arch pharyngeal pouch second pharyngeal pouch second visceral pouch the dorsal elongation of the second pouch endoderm of all mammals, with the exception of rodents, gives rise to the epithelial lining of palatine tonsils; in rodents, the ventral portion of the second pouch appears to degenerate whereas the remaining part is incorporated into the lateral border of the pharynx; it appears that rodents no longer require tonsils as their function is carried out by the NALT (Nose/Nasal-Associated Lymphoid Tissue) system in the upper respiratory tract. uberon visceral pouch 2 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. 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 UBERON:0007135 ZFA:0000131 presumptive central nervous system uberon tracheobronchial tree FMA:7393 The structure from the trachea, bronchi, and bronchioles that forms the airways that supply air to the lungs. The lining of the tracheobronchial tree consists of ciliated columnar epithelial cells. UBERON:0004102 UBERON:0007196 arbor tracheobronchialis tracheobronchial system uberon mesenchyme derived from head neural crest EFO:0003572 EHDAA2:0000735 EMAPA:16169 EMAPA:16271 EMAPA_RETIRED:16271 Mesenchyme that develops_from a cranial neural crest. TAO:0000787 UBERON:0007213 ZFA:0000787 head mesenchyme from cranial neural crest head mesenchyme from neural crest head neural crest derived mesenchyme uberon neonate stage BTO:0001762 EV:0300037 HsapDv:0000082 MmusDv:0000096 NIF_Organism:birnlex_695 OGES:000025 Of or pertaining to the period of time immediately following birth, or to the newborn. UBERON:0007221 consider splitting infant/newborn fledgling stage hatchling hatchling stage infant stage neonatal stage nestling stage newborn stage pouch stage puggle puggle stage uberon 1st arch mandibular component EHDAA2:0000031 EHDAA:583 EMAPA:16382 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] UBERON:0007237 VHOG:0000510 relationship to Meckel's cartilage to be added uberon ventral mandibular arch ventral pharyngeal arch 1 ventral visceral arch 1 pelvic appendage skeleton The collection of all skeletal elements in a pelvic appendage region. UBERON:0007273 uberon presumptive hindbrain BAMS:HB CALOHA:TS-2118 EFO:0003440 EHDAA2:0001630 FMA:295640 TAO:0000569 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]. 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. UBERON:0007277 ZFA:0000569 embryonic rhombencephalon future hindbrain presumptive rhombencephalon rhombencephalon uberon presumptive endocardium 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 UBERON:0007280 ZFA:0001724 uberon presumptive midbrain hindbrain boundary EFO:0003446 Embryonic structure that gives rise to the midbrain hindbrain boundary. TAO:0001187 UBERON:0007281 XAO:0004086 ZFA:0001187 presumptive MHB presumptive midbrain-hindbrain boundary uberon presumptive segmental plate A presumptive structure that has the potential to develop into a presomitic mesoderm. EFO:0003421 TAO:0000053 UBERON:0007282 ZFA:0000053 presumptive segmental plates uberon presumptive neural plate A presumptive structure that has the potential to develop into a neural plate. EFO:0003424 Region of the gastrula which gives rise to the neural plate.[TAO] TAO:0000063 UBERON:0007284 ZFA:0000063 consider merging prospective neuroectoderm prospective vegetal ectoderm uberon presumptive paraxial mesoderm A presumptive structure that has the potential to develop into a paraxial mesoderm. EFO:0003443 TAO:0000591 UBERON:0007285 XAO:0004134 ZFA:0000591 future paraxial mesoderm uberon presumptive pronephric mesoderm A presumptive structure that has the potential to develop into a pronephric mesoderm. EFO:0003619 TAO:0001070 UBERON:0007297 ZFA:0001070 nephron primordium uberon pancreatic lobule A dense accumulation of exocrine glands in the pancreas often surrounding islets of Langerhans. FMA:16012 In mice many lobules lack islets, in contrast to other mammals including humans MA:0000721 TODO - check UBERON:0007324 lobulus pancreaticus pancreas lobe pancreatic lobule uberon pancreatic duct A duct that is part of the pancreas and connected to the duodenum. Duct connecting the pancreas with the intestine. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] EHDAA:9194 EMAPA:32952 FMA:10419 MA:0000124 TAO:0001372 These data show that ducts within the zebrafish pancreas originally arise in situ from isolated progenitor cells rather than arising from reiterative branching of the pancreatic epithelium. This process of pancreatic duct formation in zebrafish may be analogous to the mechanism of duct formation in the mammalian mammary and salivary glands. (...) A related mechanism of duct formation has also been proposed to occur within the mammalian pancreatic epithelium.[uncertain][VHOG] UBERON:0007329 VHOG:0000254 ZFA:0001372 duct of pancreas ductus pancreaticus in EHDAA2, the dorsal and ventral ducts are classified as epithelial sacs - review after overhaul of duct/epithelia terms pancreas duct this class groups together accessory (dorsal) and main (ventral) pancreatic ducts uberon outer epithelium BSA:0000073 BTO:0000313 FBbt:00004993 HAO:0000298 TADS:0000109 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]. UBERON:0007376 WBbt:0005733 epidermis epidermis (sensu Metazoa) hypoderm hypodermis outer epidermal layer outer epithelial layer this grouping class exists primarily to align with GO - see GO:0008544. uberon stratum compactum AAO:0010600 Portion of the dermis characterized by a well-arranged, plywood-like, collagenous network. Portion of the dermis characterized by a well-arranged, plywood-like, collagenous network. Le Guellec et al, 2004.[TAO] TAO:0001182 UBERON:0007377 ZFA:0001182 connective tissue in the skin is usually diffuse and irregular, although in some species collagen bundles are arranged in a distinct ordered layer in the dermis dermal deep region relationship loss: develops_from collagenous dermal stroma (TAO:0001186)[TAO] uberon enveloping layer of ectoderm EFO:0003425 EVL 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. 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] TAO:0000086 UBERON:0007383 ZFA:0000086 enveloping layer relationship loss: develops_from superficial blastomere (TAO:0001484)[TAO] uberon epithelial sac AEO:0000115 An epithelial tube that is open at one end only. EHDAA2:0003115 UBERON:0007499 uberon epithelial tube open at both ends AEO_RETIRED:0000116 An epithelial tube open at both ends that allows fluid flow. RETIRED_EHDAA2:0003116 UBERON:0007500 uberon epithelial vesicle A closed epithelium with a lumen. AEO:0000119 EHDAA2:0003119 EHDAA2:0003119 UBERON:0007503 uberon dense mesenchyme tissue AEO:0000146 EHDAA2:0003146 EHDAA2:0003146 Mesenchyme with little extracellular matrix. UBERON:0007524 uberon migrating mesenchyme population AEO:0000152 EHDAA2:0003152 EHDAA2:0003152 Mesenchymal cells that are migrating. UBERON:0007530 this class will be an important part of the NC reorganization uberon ciliated columnar oviduct epithelium A ciliated columnar epithelium that is part of a oviduct. FMA:62016 MA:0001719 UBERON:0007589 epithelium of uterine tube in FMA, epithelium of uterine tube is a subclass of ciliated columnar epithelium. MA introduces subtypes: ciliated columnar and cuboidal. We map the FMA type according to its relationships, not its label uberon uterine tube epithelium ciliated columnar epithelium Ciliated columnar epithelium in the pulmonary system is interspersed with goblet cells that secrete mucous to form a mucosal layer apical to the epithelial layer. The rowing-like action of epithelial cilia work in tandem with goblet cells to propel mucus away from the lungs, preventing particulate matter from causing infection[http://www.bio.davidson.edu/people/kabernd/berndcv/lab/epithelialinfoweb/ciliated%20columnar%20epithelium.html] FMA:64798 In humans, Ciliated columnar epithelial cells are found mainly in the tracheal and bronchial regions of the pulmonary system and also in the fallopian tubes of the female reproductive system Simple columnar epithelium in which the luminal side of the cells bears cilia. Examples: epithelium of trachea, epithelium of uterine tube.[FMA] UBERON:0007592 uberon ciliated epithelium Epithelium bearing vibratile cilia on the free surface. UBERON:0007601 uberon layer of synovial tissue 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 UBERON:0007616 stratum synoviale synovial layer synovial membrane synovial tissue synovium uberon synovial cavity of joint An anatomical cavity that surrounded_by a synovial joint. FMA:11356 UBERON:0007617 articular cavity (synovial joint) cavitas articularis (junctura synovialis) cavity of synovial joint joint cavity synovial cavity uberon pigment epithelium of eye GAID:907 MESH:D010857 UBERON:0007625 epithelial layer of the retina, ciliary body, or iris composed of cells containing pigment granules. eye pigment epithelium uberon future meninx A developing mesenchymal capsule that covers the developing brain and spinal cord and is the precursor of the meningeal cluster. In mammals this gives rise to the arachnoid mater, pia mater and dura mater. In cyclostomes and fishes, the future meninx gives rise to a single meningeal layer, the primitive meninx. EHDAA2:0004453 UBERON:0004065 UBERON:0007645 decide whether to treat the endo and ecto meninx as subtypes or parts of the future meninx meninx primitiva primary meninx primitive meninx primordial meninx the outermost mesenchymal covering of the developing brain and spinal cord that is composed of tough fibrous connective tissue from which the arachnoid mater, pia mater and dura mater are formed[MP:0009726]d uberon anatomical junction 2 An anatomical structure that connects two structures FMA:5898 UBERON:0007651 anatomical junction junction uberon uriniferous tubule FMA:17691 UBERON:0007684 functional unit of the kidney that forms urine, consisting of two parts, the nephron and the collecting tubule. uberon kidney field UBERON:0007687 kidney anlage region of the embryo into the area in which the kidney rudiment will develop. uberon anlage AEO:0000170 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. EFO:0001649 EHDAA2:0003170 FBbt:00005426 UBERON:0007688 developmental field field future organ organ field uberon thyroid diverticulum UBERON:0007689 diverticulum thyroideum endodermal bud derived from the endodermal epithelium of the embryonic pharyngeal floor[MP]. The thyroid diverticulum is the embryological structure from which thyroid follicular cells derive. It grows from the floor of the pharnyx[WP]. saccus thyroideus uberon early pharyngeal endoderm . EFO:0003626 EHDAA2:0001457 EHDAA:962 EMAPA:32754 FMA:293087 TAO:0001104 UBERON:0007690 ZFA:0001104 early pharyngeal arch endoderm pharyngeal arch endoderm pharyngeal endoderm pharyngeal region endoderm relation conflict: ZFA vs EHDAA2. Note EHDAA2 term renamed to 'early PA endoderm' uberon transduate Body substance in liquid state, which is derived from plasma by passage through the (intact) wall of capillaries without further processing by secretory cells or glands. FMA:12276 GAID:1195 MESH:D005122 UBERON:0007779 ncithesaurus:Transudate transudative uberon serous fluid Any fluid produced by a serous gland. FMA:20932 UBERON:0007794 serous gland fluid the FMA def is Transudate contained in a serous sac uberon vascular system Anatomical system that consists of all blood and lymph vessels. BTO:0001085 CALOHA:TS-2053 EHDAA2:0004520 EMAPA:35905 Gefaesssystem@ge MA:0002718 The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]. UBERON:0007798 UMLS:C0489903 consider merging with vasculature in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system uberon craniocervical region CALOHA:TS-2356 EV:0100009 FMA:280881 MA:0000006 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. UBERON:0007811 UMLS:C0460004 WikipediaCategory:Head_and_neck cephalic area cephalic part of animal cephalic region galen:HeadAndNeck head and neck head or neck uberon appendage girdle region An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There are only two instances of appendage girdle regions per organism.[VSAO] FMA:24874 UBERON:0007823 UBERON:0007824 VSAO:0000303 fin girdle fin girdle region girdle girdle region limb girdle limb girdle region this encompasses non-skeletal tissue uberon pelvic girdle skeleton AAO:0000426 AAO:0000768 Anatomical cluster by which the hind limbs are supported and attached to the vertebral column.[AAO] Anatomical cluster that consists of the paired basipterygia which support the pelvic fin.[TAO] EFO:0000947 EHDAA2:0001426 EHDAA:7149 EHDAA:8324 EMAPA:18028 FMA:87592 Girdle skeleton consisting of a set of bones linking the axial series to the hindlimb/fin skeleton and offering anchoring areas for hindlimb/fin and caudal musculature.[VSAO] MAT:0000182 MIAA:0000182 Note that the VSAO and many ontologies use the label 'pelvic girdle' to denote the skeletal region specifically. We place the EHDAA2 class here, note that this includes the pre-cartilage condensation as parts Skeletal subdivision consisting of a set of bones linking the axial series to the hindlimb zeugopodium and offering anchoring areas for hindlimb and caudal musculature. TAO:0000565 The pelvic girdle is never joined by contributions of dermal bone. From its first appearance in placoderms, the pelvic girdle is exclusively endoskeletal. It arose from pterygiophores, perhaps several times, in support of the fin.[well established][VHOG] UBERON:0007832 VHOG:0000305 VSAO:0000155 XAO:0003064 ZFA:0000565 galen:PelvicGirdle need to resolve whether this is a paired structure or a single belt (Paired in FMA - implicitly paired in VSAO) pelvic girdle pelvic girdle skeleton skeletal parts of pelvic girdle skeleton of pelvic girdle uberon cartilage element AAO:0011130 CALOHA:TS-0118 EMAPA:32730 FMA:55107 Skeletal element that is composed of cartilage tissue and may be permanent or transient. TAO still mixes tissue and element UBERON:0007844 VSAO:0000000 XAO:0004013 ZFA:0001501 cartilage cartilage organ cartilaginous element chondrogenic element uberon regular connective tissue 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 UBERON:0007845 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). uberon dense regular connective tissue 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] FMA:64781 Regular connective tissue, the intercellular matrix of which consists predominantly of collagen fiber bundles arranged in parallel arrays.[FMA] UBERON:0007846 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 heart endothelium An endothelium that is part of a heart [Automatically generated definition]. BTO:0004293 UBERON:0008307 cardiac endothelium 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. uberon inner cell mass derived epiblast An embryonic structure that is derived from the inner cell mass and lies above the hypoblast and gives rise to the three primary germ layers EHDAA2:0000444 EHDAA:42 EHDAA:75 EMAPA:16050 The epiblast cells (appearing on day 8 of human embryonic development) make up a columnar epithelium with dense microvilli on the apical surface. During gastrulation, the epiblast cells undergo epithelial-to-mesenchymal transition and delaminate to become the loose mesenchyme of the primitive streak. The epiblast is present in postimplantation mouse embryos between E5.5-E7.5. UBERON:0008780 UMLS:C1516906 embryonic epiblast uberon lower limb segment A limb segment that is part of a hindlimb. FMA:24877 UBERON:0008784 free lower limb segment free lower limb subdivision segment of free lower limb subdivision of free lower limb uberon parotid gland primordium EHDAA2:0001413 EHDAA:9246 UBERON:0008801 uberon 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]. Currently defined in a vertebrate specific manner. The arch system has origins in basal deuterostomes, consider generalizing EHDAA2:0000187 FMA:293041 UBERON:0008814 UMLS:C1519038 pharyngeal apparatus pharyngeal arch region pharyngeal arches and clefts pharyngeal system uberon embryonic head A head that is part of a embryo. CALOHA:TS-0246 FBbt:00000155 FMA:293011 UBERON:0008816 uberon hepatic diverticulum AAO:0011057 An out-pocket of thickened ventral foregut epithelium adjacent to the developing heart. Constitutes the first morphological sign of the embryonic liver. The anterior portion of the hepatic diverticulum gives rise to the liver and intrahepatic biliary tree, while the posterior portion forms the gall bladder and extrahepatic bile ducts. EHDAA2:0000740 EHDAA:1530 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. UBERON:0008835 UMLS:C1512407 XAO:0000101 diverticulum hepaticum in mice, the hepatic diverticulum forms by E9 and expands into an obvious liver bud by E10 liver diverticulum uberon liver bud BTO:0001642 UBERON:0008836 uberon pyloric canal FMA:14580 The short narrow part of the stomach extending from the pyloric antrum to the pyloric sphincter UBERON:0008858 canalis pyloricus canalis pyloricus uberon pyloric gastric gland EMAPA:27211 FMA:14922 The gastric glands in the pyloric region of the stomach; the pyloric glands secrete mucin, which coats the stomach and protects it, and hormones such as gastrin and enkephalin[MP]. UBERON:0008861 UMLS:C0227239 check relationship to pylorus vs antrum glandula pylorica pyloric antrum gland pyloric gland pyloric mucuous gland uberon splanchnocranium AAO:0010157 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] Subdivision of endoskeleton derived from pharyngeal arches TAO:0001216 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] UBERON:0008895 VHOG:0000315 VSAO labels this term 'pharyngeal arch' (2012-06-01) - however, it clearly means pharyngeal arch skeleton. VSAO:0000149 XAO:0003176 ZFA:0001216 branchial arch skeleton gill 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 pharyngeal arch pharyngeal arch skeleton pharyngeal endoskeleton pharyngeal skeleton uberon visceral cranium visceral skeletal system visceral skeleton viscerocranium fin AAO:0010374 AEO:0001004 An external projection of an aquatic animal as a fish used in propelling or guiding the body[BTO]. BTO:0004649 EFO:0000875 MAT:0000087 MESH:D058500 MIAA:0000087 OpenCyc:Mx4rvVjcBZwpEbGdrcN5Y29ycA Surface structure involved in locomotion.[TAO] Surface structure involved in locomotion.[VSAO] TAO:0000108 This class groups together various structures that may have arisen through convergent evolution, including, for example, the dorsal fin of a cetacean UBERON:0008897 VSAO:0000099 XAO:0000002 ZFA:0000108 fins uberon lung parenchyma A parenchyma that is part of a lung. EMAPA:35522 FMA:27360 MA:0003168 UBERON:0008946 parenchyma of lung pulmonary parenchyma respiratory portion of lung uberon respiratory primordium EHDAA2:0004069 UBERON:0008947 UMLS:C1514898 uberon renal parenchyma BTO:0003604 FMA:15574 The functional tissue of the kidney, consisting of the nephrons. UBERON:0008987 kidney parenchyma parenchyma of kidney uberon stomach region An organ part that is part of a stomach. EMAPA:35821 MA:0002561 UBERON:0009034 uberon indifferent gonad A gonad prior to differentiating into a definitive testis or ovary. EHDAA2:0000716 UBERON:0009117 UMLS:C1512703 gonad rudiment typically part of the embryo - however, in male tammar wallabies the gonads are indifferent at the neonatal stage[8827321] uberon pleuroperitoneal membrane A fold of tissue which extends into the peritoneal cavity of the developing embryo and participates in the separation of the pleural and peritoneal cavities. EHDAA2:0001483 EMAPA:17709 In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart [of other tetrapods] is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG] UBERON:0009133 UBERON:0009146 UMLS:C1283968 VHOG:0000757 pleuroperitoneal fold pleuroperitoneal membranes uberon craniocervical region vein A vein that is part of a craniocervical region. EHDAA2:0004542 UBERON:0009141 craniocervical vein head and neck veins uberon vein of head and neck entire embryonic mesenchyme EHDAA2:0001113 EHDAA:177 EMAPA:16097 Sum total of mesenchyme in the embryo. UBERON:0003313 UBERON:0009142 consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm) uberon pharyngeal region of foregut EMAPA:16549 RETIRED_EHDAA2:0001454 UBERON:0009145 pharyngeal region uberon indifferent external genitalia EHDAA2:0004021 UBERON:0009196 uberon nephric duct A nephric duct is a tube that drains a primitive kidney[GO]. EMAPA:28425 EMAPA:28429 UBERON:0009201 pronephric duct or mesonephric duct uberon epithelium of foregut-midgut junction An epithelium that is part of a foregut-midgut junction. EHDAA2:0000573 EMAPA:16564 UBERON:0009497 uberon anal membrane endodermal component An endoderm that is part of a anal region. EHDAA2:0004020 EMAPA:17177 UBERON:0009521 uberon endoderm of foregut-midgut junction An endoderm that is part of a foregut-midgut junction. EHDAA2:0000572 EMAPA:18403 UBERON:0009550 uberon distal segment of digit A segment of a digit containing the distal phalanx, and overlapping the distal interphalangeal joint[CJM]. The digit tip is derived from multiple and distinct embryonic origins, and includes the distal bone with associated marrow cavity and haematopoietic cells, ventral (flexor) and dorsal (extensor) tendons, sweat glands with myoepithelial and luminal secreting cells and associated neurons for innervation, dermis with resident melanocytes and dendritic cells, mesenchyme with resident fibroblasts, skin epidermis with hair follicles, a nail organ composed of six specific parts (the root, nail bed, nail plate, eponychium (cuticle), perionychium and hyponychium). Newborn and adult mice are able to regrow forelimb (finger) and hindlimb (toe) digit tips after their amputation through the distal interphalangeal joint. Regeneration of the digit tip involves the integrated regrowth of multiple tissues within 2-3 months, reaching an external morphology that is cosmetically and functionally similar to normal digits. Most importantly, regeneration of the mouse distal digit shares morphological similarities with clinical cases documenting regrowth of missing distal portions of fingers in both children and adults UBERON:0009551 digit tip distal digit segment tip of digit uberon distal limb integumentary appendage A nail, hoof or claw. MESH:D006724 UBERON:0009564 hoof or claw hoof, claw or nail keratin plate keratin sheath uberon unguis subdivision of trunk FMA:25054 UBERON:0009569 region of trunk trunk subdivision uberon midbrain mantle layer EHDAA2:0001172 EMAPA:16977 UBERON:0009581 VHOG:0000910 mantle layer lateral wall mesencephalon mantle layer lateral wall midbrain midbrain lateral wall mantle layer uberon midbrain hindbrain boundary neural plate MHB neural plate TAO:0007044 TODO - developmental relationships for lines UBERON:0009615 ZFA:0007044 midbrain-hindbrain boundary neural plate uberon presumptive midbrain A presumptive structure that has the potential to develop into a midbrain. BAMS:MES EFO:0003432 EHDAA2:0000615 EMAPA:16140 EMAPA:16472 TAO:0000148 TODO - unify naming conventions UBERON:0009616 ZFA:0000148 early midbrain future midbrain mesencephalon presumptive mesencephalon uberon head paraxial mesoderm A major contributor to neurocranium [PMID:16313393] Bilateral mesenchymal mesoderm parallel and immediately adjacent to the neural tube/notochord; it generates a subset of extra-ocular, and other head, muscles. EHDAA2:0000736 EHDAA:364 EMAPA:16171 UBERON:0009617 cephalic paraxial mesenchyme cephalic paraxial mesoderm cranial paraxial mesenchyme cranial paraxial mesoderm head paraxial mesenchyme somitomere somitomeric mesoderm uberon trunk paraxial mesoderm EHDAA2:0002094 UBERON:0009618 trunk and cervical paraxial mesenchyme trunk paraxial mesenchyme uberon hindbrain nucleus Nucleus located within the hindbrain. TAO:0002177 UBERON:0009662 ZFA:0001658 uberon early telencephalic vesicle EFO:0003562 EHDAA2:0001981 EHDAA:1993 EHDAA:2671 EMAPA:16914 UBERON:0009676 early telencephalic ventricle early telencephalic vesicle uberon dorsal pancreas EHDAA2:0001371 UBERON:0009708 pancreatis dorsalis uberon ventral pancreas EHDAA2:0001393 UBERON:0009709 pancreatis ventralis uberon entire pharyngeal arch endoderm EHDAA2:0004621 EMAPA:32754 FMA:293087 UBERON:0009722 pharyngeal arch endoderm uberon limb mesenchyme EMAPA mapping from TH EMAPA:32705 The primordial embryonic connective tissue of the developing limbs, autopods and digits, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to limb connective tissue, bone and musculature in conjunction with myotome cells. UBERON:0009749 limb mesoderm uberon cardiac mesenchyme EHDAA2:0004162 EMAPA:36438 The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing cardiac structures UBERON:0009751 decide whether to merge with cardiac mesoderm. In EHDAA2 this lasts CS12->unbounded, includes mesenchyme of individual components as parts heart mesenchyme uberon distal interphalangeal joint An inter-phalangeal joint that connects a distal phalanx to either a medial or proximal phalanx. DIJ joint DIP joint FMA:65024 UBERON:0009768 uberon renal tubule A renal tubule is a tube that filters, re-absorbs and secretes substances to rid an organism of waste and to play a role in fluid homeostasis. UBERON:0009773 renal tubule (generic) this class groups vertebrate nephron tubules with analagous structures such as insect Malpighian tubules tubule of excretory system uberon pleural sac A serous sac that has the pleura and the pleural cavity as parts. EHDAA2:0004737 FMA:9690 UBERON:0009778 despite its name the class EHDAA2:0004737 is not a true cavity, it corresponds to what we call the sac uberon glandular acinus FMA:55588 The many-lobed berry cluster of cells that is the terminous of a gland where the secretion is produced is acinar in form. UBERON:0009842 acinar acini acinus uberon urogenital sinus mesenchyme Androgen receptor (AR) activation releases instructive signals from UGM that acts on UGS epithelium (UGE) to stimulate cell proliferation, form prostate ductal progenitors (prostatic buds), and regulate cell adhesion dynamics to permit prostatic bud outgrowth EMAPA:31500 EMAPA:31519 Mesenchyme that surrounds primitive urogenital sinus. UBERON:0009845 UGM uberon embryonic cloacal epithelium An epithelium that is part of a embryonic cloaca. EHDAA2:0004585 UBERON:0009846 cloacal epithelium uberon prostate field A specific region of the urogenital sinus epithelium into the area in which the prostate gland will develop. UBERON:0009847 prostate primordium uberon digestive tract diverticulum Branch or outpocketing of the digestive tract. FBbt:00100316 UBERON:0009854 diverticulum of gut intestinal pouch uberon sac UBERON:0009856 diverticulum galen:Diverticulum pouch uberon zone of stomach A division of the stomach. The stomach can be divided based on mucosal histology (glandular epithelium and gastric glands) and the relative position and type of gastric gland. FMA:14558 UBERON:0009870 We follow Kardong in defining stomach regions by gland, but we also include 'body of stomach'. In future we may want to have different partitions of the stomach gastric zone region of stomach section of stomach uberon metapodium region Intermediate segment of the autopod, between the mesopodial region and and acropodial region. Examples: metacarpal region, metatarsal region Naming conventions for pod terms under discussion within phenoscape group UBERON:0009877 cannon region considering adding 'acropodial region' equine cannon region metacarpal or metatarsal part of limb metacarpus/metatarsus metacarpus/metatarsus region metapodial segment metapodium uberon mesopodial skeleton Limb skeleton subdivision consisting of endochondral bones increasing the freedom of movement of the autopodia, and located between zeugopodia and autopodia.[VSAO] The collection of all skeletal elements in a mesopodium. Examples: the tarsal skeleton, the carpal skeleton UBERON:0009878 VSAO:0005022 basipodium basipodium skeleton carpal/tarsal skeleton mesopodial skeleton mesopodium mesopodium skeleton relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: distally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO] skeletal parts of mesopodium uberon anterior lateral plate mesoderm ALPM EFO:0003704 TAO:0005041 UBERON:0009881 ZFA:0005041 uberon secondary heart field A specific region of the lateral mesoderm that will form the majority of the mesodermal component of the right ventricle, arterial pole (outflow tract) and venous pole (inflow tract). In general, the two studies in chick concluded that the contribution of the SHF was to the outflow tract, whereas the mouse work suggested that the second lineage contributed more broadly to the heart, including the outflow tract and much or all of the right ventricle [11-14]. These different conclusions may represent differences in the experimental approaches used or may represent bona fide differences in the contribution of the second lineage to the hearts of birds compared to mammals [11]. Alternatively, the secondary/anterior heart fields described in the chick may represent a subset of a broader field that makes a more substantial contribution to the heart, as the mouse studies suggested SHF UBERON:0009889 XAO:0004186 anterior heart field anterior/second heart field extra-cardiac population of mesodermal progenitors that gives rise to the right ventricle and outflow tract[PMID:17276708]. in mouse has left ventricular identity[PMID:22855565] second heart field uberon facial mesenchyme EMAPA:35337 FMA:302884 Mesenchyme that is part of a developing face. UBERON:0009891 face mesenchyme mesenchyme of face uberon lobule FMA:45737 UBERON:0009911 UMLS:C0921005 lobulus todo - provide definition. Clearly distinguish between lobules, lobes and acinar parts of glands (see for example lobule of mammary gland) uberon optic neural crest EHDAA2:0001315 EHDAA:1122 UBERON:0009920 uberon neurogenic placode Cranial ectodermal placode with potential to develop into a component of the nervous system, such as nerves or ganglia. EFO:0003460 Includes: trigeminal, otic, lateral line and epibranchial placodes. TAO:0001309 UBERON:0009955 While some sensory placodes (otic and olfactory) may have homologues in basal chordates (Wada et al., 1998), the so-called neurogenenic placodes (trigeminal, otic, lateral line and epibranchial placodes) appear to have emerged at a later time (Shimeld and Holland, 2000) XAO:0004620 ZFA:0001309 neurogenic placodes placodae neurogenicae uberon multicellular anatomical structure An anatomical structure that has more than one cell as a part. CARO:0010000 FBbt:00100313 UBERON:0010000 multicellular structure uberon cell cluster organ A small cluster of cells of various types which form a discrete structure, largely delimited by a morphological boundary and whose components work together to make the whole structure capable of a specific function. CARO:0010001 Examples include arthropod sensilla. FBbt:00007229 UBERON:0010001 uberon food storage organ An organ of the digestive tract that is capable of retaining and storing food BSA:0000123 TADS:0000172 TGMA:0001041 This is a very broad functionally defined grouping class that collects disparate structures from insects to vertebrates UBERON:0010039 uberon oral gland EHDAA2:0001327 EHDAA:2181 EMAPA:16572 EMAPA:16723 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 UBERON:0010047 VHOG:0000652 buccal gland gland of oral opening gland of oral region mouth gland oral cavity gland oral region gland uberon future tongue A compound organ that has the potential to develop into a tongue. EHDAA2:0000696 EHDAA:2951 UBERON:0010056 uberon open anatomical space AEO:0000221 An anatomical space with at least one opening to another space or the exterior. EHDAA2:0004616 UBERON:0010064 uberon chromaffin system FMA:79645 MESH:D002838 Organ system subdivision that consists primarily of chromaffin cells and their supporting structures. UBERON:0010074 argentaffin system chromaffin tissue in adult cylostomes and teleosts, the interrenal bodies are separate from chromaffin bodies uberon future common hepatic duct An extrahepatic bile duct that has the potential to develop into a common hepatic duct. EHDAA2:0000595 UBERON:0010081 uberon future dermis EHDAA2:0000598 Mesenchyme that has the potential to develop into a dermis. UBERON:0010083 check development uberon future diaphragm A structure that will develop into a diaphragm. EHDAA2:0000599 UBERON:0010084 uberon future metencephalon A developing anatomical structure that has the potential to develop into a metencephalon. EHDAA2:0000623 UBERON:0010092 uberon future myelencephalon A developing anatomical structure that has the potential to develop into a myelencephalon. EHDAA2:0000640 UBERON:0010096 uberon autopod plate The distal elements of the developing limb of vertebrates that will give rise to the pedal appendages (e.g. manus, pes, paw) UBERON:0010130 limb plate uberon conducting tissue of heart Any portion of cardiac muscle tissue that is part of the conducting system of heart or the Purkinje fibers. EHDAA2:0004528 FMA:83378 UBERON:0010131 specialized conducting tissue of heart specialized muscle tissue of heart uberon male accessory sex gland Any gland, other than the gonad, associated with the genital tract, such as the ampulla of the ductus deferens and the bulbourethral, prostate and vesicular glands of the male. BTO:0004798 UBERON:0010147 male accessory gland uberon lumen of blood vessel An anatomical cavity that surrounded_by a blood vessel. FMA:312610 UBERON:0010161 blood vessel lumen uberon protuberance A roughly circular bulge in a surface. AEO:0000205 EHDAA2:0003250 FMA:82506 UBERON:0010188 requires review uberon aortic system EHDAA2:0004512 UBERON:0010191 uberon future cardiac atrium FMA:71005 Multi-tissue structure that is part of the heart tube and will become the cardiac atrium. TAO:0002228 UBERON:0010227 ZFA:0001718 presumptive atrium heart tube primordial atrium primordial cardiac atrium uberon eyeball of camera-type eye FMA:12513 MIAA:0000283 See notes for camera-type eye The core globe-shaped component of the camera-type eye. UBERON:0010230 VHOG:0001616 bulbus oculi eye eye globe eyeball globe uberon midbrain basal plate DHBA:12322 EFO:0003567 EHDAA2:0004375 Portion of tissue that is dorsolateral to the floor plate and part of the midbrain. TAO:0000761 UBERON:0010285 ZFA:0000761 basal plate midbrain basal plate midbrain region uberon midbrain neural tube Portion of neural tube that gives rise to the midbrain. TAO:0007039 UBERON:0010286 ZFA:0007039 uberon we follow ZFA in temporally dividing midbrain NT from presumptive midbrain, but in future this may be collapsed extraembryonic epithelium An epithelium that is part of a extraembryonic structure. UBERON:0010303 extra-embryonic epithelium uberon immature eye 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 UBERON:0010312 ZFA:0001678 future eye uberon neural crest-derived structure An anatomical structure that develops from the neural crest. Grouping term for query purposes UBERON:0010313 uberon structure with developmental contribution from neural crest An anatomical structure that has some part that develops from the neural crest. Grouping term for query purposes UBERON:0010314 uberon germ layer / neural crest UBERON:0010316 uberon cranial skeletal system AAO:0000109 AAO:0000971 AAO:0010185 Bony structure that encases the central nervous system and the primary sense organs of sight, olfaction, hearing, and equilibrium.[AAO] Skeletal subdivision of the head including skull (cranium plus mandible), pharyngeal and/or hyoid apparatus. Skeletal system which is part of the skull, including the splanchnocranium, chondrocranium, and dermatocranium.[TAO] TAO:0000737 UBERON:0010323 VSAO:0000049 XAO:0003075 ZFA:0000737 cranial skeleton cranium osteocranium 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 uberon 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) paired limb/fin bud mesenchyme Mesenchyme that is part of a limb/fin bud. UBERON:0010329 uberon extraembryonic membrane mesenchyme Mesenchyme that is part of a extraembryonic membrane. UBERON:0010333 uberon endochondral element A skeletal element that has the potential to participate in endochondral ossification, and may participate in intramembranous ossification. UBERON:0010363 VSAO:0000139 XAO:0004017 ZFA:0005620 endochondral replacement element https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern uberon pulmonary lobule FMA:75739 The smallest anatomical unit of the lung, measuring 0.50 to 2.00 cm in diameter. Each lobule is composed of 4-8 terminal bronchioles and their distal alveolar ducts and sacs. The lobules are separated by fibrous interlobular septa. UBERON:0010368 lobulus pulmonis uberon ecto-epithelium Epithelium composed of cells that develops from the ectoderm[FMA,modified]. FMA:69064 UBERON:0010371 ectoderm-derived epithelium uberon pancreas dorsal primordium EHDAA2:0001384 FMA:79793 UBERON:0010375 consider merging with dorsal pancreatic bud. Starts at CS12 in human (EHDAA2, embryology.ch 'bud anlagen') dorsal pancreas uberon pancreas ventral primordium EHDAA2:0001387 FMA:79794 Starts at CS14 in human (EHDAA2) or CS13-14 (embryology.ch 'bud anlagen') UBERON:0010376 uberon ventral pancreas mesenchyme from somatopleure EHDAA2:0001120 Mesenchyme that develops_from a somatopleure. UBERON:0010377 the way this class is defined also includes extraembryonic mesenchyme such as the amniotic mesenchyme; in future this may be restricted to embryonic derivatives uberon ocular surface region EMAPA:35336 MA:0002486 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. UBERON:0010409 eye surface eye surface region ocular surface uberon ciliary processes FMA:76551 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. UBERON:0010427 ciliary process ciliary processes ciliary processes set processus ciliares processus ciliares set of ciliary processes uberon pseudostratified columnar epithelium A simple columnar epithelium that looks stratified but is not, because its cells are arranged with their nuclei at different levels. FMA:45572 Pseudostratified epithelia function in secretion or absorption. If a specimen looks stratified but has cilia, then it is a pseudostratified ciliated epithelium, since stratified epithelia do not have cilia. UBERON:0010498 UMLS:C0836138 UMLS:C1514590 glandular in NCIT; we consider the two NCIT terms synonymous uberon pseudostratified ciliated columnar epithelium Epithelium composed of a single layer of cells, appearing as layered because the column-shaped cells vary in height so the nuclei are at different levels. The basal portions of all the cells are in contact with the basement membrane. It lines the respiratory system and the male reproductive tract. The cilia in the respiratory tract are motile, while the stereocilia in the male reproductive tract are immobile. FMA:13146 UBERON:0010499 UMLS:C0506992 epithelium pseudostratificatum columnare ciliatum (trachea et bronchi) uberon microcirculatory vessel 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 UBERON:0010523 ZFA:0005251 microcirculatory vessels uberon primitive nephron An epithelial tube that is fated to become a nephron. EHDAA2 treats this as already having a tubular structure, but in the ZFA representation this is a cluster of cells UBERON:0010532 developing nephron future nephron presumptive nephron primitive nephron uberon nephron progenitor UBERON:0010536 uberon paired limb/fin segment An appendage segment that is part of a limb/fin. UBERON:0010538 limb/fin segment uberon acropodial skeleton FMA:231315 The subdivision of the skeleton that consists of all the skeletal elements at the distalmost end of the autopodium - i.e. the bones of the digits or their cartilaginous precursors[VSAO,modified]. UBERON:0010543 VSAO:0005028 acropodial skeleton acropodium acropodium skeleton digital skeleton digits skeleton phalangeal skeleton set of phalanges skeletal parts of acropodial region skeletal parts of acropodium skeleton of digits uberon metapodial skeleton Endochondral bone complex located between the mesopodium and the acropodium and consisting of the metacarpals or metatarsals.[VSAO] Subdivision of skeleton that corresponds to metapodium region, between acropodial skeleton and mesopdoial skeleton. UBERON:0010546 VSAO:0005025 metacarpal/metatarsal skeleton metapodial skeleton metapodium metapodium skeleton relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: connected_to subdivision of skeleton (UBERON:0010912)[VSAO] relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: distally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO] skeletal parts of metapodium skeleton of metapodium uberon phalanx pre-cartilage condensation EMAPA:32720 UBERON:0010700 uberon phalanx cartilage element EMAPA:32721 UBERON:0010701 uberon digit mesenchyme EMAPA:32719 Mesenchyme of the digit region. UBERON:0010702 digital ray uberon appendage girdle complex 2012-04-23T10:46:51Z An organism subdivision that includes both an appendage and its accociated girdle region. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Anatomical group that consists of the soft and skeletal tissues of the appendicular region of the body and the appendage proper.[VSAO] FMA:7182 It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO] It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO] UBERON:0010707 VSAO:0000214 appendage complex appendage-girdle complex appendage/girdle complex girdle plus limb or fin haendel limb note that the FMA uses the term 'limb' to refer to the entire appendage complex (free limb plus girdle region) uberon pelvic complex Appendage girdle complex that when present, encompasses the pelvic appendage and the pelvic girdle.[VSAO] Appendage girdle complex that when present, encompasses the pelvic appendicular skeleton and the pelvic girdle. FMA:7184 UBERON:0010709 VSAO:0000215 lower limb lower limb and pelvic girdle lower limb and pelvis note that the FMA uses the terms 'upper limb' and 'lower limb' to refer to the entire appendage complex (free limb plus girdle region). Note the MA class 'hindlimb' may also belong here pelvic appendage/girdle complex pelvic girdle plus pelvic limb or fin pelvic girdle plus posterior limb or fin uberon limb skeleton subdivision Skeletal subdivision that is a segment of the limb skeleton. UBERON:0010712 VSAO:0005018 note the distinction between this and skeleton of limb uberon paired fin skeleton Skeletal system that consists of the paired fins (pectoral or pelvic fins).[TAO] Skeletal system that consists of the paired fins (pectoral or pelvic fins).[VSAO] TAO:0000027 The collection of all skeletal elements in a single paired fin. UBERON:0010713 VSAO:0000169 ZFA:0000027 uberon girdle skeleton AAO:0010686 Skeletal subdivision that is part of the appendage girdle region.[VSAO] The subdivision of the skeleton of either the pectoral or pelvic girdle. UBERON:0010719 VSAO:0000302 relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: part_of subdivision of skeleton (UBERON:0010912)[VSAO] relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: proximally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO] skeleton of girdle uberon bone of appendage girdle complex A bone that is part of an appendage girdle complex (i.e. any bone in a limb, fin or girdle). EMAPA:35494 MA:0000688 UBERON:0010740 bone of extended limb/fin region limb bone uberon meningeal cluster EHDAA2:0004661 EMAPA:32660 FMA:231572 In some primitive organisms, the meningeal cluster includes only the primitive meninx The collection of all meningeal layers that line a central nervous system. UBERON:0010743 cerebral meninges cluster of meninges meningeal meninges uberon subdivision of organism along appendicular axis A major subdivision of an organism that divides an organism along an axis perpedicular to the main body anterior-posterior axis. In vertebrates, this is typically a fin or limb segment. In insects, this includes segments of appendages such as antennae, as well as segments of the insect leg. FBbt:00007018 UBERON:0010758 appendage segment appendicular segment uberon limb cartilage element A skeletal element that is part of a limb and composed of cartilage tissue. UBERON:0010881 uberon limb bone pre-cartilage condensation A skeletal element that is part of a limb and composed of pre-cartilage tissue. UBERON:0010882 uberon subdivision of skeleton 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 UBERON:0010912 VSAO:0000042 skeletal subdivision subdivision of skeleton (in vivo) uberon nonsynovial joint FMA:7491 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. UBERON:0011134 solid joint uberon axial skeletal system FMA:7483 Subdivision of the skeletal system which consists of the axial skeleton plus associated joints. UBERON:0011137 http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton uberon post-cranial axial skeletal system FMA:302077 Subdivision of the skeletal system which consists of the post-cranial axial skeleton plus associated joints. UBERON:0011138 axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton uberon synovial limb joint Any synovial joint that is part of a (free) limb. FMA:258776 Most limb joints are synovial, but a few such as the tibiofibular joints are syndesmoses. UBERON:0011139 synovial joint of free limb segment uberon upper urinary tract FMA:45658 Subdivision of urinary system which consists of the kidney and the ureters. UBERON:0011143 galen:UpperUrinaryTract uberon facial skeleton EHDAA2:0002206 EHDAA:8361 EMAPA:18022 FMA:53673 MA:0000318 Subdivision of skull that consists of the facial bones. UBERON:0011156 facial bone facial skeleton ossa facialia ossa faciei uberon viscerocranium primary subdivision of skull FMA:54964 The skull can be divided into two: the neurocranium and the facial skeleton UBERON:0011158 skull subdivision subdivision of skull uberon primary subdivision of cranial skeletal system UBERON:0011159 uberon gastrointestinal sphincter A sphincter muscle that is part of the gastrointestinal system UBERON:0011185 UMLS:C1517464 uberon central nervous system cell part cluster A multi cell part structure that is part of a central nervous system. FMA:83143 UBERON:0011215 cell part cluster of neuraxis neuraxis layer uberon organ system subdivision A subdivision of an anatomical system. FBbt:00007330 FMA:67509 UBERON:0011216 uberon intra-ocular muscle AAO:0010038 EMAPA:18808 FMA:49150 Muscles within the eye (bulbus oculi).[AAO] UBERON:0011222 intrinsic muscle of eyeball intrinsic ocular muscle uberon appendicular skeletal system FMA:7484 Skeletal system which consists of the appendicular skeleton plus associated joints.[VSAO] Subdivision of the skeletal system which consists of the appendicular skeleton plus associated joints. UBERON:0011249 VHOG:0001666 VSAO:0000306 https://github.com/obophenotype/uberon/wiki/Appendages-and-the-appendicular-skeleton uberon autopod bone A bone that is part of a autopod region. Note that this incudes the carpal and tarsal bones. UBERON:0011250 https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern uberon embryonic skin basal layer EHDAA2:0001845 UBERON:0011272 basal cell layer of skin compare with 'stratum basale of epidermis'. This class is the source for many adult structures - see WP2062. See also: 'enveloping layer of ectoderm' outer epithelium of body uberon paired limb/fin skeleton Skeletal subdivision that is part of the paired limb/fin.[VSAO] The collection of all skeletal elements in an individual limb or fin. UBERON:0011582 VSAO:0000301 limb/fin skeleton skeletal parts of limb/fin skeleton of limb/fin uberon stylopodial skeleton Proximal element of a free limb skeleton consisting of the femur and humerus in the forelimb stylopodium and hindlimb stylopodium respectively[VSAO, modified]. Proximal element of the limb skeleton consisting of the femur and humerus in the forelimb stylopodium and hindlimb stylopodium respectively.[VSAO] UBERON:0011583 VSAO:0005007 mesomere 1 propodial propodial skeleton propodium proximal metapterygial mesomere stylopod stylopodial stylopodium stylopodium skeleton uberon zeugopodial skeleton Section of the forelimb skeleton located between the stylopodium and the autopodium. UBERON:0011584 VSAO:0005010 epipodial skeleton epipodium mesomere 2 mesomere 2 skeleton skeleton of zeugopod uberon zeugopod skeleton zeugopodial zygopodial zygopodium cell condensation 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). UBERON:0011585 VSAO:0000006 XAO:0004021 consider obsoleting, coordinate with VSAO uberon jaw region 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 UBERON:0011595 http://eol.org/collections/11578 uberon 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. Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem UBERON:0011676 axial subdivision of organism body segment main body segment uberon embryonic cardiovascular system A cardiovascular system that is part of a conceptus. EHDAA2:0000216 FMA:305965 UBERON:0011695 conceptus cardiovascular system embryonic circulatory system fetal circulatory system uberon cardiac valve leaflet EMAPA:35903 MA:0003179 UBERON:0011741 uberon valve leaflet vagus nerve nucleus A cranial nerve nucleus that is associated with a vagus nerve. FMA:54573 UBERON:0011775 nodosal nucleus nucleus of Xth nerve nucleus of vagal X nerve nucleus of vagal nerve nucleus of vagus nerve tenth cranial nerve nucleus uberon vagal X nucleus vagal nucleus vagus nucleus nerve of head region A nerve that is part of a head. UBERON:0011779 cephalic nerve head nerve uberon non-neurogenic ectodermal placode Ectodermal placode that does not develop into a component of the nervous system. UBERON:0011814 uberon atrioventricular region An anatomical junction that divides and overlaps with and atrium and a ventricle in the heart. EHDAA2:0004149 FMA:85125 UBERON:0011820 atrial ventricular junction atrioventricular junction uberon irregular connective tissue 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:0011821 uberon dense irregular connective tissue FMA:20109 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] UBERON:0011822 UMLS:C0738366 irregular dense connective tissue typus irregularis (textus connectivus collagenosus compactus) uberon dense connective tissue AAO:0000121 Connective tissue in which the fibrous component predominates. The cells, ground substance, and tissue fluid represent a minor component[NCIT] 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 UBERON:0011823 UMLS:C1511770 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. uberon fibrous connective tissue FMA:75634 UBERON:0011824 uberon loose connective tissue FMA:19783 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. UBERON:0011825 UMLS:C1253917 textus connectivus collagenosus laxus textus connectivus laxus uberon acinus of exocrine gland An acinus that is part of a exocrine gland. UBERON:0011858 exocrine gland acinus uberon collection of collagen fibrils FMA:63212 MESH:D024022 NIF_Subcellular:sao7547390221 UBERON:0011860 the FMA class specifically refers to ureter uberon anterior uvea Front (ventral) portion of the vascular, pigmentary, or middle coat of the eye, including the ciliary body and the iris. Haller tunica vascula UBERON:0011892 anterior part of uveal tract anterior uveal tract anterior vascular layer of the eyeball anterior vascular tunic of the eye ciliary body and iris tunica vasculosa bulbosa uberon vasculosa oculi ventral uveal tract epimysium 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. FMA:9726 The Epimysium also protects muscles from friction against other muscles and bones UBERON:0011899 UMLS:C0504096 epimysia fascia of muscle organ uberon stomach glandular region A region of the stomach that is lined with glandular epithelium. EMAPA:17623 MA:0001613 UBERON:0011953 UMLS:C0227197 as currently defined, this would include the cardiac antrum; however, the intent may be to exclude the cardiac glands and in mice for this to be part of the region distal to the margo plicatus glandular stomach uberon coelom 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. EHDAA2:0004731 The aggregate of the coelemic cavity lumen plus the membranes that line the lumen. UBERON:0011997 coelem coelomic coelomic cavity enterocoelom haemocoelom schizocoelom uberon epithelium-associated lymphoid tissue FMA:62811 UBERON:0012069 uberon perinatal stage In birds, the paranatal stage starts when the beak penetrates into the air pocket (air cell) between the inner and outer shell membranes The period spanning the range immediately before and after birth UBERON:0012101 paranatal stage uberon buccal salivary gland A salivary gland that is part of a cheek. FMA:59793 UBERON:0012102 uberon segment of autopod UBERON:0012139 uberon digitopodium region A segment of the autopod consisting of both acropodial region and metapodial region, but excluding the mesopodial/basopodial region. UBERON:0012140 acropodium (Wagner) https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod some sources call this the acropodium. see https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod uberon skeleton of digitopodium A subdivision of the autopod skeleton consisting of both acropodial skeleon and metapodial skeleton, but excluding the mesopodial/basopodial skeleton. UBERON:0012150 digitopodium https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod skeleton of digits some sources call this the acropodium. see https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod uberon head or neck skin A zone of skin that is part of a craniocervical region. MA:0000574 UBERON:0012180 UMLS:C1522650 uberon abdominal aorta artery An artery that originates from the abdominal aorta UBERON:0012254 abdominal artery artery of abdomen uberon columnar epithelium An epithelium that consists of columnar epithelial cells. Columnar epithelia are epithelial cells whose heights are at least four times their width. Columnar epithelia are divided into simple (or unilayered), and the rarer stratified (or multi-layered).[WP, modified] UBERON:0012274 uberon meso-epithelium Epithelium that derives from the mesoderm. [Automatically generated definition]. FMA:86452 UBERON:0012275 mesoderm-derived epithelium mesoepithelium uberon endometrium glandular epithelium EMAPA:35308 FMA:86488 MA:0002732 UBERON:0012276 glandular part of endometrium uberon uterine glands uterine glands set embryonic cloacal fold EHDAA2:0004009 One of the pair of mesenchymal swellings (folds) located on either side of the cloacal membrane during the indifferent stage of embryonic development; cranial to the cloacal membrane the folds unite to form the genital tubercle; caudally the folds are subdivided into urogenital folds anteriorly and anal folds posteriorly UBERON:0012292 We presume this is distinct from AAO:0001003, an external integumentary structure - check with amphibian anatomy ontology developers. AO notes: the text def states mesenchymal swelling, EHDAA2 splits into mesenchymal and epithelial parts cloacal fold uberon embryonic facial prominence FMA:293103 One of five swellings formed during the development of the face UBERON:0012314 embryonic facial process facial primordium primordium of face uberon fin skeleton Skeletal subdivision consisting of all the skeletal elements in a single fin. UBERON:0012353 skeleton of fin uberon acropodium region The segment of the autopod that is distal to the metapodial region and consists of the digits. UBERON:0012354 acropodial limb segment acropodial region acropodial segment of autopod class refers to an entire limb segment, not just the bones set of digits uberon digitopodium bone A bone that is part of a the digitopodium skeleton - i.e. the acropodial skeleton or the metapodial skeleton. UBERON:0012357 digit bone uberon internal anal region EHDAA2:0004588 UBERON:0012361 uberon hemopoietic tissue Blood-forming tissue, consisting of reticular fibers and cells. Also known as hemopoietic tissue Bone marrow in humans, kidney interstitium in Danio, within a stroma of reticuloendothelial tissue CALOHA:TS-2142 FMA:14073 UBERON:0012429 UMLS:C0229619 bone marrow tissue haemopoietic tissue hematopoietic tissue textus haemopoieticus uberon tunica fibrosa of eyeball FMA:58102 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. UBERON:0012430 corneosclera fibrous layer of eyeball fibrous tunic tunica fibrosa uberon external anal region EHDAA2:0004589 UBERON:0012469 uberon skeleton of pelvic complex FMA:24140 The collection of all skeletal elements in a pelvic complex - i.e. the combination of free limb or fin plus pelvic girdle. UBERON:0012476 bones of lower limb lower limb skeleton ossa membri inferioris pelvic complex skeleton set of bones of lower limb skeleton of posterior limb/fin and girdle uberon cloacal epithelium An epithelium that is part of a cloaca. EMAPA:27577 EMAPA:27640 EMAPA:36070 UBERON:0012481 ZFA:0005783 cloacal endoderm cloacal epithelium (cle) (syn: cloacal endoderm) (TS17-TS20): the cloacal epithelium is derived from endoderm and lines the cloacal cavity. It is marked by Shh and Cdh1 and lines the cloacal lumen. The cloacal epithelium gives rise to the urogenital sinus epithelium, hindgut epithelium and the urethral plate epithelium. uberon systemic vein Any vein within the general circulation that transports blood back to the right atrium of the heart. FMA:66644 UBERON:0013140 UMLS:C0447117 systemic venous tree organ part uberon future brain vesicle TODO - resolve space vs structure inconsistency; consider adding all secondary vesicles (e.g. diencephalic; my/metencephalic. See http://www.dartmouth.edu/~rswenson/NeuroSci/chapter_4.html). Note that some sources may treat the term vesicle as the progenitor of the whole brain region; for example 'The retina develops directly from the neural tube as an outpouching from the diencephalic vesicle' UBERON:0013150 brain vesicle early brain vesicle primary brain vesicle primitive brain vesicle secondary brain vesicle uberon serous acinus FMA:86279 The secretory unit of a serous gland. The acinar portion is composed of serous secreting cells. UBERON:0013232 acinus of serous gland uberon embryonic urethral groove In humans, the urethral groove is a temporary linear indentation on the underside (ventral side) of the male penis during embryonic development. It typically appears around 8 weeks of gestation and becomes closed into a normal male urethra by the 12th week The precursor of the urethra UBERON:0013241 sulcus urethralis primarius uberon urethral groove urethral sulcus space surrounding organism The space that surrounds an organism. UBERON:0013514 external to organism outside of body uberon subdivision of oviduct A section through the tube or network of tubes that connects the ovaries to the outside of the body. FMA class may only represent the uterine portion FMA:18302 UBERON:0013515 subdivision of fallopian tube subdivision of oviduct subdivision of uterine tube uberon uterine tube zone zone of uterine tube subdivision of tube UBERON:0013522 uberon anatomical conduit space 2 2 An anatomical space which is the lumen of some anatomical conduit and connects two or more spaces together[FMA,modified]. FMA:9338 UBERON:0013686 foramen space uberon 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. UBERON:0013701 uberon body proper AEO:0000103 BTO:0001489 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]. EMAPA:36031 FMA:231424 The region of the organism associated with the visceral organs. UBERON:0013702 body uberon whole body integumentary projection Anatomical projection that is part of the integumentl system. UBERON:0013703 skin projection uberon integumentary system layer A organ component layer that is part of a integumental system. UBERON:0013754 layer of skin skin layer uberon venous blood A blood that is part of a vein. FMA:83067 UBERON:0013756 blood in vein portion of venous blood uberon venous blood 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. UBERON:0013765 digestive organ digestive system organ uberon great vessel of heart EMAPA:36460 Great vessels is a term used to refer collectively to the large vessels that bring blood to and from the heart. Groupings may vary - typically pulmonary vessels and aorta and vena cavae UBERON:0013768 great vessel great vessel of thorax uberon future telencephalon EHDAA2:0004424 EMAPA:36024 Embryonic structure that gives rise to the telencephalon. TAO:0000571 UBERON:0014371 ZFA:0000571 paired anteriolateral division of the embryonic prosencephalon plus the lamina terminalis from which the olfactory lobes, cerebral cortex, and subcortical nuclei are derived[MP] presumptive telencephalon uberon mesenchyme derived from neural crest EMAPA:32735 FMA:293883 Mesenchyme that develops_from the neural crest[Automatically generated definition]. UBERON:0014387 mesenchyme from neural crest neural crest derived mesenchyme neural crest mesenchyme uberon thoracic skeleton EHDAA2:0002013 FMA:77169 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. UBERON:0014477 skeleton of thorax thoracic part of axial skeleton thoracic skeleton uberon interlobular duct A duct that is located between lobules, within the thin connective tissue septa that separate lobules. All interlobular ducts are excretory. UBERON:0014716 uberon intralobular duct A duct that is located within a lobule, with no more connective tissue intervening between ducts and secretory units (i.e., acini or tubules) than between adjacent secretory units. Intercalated and striated ducts are intralobular UBERON:0014719 intralobular ductule uberon chorda tendinea of left ventricle Chorda tendinea which is attached to the leaflet of mitral valve and is continuous with the endocardium of papillary muscle of left ventricle. FMA:9349 UBERON:0014851 uberon 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). 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 UBERON:0014892 VHOG:0000319 XAO:0000174 ZFA:0005277 skeletal muscle uberon primordial vasculature A portion of tissue that will develop into vasculature. EFO:0003708 TAO:0005076 UBERON:0014903 ZFA:0005076 uberon phalanx endochondral element A phalanx bone or its cartilage or pre-cartilage precursor. UBERON:0015023 phalanx element phalanx skeletal element uberon limb endochondral element A limb bone or its cartilage or pre-cartilage precursor. UBERON:0015061 limb bone endochondral element limb bone skeletal element uberon autopod endochondral element A endochondral element that is part of a autopod region. UBERON:0015063 uberon autopod cartilage A autopod endochondral element that is composed primarily of a cartilage tissue. UBERON:0015064 uberon lateral structure 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:0015212 uberon 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. SPD:0000130 UBERON:0015228 cardiac pump cardiac structure circulatory vessel heart heart or heart like organ uberon heart plus pericardium MA:0002449 UBERON:0015410 heart/pericardium uberon heterogeneous tissue FMA:62798 UBERON:0015757 portion of heterogeneous tissue uberon eye epithelium A epithelium that is part of a camera-type eye. EMAPA:35957 MA:0003162 UBERON:0015808 uberon foregut epithelium A epithelium that is part of a foregut. EMAPA:32922 MA:0003204 UBERON:0015833 uberon lobe of cerebral hemisphere BTO:0000445 FMA:61823 Subdivision of telencephalon which is one of a number of subdivisions of each hemisphere separated by both real landmarks (sulci and fissures) and arbitrary boundaries[FMA,modified]. UBERON:0000322 UBERON:0016526 We use the term lobe broadly as a rough regional area, encompassing homologous regions in smooth-brained mammals. We subdivide the lobes into white matter and neocortical parts. cerebral cortical segment cerebral hemisphere lobe cerebral lobe lobe of cerebral cortex lobe parts of cerebral cortex lobes of the brain lobi cerebri regional organ part of cerebral cortex segment of cerebral cortex uberon pit AEO:0000204 An roughly circular indentation in a surface. UBERON:0016566 uberon future central nervous system Primordium that develops into the central nervous system UBERON:0016879 UBERON:3000469 future CNS presumptive central nervous system uberon future nervous system AAO:0000477 Primordium that develops into the nervous system UBERON:0016880 UBERON:3000477 presumptive nervous system uberon entire extraembryonic component AEO:0000195 EHDAA2:0000003 EMAPA:16042 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. UBERON:0016887 extra-embryonic component extraembryonic component uberon transitional anatomical structure AEO:0000132 An embryonic anatomical entity that will turn into one or more other anatomical entities, perhaps with other anatomical entities, later in development. UBERON:0016888 uberon developing mesenchymal structure A mesenchyme-derived anatomical entity undergoing a transtion to become another structure. AEO:0001016 UBERON:0017650 uberon abdominal viscera A viscus that is part of a abdomen. FMA:32413 FMA:67355 UBERON:0017672 abdominal viscera abdominal viscera set set of abdominal viscera uberon skeletal musculature 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:0018254 uberon layer of muscle tissue Any organ component layer that consists of muscle tissue. FMA:45634 NCITA class may refer to smooth muscle only UBERON:0018260 uberon heart vasculature An interconnected tubular multi-tissue structure that contains fluid that is actively transported around the heart. FMA:73747 UBERON:0018674 ZFA:0005811 cardiac vasculature uberon nursing stage A mammalian developmental stage that covers the period from birth until weaning. UBERON:0018685 suckling stage uberon bladder organ A membranous sac in animals that serves as the receptacle of a liquid or contains gas. BTO:0000123 UBERON:0018707 bladder uberon reproductive system mucosa BTO:0002439 UBERON:0019042 genital mucosa uberon chorioretinal region The part of the eye that consists of both the retina and the optic choroid UBERON:0019207 chorioretina choroid and retina retinachoroid retinachoroidal region uberon sensory organ epithelium EMAPA:35952 MA:0003174 UBERON:0019304 uberon surface of eyeball FMA:58315 UBERON:0022288 surface of region of wall of eyeball uberon 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]. UBERON:0022303 lamina layer 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 uberon visceral serous membrane FMA:15860 Serous membrane layer that is adjacent to and lines an organ. UBERON:0022350 uberon visceral wall of serous membrane parietal serous membrane FMA:15859 MA:0002448 Serous membrane layer that lines to a body cavity. UBERON:0022351 cavity lining parietal wall of serous membrane uberon developing neuroepithelium AEO:0001008 An embryonic or larval epithelium that is committed to form part of the nervous system. BTO:0000314 EHDAA2_RETIRED:0004654 FMA:64807 UBERON:0034705 embryonic neuroepithelium neurepithelium neuroepithelium uberon proliferating neuroepithelium AEO:0001009 An epithelium that is undergoing proliferation to provide large numbers of neuronal cells. UBERON:0034706 uberon differentiating neuroepithelium A neuroepithelium some of whose cells are undergoing terminal differentiation to become neuronal cells. AEO:0001010 UBERON:0034707 uberon cranial neuron projection bundle Any of the cranial nerves, or their central nervous system analogs (the optic tract, the epiphyseal tract). These analogs are not true nerves, and are instead evaginated sensory afferents emanating from the brain UBERON:0034713 cranial nerve fiber bundle cranial nerve fiber tract cranial nerve or tract neuron projection bundle from brain uberon morphological feature A part of an organism or organ that is continuous with its surroundings and distinguished from its surroundings based on morphology. UBERON:0034768 uberon lymphomyeloid tissue FMA:79770 UBERON:0034769 uberon bodily gas Any substance in the body or expelled from the body that is in a gaseous state. FMA:84580 UBERON:0034873 gas in anatomical space portion of gas in anatomical space uberon air in respiratory system Any portion of gas located in a part of the respiratory system that is composed primarily of air. FMA:84581 UBERON:0034874 respiratory air respiratory system air uberon prechordal mesoderm UBERON:0034878 prechordal mesenchyme the area of axial mesoderm that develops into the prechordal plate uberon infant stage Nursing stage that follows the neonate stage in mammals and ends at weaning. UBERON:0034920 uberon multi organ part structure An multicellular anatomical structure that has subparts of multiple organs as a part. CARO:0020001 UBERON:0034921 anatomical cluster uberon cell cluster A cluster of cells, largely surrounded by a morphological boundary. CARO:0020002 FMA:62807 UBERON:0034922 uberon anatomical collection A collection of anatomical structures that are alike in terms of their morphology or developmental origin. UBERON:0034925 resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected uberon external soft tissue zone A region or zone on the surface of an organism that encompasses skin and any adnexa, down through muscles and bounded by underlying skeletal support structures. UBERON:0034929 uberon epithelium of biliary system BTO:0001513 The epithelial layer covering the biliary system. This includes the epithelium of the gallbladder (when present) as well as the intrahepatic and extrahepatic bile ducts. UBERON:0034932 biliary epithelium biliary system epithelium biliary tract epithelium uberon zone of organ FMA:55268 UBERON:0034944 organ region with floating fiat boundary organ sector organ zonal region organ zone uberon gas in respiratory system Any portion of gas located in a part of the respiratory system. UBERON:0034947 respiratory gas respiratory system gas uberon epithelial layer of duct UBERON:0034969 duct epithelium ductal epithelium uberon excretory duct UBERON:0035050 uberon left cardiac chamber Any chamber of the left side of the heart FMA:7166 UBERON:0035553 uberon right cardiac chamber Any chamber of the right side of the heart FMA:7165 UBERON:0035554 uberon laryngeal nerve Any nerve that innervates the larynx. MESH:A08.800.050.050.925.450 UBERON:0035642 uberon future mouth FMA:293105 The primordial mouth region of the developing head. UBERON:0035804 primitive mouth primordial mouth uberon serous cavity FMA:12241 UBERON:0035809 uberon abdominopelvic cavity FMA:12267 The part of the ventral body cavity that is within the abdominal segment of the trunk, which encompasses the abdomen proper plus pelvic cavity. UBERON:0035819 cavitas abdominis et pelvis uberon peritoneal sac A serous sac that is the aggregate of the peritoneum and the peritoneal cavity, located in the abdominal cavity. EMAPA:16137 FMA:9908 MA:0000054 UBERON:0035820 peritoneal component uberon preplacodal ectoderm Non neural ectoderm that surrounds the presumptive neural plate and gives rise to neurogenic placodes. This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon ZFA:0007013 teleost_anatomy_curators uberon/phenoscape-anatomy external integument structure 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 digit plus metapodial segment A subdivision of the autopod consisting of digit plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis. UBERON:5002544 digit digit ( phalanges plus metapodial) plus soft tissue digit digitopodial subdivision digit ray this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit. uberon individual digit of digitopodial skeleton A subdivision of the skeleton of the autopod consisting of the phalanges of a single digit plus the associated metapodial element. UBERON:5102544 digit digit skeleton this class represents a series of phalanges plus a metapodial element. In comparative anatomy terminology we would call this a 'digit', but the label 'digit' is sometimes used to exclude metapodials and to include soft tissue. This series of elements is hypothesized to be homologous to radials. uberon prostate gland BTO:0001129 CALOHA:TS-0828 EFO:0000858 EMAPA:19287 EV:0100104 FMA:9600 GAID:392 MA:0000404 MAT:0000078 MESH:D011467 MIAA:0000078 OpenCyc:Mx4rv6trqZwpEbGdrcN5Y29ycA TODO - FMA treats the gland as part of the prostate - see also FMA:74119. The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid. UBERON:0002367 UMLS:C0033572 VHOG:0001261 galen:ProstateGland male prostate prostata prostate prostatic uberon