Alan Ruttenberg Alexander Diehl Ann Maglia Anna Anagnostopoulos Bgee Project - http://bgee.unil.ch Bill Bug Brian K Hall Carlo Torniai Catherine Leroy Ceri Van Slyke Cynthia Smith David Hill David Osumi-Sutherland Duncan Davidson Frederic Bastian Gene Ontology Consortium George Gkoutos Hilmar Lapp James Balhoff James Malone Jonathan Bard Lydie Lane Marc Robinson-Rechavi Mark Engelstad - https://orcid.org/0000-0001-5889-4463 Maryann Martone NIF Project - http://neuinfo.org/ Onard Mejino PATO Project Paul Schofield Paul Sereno Paula Duek Roggli Paula Mabee Phenoscape Project Rebecca Foulger Robert Druzinsky Sarah Whitcher Kansa - https://orcid.org/0000-0001-7920-5321 Shahim Essaid Suzanna Lewis Terry Hayamizu Terry Meehan Trish Whetzel Yvonne Bradford neXtProt project Alex Dececchi Anne Niknejad Aurelie Comte Chris Mungall - http://orcid.org/0000-0002-6601-2165 David Blackburn Erik Segerdell Melissa Haendel Nizar Ibrahim Wasila Dahdul Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data. http://uberon.org ISBN:0030229073 Invertebrate Zoology, Barnes ISBN:0073040584 Vertebrates, Kardong ISBN:0123813611 Comparative Anatomy and Histology: A Mouse and Human Atlas, Treuting and Dintzis ISBN:0226313379 Fins into Limbs: Evolution, Development, and Transformation, Hall ISBN:0443065837 Human embryology, Larsen ISBN:0471888893 Comparative Vertebrate Neuroanatomy: Evolution and Adaptation by Butler and Hodos ISBN:0683400088 Stedman's Medical Dictionary ISBN:1588900649 Color Atlas and Textbook of Human Anatomy: Nervous system and sensory organs By Werner Kahle, Michael Frotscher ISBN:1588903958 Principles and practice of pediatric neurosurgery By A. Leland Albright, P. David Adelson, Ian F. Pollack ISBN:1607950324 Craniofacial Embryogenetics & Development, 2nd edition, Sperber ISBN:978-0-12-369548-2 Principles of Developmental Genetics, Sally A Moody ISBN:9780120749034 The laboratory rat ISBN:9780397517251 Surgical anatomy of the hand and upper extremity. By James R. Doyle and Michael J. Botte ISBN:9780674021839 The Tree of Life - Guillaume Lecointre, Herve Le Guyader ISBN:9780878932504 Developmental Biology MESH PMID:11433360 Placental development: lessons from mouse mutants PMID:16417468 Forgotten and novel aspects in pancreas development, Pieler and Chen http://wiki.phenotypercn.org/wg/phenotypercn/index.php?title=Neural_Crest_Workshop http://wiki.phenotypercn.org/wiki/August_2012_Notes https://docs.google.com/document/d/16JZOuH9sh_a8uIXA4cqg0Q1H6MV5yCj3-rhuKsZoV_U/edit https://docs.google.com/document/d/1MnUgispgGfNQoezYzWzzGTnkAnI0gzRnJIwdip6MMtw/edit https://docs.google.com/document/d/1cPWBqrl_Qy7XHEWFqtR_PgQX61yRkgGuLaiDpnEXxkE/edit https://docs.google.com/document/d/1r9kNPpFYGdu0SpJDLyFAVQczBlG0wAZCBMd18gG3Ot8/edit# https://docs.google.com/spreadsheet/ccc?key=0Aj8NJdyb-leqdDM0R3hTVTRHRExDVjRCSkZEbDc5N1E#gid=0 Uber-anatomy ontology http://genomebiology.com/2012/13/1/R5 http://www.ncbi.nlm.nih.gov/pubmed/22293552 https://github.com/cmungall/uberon/ https://obo.svn.sourceforge.net/svnroot/obo/uberon/ https://github.com/obophenotype/uberon/issues/ https://lists.sourceforge.net/lists/listinfo/obo-anatomy uberon 1.2 AEO BILA BSPO CARO EFO GO OG VSAO EHDAA EV NCIT OGES SCTID VHOG AAO part_of NCBITaxon:8292 DHBA part_of NCBITaxon:9606 DMBA part_of NCBITaxon:10090 EHDAA2 part_of NCBITaxon:9606 EMAPA part_of NCBITaxon:10090 FBbt part_of NCBITaxon:7227 FBdv part_of NCBITaxon:7227 FMA part_of NCBITaxon:9606 HAO part_of NCBITaxon:7399 HBA part_of NCBITaxon:9606 HsapDv part_of NCBITaxon:9606 MA part_of NCBITaxon:10090 MBA part_of NCBITaxon:10090 MFO part_of NCBITaxon:8089 MmusDv part_of NCBITaxon:10090 OlatDv part_of NCBITaxon:8089 PBA part_of NCBITaxon:9443 SPD part_of NCBITaxon:6893 TADS part_of NCBITaxon:6939 TAO part_of NCBITaxon:32443 TGMA part_of NCBITaxon:44484 WBbt part_of NCBITaxon:6237 WBls part_of NCBITaxon:6237 XAO part_of NCBITaxon:8353 ZFA part_of NCBITaxon:7954 ZFS part_of NCBITaxon:7954 Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/TEMP>) VersionIRI(<null>))) [Axioms: 437 Logical Axioms: 0] Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/uberon-bridge-to-bfo.owl>) VersionIRI(<null>))) [Axioms: 20 Logical Axioms: 9] Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/uberon/disjoint_union_over.owl>) VersionIRI(<null>))) [Axioms: 38 Logical Axioms: 38] Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/uberon/ext.owl>) VersionIRI(<null>))) [Axioms: 26525 Logical Axioms: 4920] Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/uberon/reflexivity_axioms.owl>) VersionIRI(<null>))) [Axioms: 2 Logical Axioms: 2] http://uberon.org IAO:0000112 uberon example_of_usage true example_of_usage example of usage definition IAO:0000116 uberon editor_note true editor_note editor note IAO:0000232 uberon curator_notes true curator_notes curator notes expand expression to expand assertion to term replaced by S never_in_taxon T iff: S SubClassOf in_taxon only not T Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: ?X and (RO_0002162 some ?Y) RO:0002161 uberon never_in_taxon true true never_in_taxon never_in_taxon S never_in_taxon T iff: S SubClassOf in_taxon only not T Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y) RO:0002171 uberon mutually_spatially_disjoint_with true true mutually_spatially_disjoint_with mutually_spatially_disjoint_with S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage. RO:0002173 uberon ambiguous_for_taxon true true ambiguous_for_taxon ambiguous_for_taxon S ambiguous_for_taxon T if the class S does not have a clear referent in taxon T. An example would be the class 'manual digit 1', which encompasses a homology hypotheses that is accepted for some species (e.g. human and mouse), but does not have a clear referent in Aves - the referent is dependent on the hypothesis embraced, and also on the ontogenetic stage. PHENOSCPAE:asilomar_mtg S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T. RO:0002174 uberon dubious_for_taxon true true 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 dubious_for_taxon S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T. 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 RO:0002175 applicable for taxon uberon present_in_taxon true true present_in_taxon present_in_taxon 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 A is has_no_connections_with B if there are no parts of A or B that have a connection with the other. Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (RO_0002170 some (BFO_0000050 some ?Y)) RO:0002475 uberon has_no_connections_with true true has_no_connections_with has_no_connections_with A is has_no_connections_with B if there are no parts of A or B that have a connection with the other. 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. UBPROP:0000001 uberon external_definition true external_definition This annotation property may be replaced with an annotation property from an external ontology such as IAO external_definition 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. A textual description of an axiom loss in this ontology compared to an external ontology. UBPROP:0000002 uberon axiom_lost_from_external_ontology true axiom_lost_from_external_ontology This annotation property may be replaced with an annotation property from an external ontology such as IAO axiom_lost_from_external_ontology A textual description of an axiom loss in this ontology compared to an external ontology. Notes on the homology status of this class. UBPROP:0000003 uberon homology_notes true homology_notes This annotation property may be replaced with an annotation property from an external ontology such as IAO homology_notes Notes on the homology status of this class. 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. UBPROP:0000005 uberon external_comment true external_comment This annotation property may be replaced with an annotation property from an external ontology such as IAO external_comment 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. UBPROP:0000006 uberon implements_design_pattern true implements_design_pattern implements_design_pattern 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'. UBPROP:0000007 uberon has_relational_adjective true has_relational_adjective has_relational_adjective Notes on the how instances of this class vary across species. UBPROP:0000008 uberon taxon_notes true taxon_notes taxon_notes Notes on the how instances of this class vary across species. 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 uberon function_notes true function_notes function_notes Notes on the evolved function of instances of this class. 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 uberon structure_notes true structure_notes structure_notes Notes on the structure, composition or histology of instances of this class. 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 uberon development_notes true development_notes development_notes Notes on the ontogenic development of instances of this class. 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 uberon external_ontology_notes true external_ontology_notes external_ontology_notes Notes on how similar or equivalent classes are represented in other ontologies. 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 uberon terminology_notes true terminology_notes terminology_notes Notes on how lexical conventions regarding this class, in particular any issues that may arise due to homonyny or synonymy. Notes on how instances of this class functon biomechanically. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000014 uberon action_notes true action_notes actions_notes Notes on how instances of this class functon biomechanically. Notes on the location, position or part-parents of instances of this class. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000015 uberon location_notes true location_notes location_notes Notes on the location, position or part-parents of instances of this class. UBPROP:0000100 uberon is_count_of true is_count_of is count of 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 uberon preceding_element_is true preceding_element_is preceding element is 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) A property used to indicate the position of an element where that element is of a type that is serially repeated linearly along some axis for which a total ordering exists. The ordering may represent an ancestral condition UBPROP:0000102 uberon repeated_element_number true repeated_element_number The range is currently non-negative integer repeated element number A property used to indicate the position of an element where that element is of a type that is serially repeated linearly along some axis for which a total ordering exists. The ordering may represent an ancestral condition 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. gill arch N = PA N-2. the term branchial_arch is ambiguous. UBPROP:0000103 uberon pharyngeal_arch_number true pharyngeal_arch_number pharyngeal arch number 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. x ray_number N if and only if (i) x is a ray, and (ii) x is ancestrally associated with ray number N in a series of phalanges repeated along a radio-ulnar or equivalent axis, with ray_number 1 being the anteriormost ray. UBPROP:0000104 uberon ray_number true ray_number The correct terminology is yet to be established; in tetrapods 'ray' might mean the mereological sum of the phalanges of a manual digit plus a metatarsal bone (or equivalent for hindlimb) ray number x ray_number N if and only if (i) x is a ray, and (ii) x is ancestrally associated with ray number N in a series of phalanges repeated along a radio-ulnar or equivalent axis, with ray_number 1 being the anteriormost ray. 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 UBPROP:0000105 uberon phalanx_number true phalanx_number 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 phalanx number 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 x rib_number N if and only if (i) x is a rib, and (ii) x is rib number N in a series of ribs repeated along an anterior-posterior axis, with rib_number 1 being the anteriormost rib. Note that this property counts ribs, *not* the adjoining vertebrae. In the early tetrapods, every vertebra bore a pair of ribs, although those on the thoracic vertebrae are typically the longest. In most subsequent forms, many of these early ribs have been lost, and in living amphibians and reptiles, there is great variation in rib structure and number. For example, turtles have only eight pairs of ribs, which are developed into a bony or cartilagenous carapace and plastron, while snakes have numerous ribs running along the full length of their trunk. Frogs typically have no ribs, aside from a sacral pair, which form part of the pelvis. Mammals usually also only have distinct ribs on the thoracic vertebra, although fixed cervical ribs are also present in monotremes. In marsupials and placental mammals, the cervical and lumbar ribs are found only as tiny remnants fused to the vertebrae, where they are referred to as transverse processes. In general, the structure and number of the true ribs in humans is similar to that in other mammals. Unlike reptiles, caudal ribs are never found in mammals. Note that in TAO, ribs are numbered by *vertebrae* UBPROP:0000106 uberon rib_number true rib_number rib number x rib_number N if and only if (i) x is a rib, and (ii) x is rib number N in a series of ribs repeated along an anterior-posterior axis, with rib_number 1 being the anteriormost rib. Note that this property counts ribs, *not* the adjoining vertebrae. Note that in TAO, ribs are numbered by *vertebrae* TAO x vertebra_number N if and only if (i) x is a vertebra, and (ii) x is vertebra number N in a series of vertebras repeated along an anterior-posterior axis, with vertebra_number 1 being the anteriormost vertebra (also known as the atlas). UBPROP:0000107 uberon vertebra_number true vertebra_number vertebra number x vertebra_number N if and only if (i) x is a vertebra, and (ii) x is vertebra number N in a series of vertebras repeated along an anterior-posterior axis, with vertebra_number 1 being the anteriormost vertebra (also known as the atlas). x somite_number N if and only if (i) x is a somite, and (ii) x is somite number N in a series of somites repeated along an anterior-posterior axis, with somite_number 1 being the anteriormost somite. UBPROP:0000108 uberon somite_number true somite_number somite number x somite_number N if and only if (i) x is a somite, and (ii) x is somite number N in a series of somites repeated along an anterior-posterior axis, with somite_number 1 being the anteriormost somite. x paired_appendage_number N if and only if (i) x is a paired_appendage, and (ii) x is paired_appendage number N in a series of paired_appendages repeated along an anterior-posterior axis, with paired_appendage_number 1 being the anteriormost paired_appendage. In vertebrates, this is the pectoral appendage UBPROP:0000109 uberon paired_appendage_number true paired_appendage_number paired_appendage number x paired_appendage_number N if and only if (i) x is a paired_appendage, and (ii) x is paired_appendage number N in a series of paired_appendages repeated along an anterior-posterior axis, with paired_appendage_number 1 being the anteriormost paired_appendage. In vertebrates, this is the pectoral appendage x appendage_segment_number N if and only if (i) x is a appendage_segment, and (ii) x is appendage_segment number N in a series of appendage_segments repeated along an proximo-distal axis, with appendage_segment_number 1 being the proximalmost appendage_segment (in tetrapods this would be the stylopod, as we do not classify girdles as appendage segments). UBPROP:0000110 uberon appendage_segment_number true appendage_segment_number Examples: in dropsphila coxa=1, trochanter=2, femur=3, tibia=4, tarsal segments 1-5=5-9, pretarsus=10 appendage segment number x appendage_segment_number N if and only if (i) x is a appendage_segment, and (ii) x is appendage_segment number N in a series of appendage_segments repeated along an proximo-distal axis, with appendage_segment_number 1 being the proximalmost appendage_segment (in tetrapods this would be the stylopod, as we do not classify girdles as appendage segments). x rhombomere_number N if and only if (i) x is a rhombomere, and (ii) x is rhombomere number N in a series of rhombomeres repeated along an anterior-posterior axis, with rhombomere_number 1 being the anteriormost rhombomere. UBPROP:0000111 uberon rhombomere_number true rhombomere_number rhombomere number x rhombomere_number N if and only if (i) x is a rhombomere, and (ii) x is rhombomere number N in a series of rhombomeres repeated along an anterior-posterior axis, with rhombomere_number 1 being the anteriormost rhombomere. x tooth_number N if and only if (i) x is a tooth, and (ii) x is ancestrally tooth number N in a series of teeth repeated along an anterior-posterior axis, typically on the lateral side of a structure such as a jaw, with tooth_number 1 being the anteriormost. Note that this count refers to the total number of teeth starting from the first, regardless of the type of tooth. If sub-systems are required for numbering within a series of teeth of the same type, consider a subproperty. For example, in a human, maxillary canine = tooth 3 of upper jaw = canine_tooth 1 of upper jaw UBPROP:0000112 uberon tooth_number true tooth_number tooth number Syntax: upper/lower = I.C.P.M / I.C.P.M. When used with generic tooth class applies to both deciduous and primary. Should also be used with a taxon property. UBPROP:0000113 uberon dental_formula true dental_formula dental formula Syntax: upper/lower = I.C.P.M / I.C.P.M. When used with generic tooth class applies to both deciduous and primary. Should also be used with a taxon property. UBPROP:0000201 uberon source_atlas true source_atlas source atlas 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 uberon fma_set_term true fma_set_term fma_set_term 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 FMA abbreviation brain name abbreviations (drosophila) preferred term in the context of comparative anatomy A historic synonym, no longer encouraged developmental term dubious or contested synonym a synonym made on the basis of a possibly homologous structure in another species preferred term when talking about an instance of this class in Homo sapiens indicates that a synonym is used in an inconsistent or confusing way, typically between species latin term a mis-spelling that is in common use and thus recorded synonym that is inappropriate for amniotes synonym that is inappropriate for mammals expert consultation and attribution required plural term taxonomic disambiguation a systematic synonym used as the base name for design patterns Classes tagged with this subset property were added upon request from the Human Cell Atlas (HCA). CUMBO cyclostome structures brain region defined by cyto-architecture classes that are defined by relative position counting from first in a series of elements along an axis in an individual organism rather than by strict homology developmental_classification Indicates that subclasses in AOs may be inappropriately linked 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 subset of classes that have logical defs text defs and synonyms aligned with FEED functional_classification Subset consisting of classes creating for grouping purposes uberon homologous_in true Status: experimental homologous_in 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 core classes typically found across metazoa. one purpose is to create a rough set of terms that could be used to start a new metazoan AO. Note this subset is not yet fully fleshed out abstract class brought in to group ontology classes but not informative organs, excluding individual muscles and skeletal elements Phenotype slim A subset specifically created for the 2012 Phenotype RCN meeting. Includes some human-specific terms that may eventually be removed when they are adequately represented with part of relationships in FMA Uberon slim - subset that excludes obscure terms and deep compositional terms Indicates that the class encompasses classes from other AOs that have not been verified 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 uberon dc-contributor true dc-contributor contributor uberon dc-creator true dc-creator creator uberon dc-description true dc-description description uberon dc-publisher true dc-publisher publisher uberon dc-source true dc-source derived from resource uberon dc-title true dc-title title uberon dcterms-isReferencedBy true dcterms-isReferencedBy is referenced by uberon dcterms-license true dcterms-license license uberon doap-GitRepository true doap-GitRepository Git repository uberon doap-SVNRepository true doap-SVNRepository SVN repository uberon doap-bug-database true doap-bug-database bug database uberon doap-mailing-list true doap-mailing-list mailing list uberon doap-wiki true doap-wiki wiki subset_property synonym_type_property consider has_alternative_id has_broad_synonym database_cross_reference has_exact_synonym has_narrow_synonym has_obo_format_version has_obo_namespace has_related_synonym has_scope has_synonym_type in_subset shorthand treat-xrefs-as-equivalent treat-xrefs-as-has-subclass treat-xrefs-as-is_a treat-xrefs-as-reverse-genus-differentia uberon seeAlso true seeAlso see also uberon depicted_by true depicted_by depicted by uberon foaf-homepage true foaf-homepage homepage uberon foaf-page true foaf-page page BFO:0000050 uberon part_of part_of part of BFO:0000051 uberon has_part has_part has part X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X) BFO:0000062 is preceded by takes place after uberon preceded_by preceded_by preceded_by is preceded by SIO:000249 takes place after Allen:precedes BFO:0000063 uberon precedes precedes precedes BFO:0000067 uberon contains_process contains_process contains process true true x anterior_to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail: bearer cjm 2009-07-31T02:15:46Z BSPO:0000096 uberon anterior_to anterior_to anterior_to x anterior_to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail: bearer x distal_to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal). BSPO:0000097 uberon distal_to distal_to distal_to x distal_to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal). x dorsal_to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly). BSPO:0000098 uberon dorsal_to dorsal_to dorsal_to x dorsal_to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly). x posterior_to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail. BSPO:0000099 caudal_to uberon posterior_to posterior_to posterior_to x posterior_to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail. x proximal_to y iff x is closer to the point of attachment with the body than y. BSPO:0000100 uberon proximal_to proximal_to proximal_to x proximal_to y iff x is closer to the point of attachment with the body than y. x ventral_to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly). BSPO:0000102 uberon ventral_to ventral_to ventral_to x ventral_to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly). Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines. BSPO:0000107 uberon deep_to deep_to deep_to Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines. Near the outer surface of the organism. Thus, skin is superficial to the muscle layer. BSPO:0000108 uberon superficial_to superficial_to superficial_to Near the outer surface of the organism. Thus, skin is superficial to the muscle layer. X in_left_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the left portion. BSPO:0000120 uberon in_left_side_of in_left_side_of in_left_side_of https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern X in_left_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the left portion. BSPO:PATO_mtg_2009 X in_right_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the right portion. BSPO:0000121 uberon in_right_side_of in_right_side_of in_right_side_of https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern X in_right_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the right portion. BSPO:PATO_mtg_2009 X posterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the posterior portion. BSPO:0000122 uberon in_posterior_side_of in_posterior_side_of in_posterior_side_of X posterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the posterior portion. BSPO:PATO_mtg_2009 X anterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the anterior portion. BSPO:0000123 uberon in_anterior_side_of in_anterior_side_of in_anterior_side_of X anterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the anterior portion. BSPO:PATO_mtg_2009 X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion. BSPO:0000124 uberon in_proximal_side_of in_proximal_side_of in_proximal_side_of X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion. BSPO:PATO_mtg_2009 X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion. BSPO:0000125 uberon in_distal_side_of in_distal_side_of in_distal_side_of X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion. BSPO:PATO_mtg_2009 X in_lateral_side_of Y <=> if X is in_left_side_of Y or X is in_right_side_of Y. X is often, but not always a paired structure BSPO:0000126 uberon in_lateral_side_of in_lateral_side_of in_lateral_side_of https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern X in_lateral_side_of Y <=> if X is in_left_side_of Y or X is in_right_side_of Y. X is often, but not always a paired structure X superficial_part_of Y <=> if Y is subdivided into two superficial and deep portions, X is part_of the superficial portion. BSPO:0001100 uberon in_superficial_part_of in_superficial_part_of in_superficial_part_of X superficial_part_of Y <=> if Y is subdivided into two superficial and deep portions, X is part_of the superficial portion. X superficial_part_of Y <=> if Y is subdivided into two superficial and deep portions, X is part_of the deep portion. BSPO:0001101 uberon in_deep_part_of in_deep_part_of in_deep_part_of X superficial_part_of Y <=> if Y is subdivided into two superficial and deep portions, X is part_of the deep portion. X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y BSPO:0001106 uberon proximalmost_part_of proximalmost_part_of proximalmost_part_of X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y This relation holds when both the deep_to and ajdacent_to relationship similarly hold. BSPO:0001107 uberon immediately_deep_to immediately_deep_to immediately_deep_to This relation holds when both the deep_to and ajdacent_to relationship similarly hold. X distalmost_part_of Y <=> X is part_of Y and X is adjacent_to the distal boundary of Y BSPO:0001108 uberon distalmost_part_of distalmost_part_of distalmost_part_of X distalmost_part_of Y <=> X is part_of Y and X is adjacent_to the distal boundary of Y BSPO:0001113 uberon preaxialmost_part_of preaxialmost_part_of preaxialmost_part_of x preaxial_to y iff x is further along the preaxial-postaxial axis than y, towards the postaxial side. BSPO:0001114 uberon posterior_to (developmentally) postaxial_to postaxial_to postaxial_to x preaxial_to y iff x is further along the preaxial-postaxial axis than y, towards the postaxial side. posterior_to (developmentally) MA:th BSPO:0001115 uberon postaxialmost_part_of postaxialmost_part_of postaxialmost_part_of X intersects_median_plane of iff X crosses the midine plane of Y. BSPO:0005001 uberon intersects_midsagittal_plane_of intersects_midsagittal_plane_of intersects_midsagittal_plane_of BSPO:0015009 uberon immediately_anterior_to immediately_anterior_to immediately_anterior_to BSPO:0015012 uberon immediately_posterior_to immediately_posterior_to immediately_posterior_to BSPO:0015014 uberon immediately_superficial_to immediately_superficial_to immediately_superficial_to BSPO:0015101 uberon in_dorsal_side_of in_dorsal_side_of in_dorsal_side_of BSPO:0015102 uberon in_ventral_side_of in_ventral_side_of in_ventral_side_of nearer to the oral opening of the organism, on the oral-aboral axis. BSPO:0015201 uberon oral_to oral_to oral_to nearer to the oral opening of the organism, on the oral-aboral axis. BSPO:cjm nearer to the aboral opening of the organism, on the oral-aboral axis. BSPO:0015202 uberon aboral_to aboral_to aboral_to nearer to the aboral opening of the organism, on the oral-aboral axis. BSPO:cjm x preaxial_to y iff x is further along the preaxial-postaxial axis than y, towards the front. BSPO:1000000 uberon anterior_to (developmentally) lateral (radial) to medial (tibial) to preaxial_to preaxial_to preaxial_to x preaxial_to y iff x is further along the preaxial-postaxial axis than y, towards the front. anterior_to (developmentally) MA:th RO:0000053 uberon bearer_of bearer_of bearer of RO:0000056 uberon participates_in participates_in participates in RO:0000086 uberon has_quality has_quality has quality RO:0001015 uberon location_of location_of location_of RO:0001019 uberon contains contains contains RO:0001025 uberon located_in located_in located_in RO:0002000 uberon boundary_of boundary_of boundary of RO:0002002 uberon has_boundary has_boundary has boundary RO:0002005 nerve supply uberon innervated_by innervated_by http://code.google.com/p/obo-relations/issues/detail?id=6 innervated_by nerve supply FMA:85999 RO:0002007 uberon bounding_layer_of bounding_layer_of A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. bounding layer of Relation between occurrents, shares start and end boundaries. RO:0002082 coincides_with is_equal_to uberon simultaneous_with simultaneous_with simultaneous_with Relation between occurrents, shares start and end boundaries. Allen:is_equal_to X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]. RO:0002087 directly preceded by is directly preceded by is immediately preceded by starts_at_end_of uberon immediately_preceded_by immediately_preceded_by immediately_preceded_by A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]. SIO:000251 is immediately preceded by SIO:000251 A overlaps B if they share some part in common. BFO_0000051 some (BFO_0000050 some ?Y) RO:0002131 uberon overlaps overlaps overlaps RO:0002134 uberon innervates innervates http://code.google.com/p/obo-relations/issues/detail?id=6 innervates RO:0002150 uberon continuous_with continuous_with continuous_with RO:0002158 uberon homologous_to homologous_to homologous_to RO:0002159 uberon serially_homologous_to serially_homologous_to serially_homologous_to S only_in_taxon T iff: S SubClassOf in_taxon only T RO:0002160 uberon only_in_taxon only_in_taxon only_in_taxon S only_in_taxon T iff: S SubClassOf in_taxon only T RO:0002162 uberon in_taxon in_taxon in taxon Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship. RO:0002170 uberon connected_to connected_to Connection does not imply overlaps. 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. Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship. this is currently used for both structural relationships (such as between a valve and the chamber it connects) and abstract relationships (anatomical lines and the entities they connect) RO:0002176 uberon connects connects connects Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship. RO:0002177 uberon attaches_to_part_of attaches_to_part_of attaches_to_part_of true relation between an artery and the structure is supplies with blood. RO:0002178 arterial supply of uberon supplies supplies source: FMA supplies arterial supply of FMA:86003 RO:0002179 drains blood from drains from uberon drains drains source: Wikipedia drains RO:0002180 uberon has_component has_component has component RO:0002202 uberon develops_from develops_from develops_from RO:0002203 uberon develops_into develops_into develops_into RO:0002207 uberon directly_develops_from directly_develops_from directly_develops_from RO:0002215 uberon capable_of capable_of capable of RO:0002216 uberon capable_of_part_of capable_of_part_of capable of part of x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y RO:0002219 uberon surrounded_by surrounded_by surrounded_by x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y x adjacent_to y iff: x and y share a boundary RO:0002220 uberon adjacent_to adjacent_to adjacent_to inverse of surrounded_by RO:0002221 uberon surrounds surrounds surrounds inverse of surrounded_by Relation between occurrents, shares a start boundary with. RO:0002223 uberon starts starts starts Relation between occurrents, shares a start boundary with. Allen:starts RO:0002224 uberon starts_with starts_with starts with RO:0002225 uberon develops_from_part_of develops_from_part_of develops_from_part_of RO:0002226 uberon develops_in develops_in This relation take from EHDAA2 - precise semantics yet to be defined develops_in Relation between occurrents, shares an end boundary with. RO:0002229 finishes uberon ends ends ends Relation between occurrents, shares an end boundary with. Allen:starts ZFS:finishes RO:0002230 uberon ends_with ends_with ends with RO:0002254 uberon has_developmental_contribution_from has_developmental_contribution_from has developmental contribution from RO:0002255 uberon developmentally_contributes_to developmentally_contributes_to developmentally_contributes_to t1 developmentally_induced_by t2 if there is a process of organ induction (GO:0001759) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor tissue type T to T', where T' develops_from T. RO:0002256 uberon developmentally_induced_by developmentally_induced_by sources for developmentally_induced_by relationships in Uberon: Developmental Biology, Gilbert, 8th edition, figure 6.5(F) developmentally_induced_by t1 developmentally_induced_by t2 if there is a process of organ induction (GO:0001759) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor tissue type T to T', where T' develops_from T. GO:0001759 RO:0002258 uberon developmentally_preceded_by developmentally_preceded_by developmentally preceded by RO:0002285 uberon developmentally_replaces developmentally_replaces developmentally_replaces RO:0002322 adapted_for uberon confers_advantage_in confers_advantage_in confers_advantage_in RO:0002328 uberon functionally_related_to functionally_related_to functionally related to RO:0002329 uberon part_of_structure_that_is_capable_of part_of_structure_that_is_capable_of part of structure that is capable of RO:0002350 uberon member_of member_of member of RO:0002351 uberon has_member has_member has member RO:0002352 uberon input_of input_of input of RO:0002353 uberon output_of output_of output of RO:0002371 uberon attaches_to attaches_to attaches_to m has_muscle_origin s iff m is attaches_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. RO:0002372 uberon has_muscle_origin has_muscle_origin The origin is the end of a muscle that attaches to the more fixed part of the skeleton, which is the proximal end in limb muscles has_muscle_origin m has_muscle_origin s iff m is attaches_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. RO:0002373 uberon has_muscle_insertion has_muscle_insertion The insertion is the point of attachment of a muscle that moves the most when the muscle shortens, or the most distal end of limb muscles has_muscle_insertion m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. x has_fused_element y iff: there exists some z : x has_part z, z homologous_to y, and y is a distinct element, the boundary between x and z is largely fiat RO:0002374 uberon has_fused_element has_fused_element A single bone in one species may correspond to the fusion of two or more bones found as distinct elements in another. For example, tibiofibula has_fused_element tibia. A has_fused_element B does not imply that A has_part some B, rather than A has_part some B', where B' is not a subtype of B (because B is a distinct element but B' is a regional part) but has some evolutionary relationship to B. has_fused_element RO:0002376 uberon drains into tributary_of tributary_of tributary_of drains into dbpowl:drainsTo we need to check if FMA branch_of implies part_of. the relation we intend to use here should - for example, see vestibulocochlear nerve RO:0002380 uberon branching_part_of branching_part_of branching_part_of x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y RO:0002385 uberon has_potential_to_developmentally_contribute_to has_potential_to_developmentally_contribute_to has potential to developmentally contribute to x has the potential to develop into y iff x develops into y or if x is capable of developing into y RO:0002387 uberon has_potential_to_develop_into has_potential_to_develop_into has potential to develop into x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y RO:0002388 uberon has_potential_to_directly_develop_into has_potential_to_directly_develop_into has potential to directly develop into RO:0002433 uberon contributes_to_morphology_of contributes_to_morphology_of contributes to morphology of x composed_primarily_of y iff: more than half of the mass of x is made from parts of y RO:0002473 uberon RO:0002473 composed_primarily_of composed_primarily_of composed primarily of RO:0002476 uberon child_nucleus_of child_nucleus_of child nucleus of RO:0002477 uberon child_nucleus_of_in_hermaphrodite child_nucleus_of_in_hermaphrodite child nucleus of in hermaphrodite RO:0002478 uberon child_nucleus_of_in_male child_nucleus_of_in_male child nucleus of in male Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s. RO:0002488 begins_to_exist_during uberon RO:0002488 existence_starts_during existence_starts_during existence starts during Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s. Relation between continuant and occurrent, such that c comes into existence at the start of p. RO:0002489 uberon existence_starts_with existence_starts_with existence starts with Relation between continuant and occurrent, such that c comes into existence at the start of p. RO:0002491 uberon existence_starts_and_ends_during existence_starts_and_ends_during existence starts and ends during Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely. RO:0002492 ceases_to_exist_during uberon RO:0002492 existence_ends_during existence_ends_during existence ends during Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely. Relation between continuant and occurrent, such that c ceases to exist at the end of p. RO:0002493 uberon existence_ends_with existence_ends_with existence ends with Relation between continuant and occurrent, such that c ceases to exist at the end of p. RO:0002494 transforms from uberon transformation_of transformation_of transformation of transforms from SIO:000657 RO:0002495 direct_transformation_of immediately transforms from uberon immediate_transformation_of immediate_transformation_of immediate transformation of direct_transformation_of immediately transforms from SIO:000658 RO:0002496 uberon existence_starts_during_or_after existence_starts_during_or_after existence starts during or after RO:0002497 uberon existence_ends_during_or_before existence_ends_during_or_before existence ends during or before A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision. RO:0002551 uberon has sekeletal support has supporting framework has_skeleton has_skeleton has skeleton A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision. m1 has_muscle_antagonist m2 iff m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. RO:0002568 uberon has_muscle_antagonist has_muscle_antagonist has_muscle_antagonist m1 has_muscle_antagonist m2 iff m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. RO:0002569 uberon has_branching_part has_branching_part has branching part RO:0002571 uberon lumen_of lumen_of lumen of RO:0002572 uberon luminal_space_of luminal_space_of luminal space of RO:0002576 uberon skeleton_of skeleton_of skeleton of RO:0003000 uberon produces produces produces RO:0003001 uberon produced_by produced_by produced_by UBPROP:0000004 uberon provenance_notes provenance_notes obsolete provenance_notes true true uberon anastomoses_with anastomoses with x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y. uberon anteriorly_connected_to anteriorly connected to x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y. carries uberon channel_for channel for uberon channels_from channels_from uberon channels_into channels_into x is a conduit for y iff y passes through the lumen of x. uberon conduit_for conduit for x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y. uberon distally_connected_to distally connected to x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y. uberon extends_fibers_into extends_fibers_into Relationship between a fluid and a material entity, where the fluid is the output of a realization of a filtration role that inheres in the material entity. uberon filtered_through Relationship between a fluid and a filtration barrier, where the portion of fluid arises as a transformation of another portion of fluid on the other side of the barrier, with larger particles removed filtered through uberon has_start has_start 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. uberon in_central_side_of in_central_side_of https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern 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. BSPO:cjm uberon in_innermost_side_of in_innermost_side_of uberon in_outermost_side_of in_outermost_side_of a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s add to RO uberon indirectly_supplies indirectly_supplies uberon layer_part_of layer part of x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y. uberon posteriorly_connected_to posteriorly connected to x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y. uberon protects protects x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y. uberon proximally_connected_to proximally connected to x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y. uberon sexually_homologous_to sexually_homologous_to c site_of p if c is the bearer of a disposition that is realized by a process that has p as part uberon capable_of_has_part site_of site_of uberon subdivision_of placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B subdivision of Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. uberon synapsed_by synapsed by . uberon transitively_anteriorly_connected_to transitively anteriorly connected to . 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 trunk_part_of trunk_part_of true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true true An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity. uberon UBERON:0000000 processual entity An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity. span:ProcessualEntity Lower, narrow portion of the uterus where it joins with the top end of the vagina. The narrow caudal end of the uterus that opens into the vagina. [TFD][VHOG] The evolution of mammals is associated with radical changes in their reproductive biology, particularly the structure and function of the female reproductive organs. These changes include the evolution of the uterus, cervix, vagina, placenta and specialized cell types associated with each of those structures.[well established][VHOG] cervical cervix BTO:0001421 BTO:0002249 CALOHA:TS-0134 EFO:0000979 EMAPA:29927 EV:0100114 FMA:17740 GAID:376 MA:0000392 MAT:0000292 MESH:D002584 NCIT:C12311 OpenCyc:Mx4rvVipEJwpEbGdrcN5Y29ycA UMLS:C0007874 VHOG:0001359 galen:CervixUteri canalis cervicis uteri caudal segment of uterus cervical canal of uterus cervix uteri neck of uterus uterine cervix uberon cervical canal cervix of uterus UBERON:0000002 uterine cervix Lower, narrow portion of the uterus where it joins with the top end of the vagina. The narrow caudal end of the uterus that opens into the vagina. [TFD][VHOG] 2012-09-17 VHOG:0001359 VHOG The evolution of mammals is associated with radical changes in their reproductive biology, particularly the structure and function of the female reproductive organs. These changes include the evolution of the uterus, cervix, vagina, placenta and specialized cell types associated with each of those structures.[well established][VHOG] 2012-09-17 VHOG:0001359 VHOG DOI:10.1098/rspb.2004.2848 Lynch VJ, Roth JJ, Takahashi K, Dunn CW, Nonaka DF, Stopper GF, Wagner GP, Adaptive evolution of HoxA-11 and HoxA-13 at the origin of the uterus in mammals. Proceedings of the Royal Society of London, Series B (2004) cervix EFO:0000979 UMLS:C0007874 ncithesaurus:Cervix canalis cervicis uteri FMA:17740 FMA:TA cervical canal of uterus FMA:17740 cervix uteri EMAPA:29927 neck of uterus FMA:17740 uterine cervix FMA:17740 cervical canal FMA:17740 cervix of uterus BTO:0001421 Orifice of the olfactory system. The naris is the route by which odorants enter the olfactory system[MAH]. One of paired external openings of the nasal chamber.[AAO] Naris refer to the external and interior naris (choana) of tetrapods, and to anterior and posterior naris of zebrafish. It seems now accepted that the structure is homologous: The choana, a unique 'internal nostril' opening from the nasal sac into the roof of the mouth, is a key part of the tetrapod (land vertebrate) respiratory system. It was the first component of the tetrapod body plan to evolve, well before the origin of limbs, and is therefore crucial to our understanding of the beginning of the fish-tetrapod transition. (...) Here we present new material of Kenichthys, a 395-million-year-old fossil fish from China, that provides direct evidence for the origin of the choana and establishes its homology: it is indeed a displaced posterior external nostril that, during a brief transitional stage illustrated by Kenichthys, separated the maxilla from the premaxilla.[well established][VHOG] in actinopterygians, both pairs of nares are external. In tetrapods, the exhalant empties into the buccal cavity we have classified this as an orifice, according to FMA. Note that in FMA, orifices are immaterial entities, but in ZFA this is a surface structure AAO:0000311 EHDAA2:0001225 EHDAA:9083 EMAPA:17847 MA:0000282 VHOG:0000663 galen:Naris uberon UBERON:0000003 naris ZFA Orifice of the olfactory system. The naris is the route by which odorants enter the olfactory system[MAH]. One of paired external openings of the nasal chamber.[AAO] 2012-06-20 AAO:0000311 AAO AAO:EJS Naris refer to the external and interior naris (choana) of tetrapods, and to anterior and posterior naris of zebrafish. It seems now accepted that the structure is homologous: The choana, a unique 'internal nostril' opening from the nasal sac into the roof of the mouth, is a key part of the tetrapod (land vertebrate) respiratory system. It was the first component of the tetrapod body plan to evolve, well before the origin of limbs, and is therefore crucial to our understanding of the beginning of the fish-tetrapod transition. (...) Here we present new material of Kenichthys, a 395-million-year-old fossil fish from China, that provides direct evidence for the origin of the choana and establishes its homology: it is indeed a displaced posterior external nostril that, during a brief transitional stage illustrated by Kenichthys, separated the maxilla from the premaxilla.[well established][VHOG] 2012-09-17 VHOG:0000663 VHOG DOI:10.1038/nature02843 Zhu M, Ahlberg PE, The origin of the internal nostril in tetrapodes. Nature (2004) we have classified this as an orifice, according to FMA. Note that in FMA, orifices are immaterial entities, but in ZFA this is a surface structure FMA The olfactory organ of vertebrates, consisting of nares, olfactory epithelia and the structures and skeletal framework of the nasal cavity. Organ that is the specialized structure of the face that contains olfactory neurons. The peripheral olfactory organ is paired[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]. 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] 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 NCIT:C12756 OpenCyc:Mx4rvViCbJwpEbGdrcN5Y29ycA TAO:0000047 UMLS:C0028429 ZFA:0000047 galen:Nose nasal sac nose peripheral olfactory organ uberon nasus olfactory apparatus proboscis UBERON:0000004 nose http://upload.wikimedia.org/wikipedia/commons/d/d0/Canine-nose.jpg FMA ZFA-def ZFA The olfactory organ of vertebrates, consisting of nares, olfactory epithelia and the structures and skeletal framework of the nasal cavity. UBERON:cjm Organ that is the specialized structure of the face that contains olfactory neurons. The peripheral olfactory organ is paired[ZFA:0000047]. 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]. the organ that is specialized for smell and is part of the respiratory system MP:0002233 UMLS:C0028429 ncithesaurus:Nose nasal sac ZFA:0000047 nose MA:0000281 peripheral olfactory organ ZFA:0000047 nasus olfactory apparatus UBERON:cjm FBbt:00005157 chemosensory sensory organ uberon UBERON:0000005 chemosensory organ chemosensory sensory organ FBbt:00005157 the clusters of hormone-producing cells that are scattered throughout the pancreas Anatomical structure which consists of glands developed from pancreatic ducts in the larvae and secrete insulin.[AAO] 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] 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 BTO:0000991 CALOHA:TS-0741 EFO:0000856 EMAPA:32927 EV:0100130 FMA:16016 GAID:324 MA:0000127 MAT:0000076 MESH:D007515 MIAA:0000076 NCIT:C12608 UMLS:C0022131 VHOG:0000646 XAO:0000159 pancreatic insula pancreatic islet uberon island of Langerhans island of pancreas islets of Langerhans UBERON:0000006 islet of Langerhans http://upload.wikimedia.org/wikipedia/commons/9/99/Gray1105.png the clusters of hormone-producing cells that are scattered throughout the pancreas MA:0000127 MESH:A03.734.414 MP:0005215 Anatomical structure which consists of glands developed from pancreatic ducts in the larvae and secrete insulin.[AAO] 2012-06-20 AAO:0010406 AAO AAO:BJB 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] 2012-09-17 VHOG:0000646 VHOG PMID:7600975 Slack JMW, Developmental biology of the pancreas. Development (1995) 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) UMLS:C0022131 ncithesaurus:Islet_of_Langerhans island of Langerhans BTO:0000991 island of pancreas BTO:0000991 The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands [GO]. An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin [ZFIN]. An endocrine gland derived from infundibulum of the floor of the diencephalon and an ectodermal dorsal protrusion from the buccal cavity which controls the secretion of many hormones influencing the function of various organs of the body.[AAO] An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin.[TAO] It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG] The lamprey possesses a distinct pituitary organ and hormones, the ascidian does not show distinct evidence of them [Sower S, Freamat M, Kavanaugh S. The origins of the vertebrate hypothalamic-pituitary-gonadal (HPG) and hypothalamic-pituitary-thyroid (HPT) endocrine systems: new insights from lampreys. Gen Comp Endocrinol 2009;161:20-9] Hp AAO:0010536 BAMS:PIT BAMS:Pit BIRNLEX:1353 BM:Die-Hy-HY BTO:0001073 CALOHA:TS-0798 DHBA:10505 EFO:0000857 EHDAA2:0001471 EHDAA:2183 EHDAA:4477 EMAPA:35998 EV:0100132 FMA:13889 GAID:457 HBA:4634 MA:0000176 MAT:0000077 MESH:D010902 MIAA:0000077 NCIT:C12399 OpenCyc:Mx4rv6NQYJwpEbGdrcN5Y29ycA TAO:0000118 UMLS:C0032005 VHOG:0000143 XAO:0000017 ZFA:0000118 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=399 glandula pituitaria pituitary pituitary body uberon hypophysis hypophysis cerebri UBERON:0000007 Terminology note: hypophysis and pituitary gland are often used informally as synonyms, but the hypophysis also includes the small infundibular or pituitary stalk[Neumann 2020] pituitary gland http://upload.wikimedia.org/wikipedia/commons/9/97/Gray1180.png ZFA ZFA BGEE:ANN The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands [GO]. An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin [ZFIN]. ZFIN:curator An endocrine gland derived from infundibulum of the floor of the diencephalon and an ectodermal dorsal protrusion from the buccal cavity which controls the secretion of many hormones influencing the function of various organs of the body.[AAO] 2012-06-20 AAO:0010536 AAO AAO:BJB An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin.[TAO] 2012-08-14 TAO:0000118 TAO ZFIN:curator It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG] 2012-09-17 VHOG:0000143 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.510 Hp BIRNLEX:1353 NIFSTD:NeuroNames_abbrevSource UMLS:C0032005 BIRNLEX:1353 UMLS:C0032005 ncithesaurus:Pituitary_Gland http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=399 BIRNLEX:1353 glandula pituitaria pituitary BTO:0001073 pituitary body BTO:0001073 hypophysis ZFA:0000118 hypophysis cerebri MA:0000176 A layer of dense irregular connective tissue that lines organs and supports the mucosa, as well as joins the mucosa to the bulk of underlying smooth muscle. [WP,unvetted]. submucosal BTO:0002107 FMA:85391 FMA:85392 NCIT:C13167 UMLS:C0225344 organ submucosa region of submucosa submucosa of organ submucosa of region of organ uberon submucous layer tela submucosa tunica submucosa UBERON:0000009 submucosa http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png A layer of dense irregular connective tissue that lines organs and supports the mucosa, as well as joins the mucosa to the bulk of underlying smooth muscle. [WP,unvetted]. UMLS:C0225344 ncithesaurus:Submucosa organ submucosa FMA:85391 region of submucosa FMA:85392 submucosa of organ FMA:85391 submucosa of region of organ FMA:85392 submucous layer BTO:0002107 tela submucosa BTO:0002107 A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands. Nervous structures including ganglia outside of the central nervous system. Kimmel et al, 1995.[TAO] Part of nervous system in which nerves extend throughout the body outside of the brain and spinal cord.[AAO] The peripheral nervous system (PNS) is the part of the nervous system connected to the CNS which contains cranial nerves III - XII, spinal, peripheral and autonomic nerves. (CUMBO) (...) specific vertebrate traits within the chordate phylum such as skeletal tissues, PNS, and spectacular head and brain development, are linked to the NC (neural crest) and its derivatives.[well established][VHOG] PNS AAO:0000429 BAMS:PNS BILA:0000081 BIRNLEX:1111 BTO:0001028 CALOHA:TS-0808 EFO:0000891 EHDAA2:0001445 EHDAA:2893 EMAPA:16665 EV:0100335 FBbt:00005098 FMA:9903 GAID:715 MA:0000218 MAT:0000338 MESH:D017933 MIAA:0000338 NCIT:C12465 TAO:0000142 UMLS:C0206417 UMLS:C1305921 VHOG:0000399 XAO:0000178 ZFA:0000142 pars peripherica systema nervosum periphericum uberon UBERON:0000010 peripheral nervous system http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png cjm A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands. GO:0007422 Nervous structures including ganglia outside of the central nervous system. Kimmel et al, 1995.[TAO] 2012-08-14 TAO:0000142 TAO ZFIN:curator Part of nervous system in which nerves extend throughout the body outside of the brain and spinal cord.[AAO] 2012-06-20 AAO:0000429 AAO AAO:BJB The peripheral nervous system (PNS) is the part of the nervous system connected to the CNS which contains cranial nerves III - XII, spinal, peripheral and autonomic nerves. (CUMBO) (...) specific vertebrate traits within the chordate phylum such as skeletal tissues, PNS, and spectacular head and brain development, are linked to the NC (neural crest) and its derivatives.[well established][VHOG] 2012-09-17 VHOG:0000399 VHOG DOI:10.1007/978-0-387-46954-6_6 Dupin E, Creuzet S, Le Douarin NM, The contribution of the neural crest to the vertebrate body. Advances in experimental medicine and biology (2006) PNS UMLS:C0206417 BIRNLEX:1111 UMLS:C0206417 ncithesaurus:Peripheral_Nervous_System UMLS:C1305921 BIRNLEX:1111 pars peripherica FMA:9903 FMA:TA systema nervosum periphericum FMA:9903 FMA:TA The parasympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system. Parasympathetic nerves emerge cranially as pre ganglionic fibers from oculomotor, facial, glossopharyngeal and vagus and from the sacral region of the spinal cord. Most neurons are cholinergic and responses are mediated by muscarinic receptors. The parasympathetic system innervates, for example: salivary glands, thoracic and abdominal viscera, bladder and genitalia[GO]. Part of the autonomic nervous system which has opposing physiological effects of the sympathetic nervous system. Examples include decreasing the heart rate or dilating the blood vessels.[AAO] In mammals, the autonomic nervous system is divided into two contrasting, antagonistic systems of control over visceral activity: the sympathetic system and the parasympathetic system (reference 1); In general, the teleosts may be considered phylogenetically the first class of vertebrates in which the heart is regulated by both sympathetic and parasympathetic neural pathways (reference 2).[well established][VHOG] AAO:0010488 BIRNLEX:2517 BTO:0001833 CALOHA:TS-2094 EFO:0000894 EHDA:10096 EHDAA2:0001402 EHDAA:4655 EMAPA:17270 FMA:9907 GAID:708 MA:0000223 MAT:0000101 MESH:D010275 MIAA:0000101 NCIT:C12764 TAO:0001575 UMLS:C0030510 UMLS:C1305770 VHOG:0000755 ZFA:0001575 PNS - parasympathetic parasympathetic part of autonomic division of nervous system pars parasympathica divisionis autonomici systematis nervosi uberon pars parasympathica divisionis autonomici systematis nervosi UBERON:0000011 parasympathetic nervous system http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png cjm FMA MA WP ZFA-modified-from-isa The parasympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system. Parasympathetic nerves emerge cranially as pre ganglionic fibers from oculomotor, facial, glossopharyngeal and vagus and from the sacral region of the spinal cord. Most neurons are cholinergic and responses are mediated by muscarinic receptors. The parasympathetic system innervates, for example: salivary glands, thoracic and abdominal viscera, bladder and genitalia[GO]. GO:0048486 Part of the autonomic nervous system which has opposing physiological effects of the sympathetic nervous system. Examples include decreasing the heart rate or dilating the blood vessels.[AAO] 2012-06-20 AAO:0010488 AAO AAO:BJB In mammals, the autonomic nervous system is divided into two contrasting, antagonistic systems of control over visceral activity: the sympathetic system and the parasympathetic system (reference 1); In general, the teleosts may be considered phylogenetically the first class of vertebrates in which the heart is regulated by both sympathetic and parasympathetic neural pathways (reference 2).[well established][VHOG] 2012-09-17 VHOG:0000755 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.634, DOI:10.1016/S0306-4530(98)00057-2 Porges SW, Love: an emergent property of the mammalian autonomic nervous system. Psychoneuroendocrinology (1998) UMLS:C0030510 BIRNLEX:2517 UMLS:C0030510 ncithesaurus:Parasympathetic_Nervous_System UMLS:C1305770 BIRNLEX:2517 pars parasympathica divisionis autonomici systematis nervosi FMA:9907 FMA:TA pars parasympathica divisionis autonomici systematis nervosi Part of peripheral nervous system that includes the somatic parts of the cranial and spinal nerves and their ganglia and the peripheral sensory receptors. EFO:0000892 FMA:9904 MA:0002850 MAT:0000099 MIAA:0000099 NLXANAT:100301 PNS - somatic somatic nervous system, somatic division somatic part of peripheral nervous system somatic peripheral nervous system uberon UBERON:0000012 somatic nervous system cjm Part of peripheral nervous system that includes the somatic parts of the cranial and spinal nerves and their ganglia and the peripheral sensory receptors. NLXANAT:100301 somatic nervous system, somatic division NLXANAT:100301 somatic part of peripheral nervous system UBERON:cjm somatic peripheral nervous system NLXANAT:100301 The sympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system (the other being the parasympathetic nervous system). The sympathetic preganglionic neurons have their cell bodies in the thoracic and lumbar regions of the spinal cord and connect to the paravertebral chain of sympathetic ganglia. Innervate heart and blood vessels, sweat glands, viscera and the adrenal medulla. Most sympathetic neurons, but not all, use noradrenaline as a post-ganglionic neurotransmitter [GO]. Part of the autonomic nervous system which has opposing physiological effects of the parasympathetic nervous system. Examples include increasing the heart rate or constricting the blood vessels.[AAO] The part of the autonomic nervous system which chiefly contains adrenergic fibres and tends to control and reduce secretions, decrease the contractility and hence the tone of smooth muscles and provoke the contraction of blood vessels. Essentially, it consists of preganglionic fibres from the thoracic and upper lumbar parts of the spinal cord. These fibres, by means of delicate rami communicantes, cross over to ganglia sited in a pair of ganglionated cords on each side of the vertebral column or to more peripheral ganglia. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] The autonomic nervous system is composed of three divisions: the sympathetic division, the parasympathetic division, and the enteric division. (...) In ray-finned teleost fishes, a sympathetic chain is present, and dual innervation of additional organs can be observed. A similar pattern can be found in amphibians (...). The evolution of the autonomic nervous system has been quite conservative, especially in the tetrapod lineage.[well established][VHOG] has developmental contribution from NC in verteberates (https://github.com/obophenotype/uberon/wiki/The-neural-crest) AAO:0010487 BIRNLEX:2516 BTO:0001832 CALOHA:TS-2050 EFO:0000893 EHDAA2:0001971 EHDAA:3769 EMAPA:16985 FMA:9906 GAID:710 MA:0000225 MESH:D013564 MIAA:0000100 NCIT:C12795 TAO:0001576 UMLS:C0039044 UMLS:C1269646 VHOG:0000384 ZFA:0001576 pars sympathica divisionis autonomici systematis nervosi sympathetic nervous system sympathetic part of autonomic division of nervous system uberon pars sympathica divisionis autonomici systematis nervosi UBERON:0000013 sympathetic nervous system http://upload.wikimedia.org/wikipedia/commons/7/77/Gray838.png cjm FMA MA ZFA-modified-from-isa The sympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system (the other being the parasympathetic nervous system). The sympathetic preganglionic neurons have their cell bodies in the thoracic and lumbar regions of the spinal cord and connect to the paravertebral chain of sympathetic ganglia. Innervate heart and blood vessels, sweat glands, viscera and the adrenal medulla. Most sympathetic neurons, but not all, use noradrenaline as a post-ganglionic neurotransmitter [GO]. GO:0048485 Part of the autonomic nervous system which has opposing physiological effects of the parasympathetic nervous system. Examples include increasing the heart rate or constricting the blood vessels.[AAO] 2012-06-20 AAO:0010487 AAO AAO:BJB The part of the autonomic nervous system which chiefly contains adrenergic fibres and tends to control and reduce secretions, decrease the contractility and hence the tone of smooth muscles and provoke the contraction of blood vessels. Essentially, it consists of preganglionic fibres from the thoracic and upper lumbar parts of the spinal cord. These fibres, by means of delicate rami communicantes, cross over to ganglia sited in a pair of ganglionated cords on each side of the vertebral column or to more peripheral ganglia. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000384 VHOG The autonomic nervous system is composed of three divisions: the sympathetic division, the parasympathetic division, and the enteric division. (...) In ray-finned teleost fishes, a sympathetic chain is present, and dual innervation of additional organs can be observed. A similar pattern can be found in amphibians (...). The evolution of the autonomic nervous system has been quite conservative, especially in the tetrapod lineage.[well established][VHOG] 2012-09-17 VHOG:0000384 VHOG ISBN:978-0471210054 Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.461-463 UMLS:C0039044 BIRNLEX:2516 UMLS:C0039044 ncithesaurus:Sympathetic_Nervous_System UMLS:C1269646 BIRNLEX:2516 pars sympathica divisionis autonomici systematis nervosi FMA:9906 FMA:TA pars sympathica divisionis autonomici systematis nervosi Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis. Note the distinction between the entire skin of the body, of which there is only 1 in an organism, and zones of skin, of which there can be many. Examples: skin of knee (...) it is well-established that neural crest cells contribute to both the dermal skeleton (craniofacial bone, teeth, and the caudal fin rays of teleosts) and the integument, including craniofacial dermis and all pigment cells outside the retina (...).[well established][VHOG] we assume that mouse, HOG and GAID all mean zone of skin when they say skin. We also choose skin as an exact synonym, as it is more intuitive EHDAA2:0001844 EHDAA:6530 EMAPA:17525 EV:0100152 FMA:86166 GAID:933 MA:0000151 MAT:0000284 MESH:D012867 MIAA:0000284 OpenCyc:Mx4rvVjX3ZwpEbGdrcN5Y29ycA VHOG:0000860 portion of skin region of skin skin skin region skin zone uberon UBERON:0000014 zone of skin http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg http://upload.wikimedia.org/wikipedia/commons/e/e8/HumanSkinDiagram.jpg FMA Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis. (...) it is well-established that neural crest cells contribute to both the dermal skeleton (craniofacial bone, teeth, and the caudal fin rays of teleosts) and the integument, including craniofacial dermis and all pigment cells outside the retina (...).[well established][VHOG] 2012-09-17 VHOG:0000860 VHOG DOI:10.1111/j.1469-7580.2008.01043.x Vickaryous MK, Sire JY, The integumentary skeleton of tetrapods: origin, evolution, and development. J Anat (2009) skin MA:0000151 A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures. AEO:0000192 CARO:0000010 FMA:50705 anatomical boundary uberon UBERON:0000015 Except in the case of abstracted fiat boundaries such as the midline plane of an organism, all 2D anatomical entities have a 3 dimensional projection. For example, the surface of the shell of a muscle has a distinct shape that projects into the third dimension. Note that boundaries are 2D structures. They have no thickness - and so can not be sites of gene expression or gene product localisation. For this, use boundary region terms. non-material anatomical boundary CARO A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures. CARO:0000010 anatomical boundary CARO:0000010 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. create a separate class for distributed pancreas, eg cyclostomes? 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 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] 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] endocrine and exocrine pancreas are not co-associated in hagfishes or lampreys BTO:0000650 CALOHA:TS-1302 EFO:0002542 EMAPA:35305 EV:0100129 FMA:16018 MA:0001582 NCIT:C32509 TAO:0001260 VHOG:0000049 ZFA:0001260 endocrine pancreas pars endocrina pancreatis uberon endocrine part of pancreas islets of Langerhans part of pancreas UBERON:0000016 endocrine pancreas ZFA AAO FMA XAO GO GO GO 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. GO:GO 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] 2012-09-17 VHOG:0000049 VHOG 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] 2012-08-14 TAO:0001260 TAO ZFIN:curator 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] 2012-09-17 VHOG:0000049 VHOG DOI:10.1016/j.crvi.2007.03.006 Madsen OD, Pancreas phylogeny and ontogeny in relation to a 'pancreatic stem cell'. C.R. Biologies (2007) endocrine and exocrine pancreas are not co-associated in hagfishes or lampreys endocrine part of pancreas BTO:0000650 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]. 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] 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] AAO:0010407 BTO:0000434 CALOHA:TS-1241 EMAPA:35328 EV:0100093 FMA:16017 MA:0002415 NCIT:C32546 TAO:0001249 UMLS:C0553695 VHOG:0000048 XAO:0000137 ZFA:0001249 exocrine pancreas pars exocrina pancreatis uberon exocrine component of pancreas exocrine part of pancreas UBERON:0000017 exocrine pancreas 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]. GOC:GO The exocrine pancreas is composed of acinar epithelial cells and ductal epithelium that manufacture the proteolytic enzymes and bicarbonate required for digestion.[TAO] 2012-08-14 TAO:0001249 TAO ZFIN:curator 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] 2012-09-17 VHOG:0000048 VHOG 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] 2012-09-17 VHOG:0000048 VHOG DOI:10.1016/j.crvi.2007.03.006 Madsen OD, Pancreas phylogeny and ontogeny in relation to a 'pancreatic stem cell'. C.R. Biologies (2007) UMLS:C0553695 ncithesaurus:Exocrine_Pancreas exocrine part of pancreas BTO:0000434 A light sensing organ composed of ommatidia The term compound eye is sometimes used for the multi-unit eyes of annelids, bivalves, echinoderms. We follow Richter et al and restrict this class to the arthropod structure for these structures BTO:0001921 FBbt:00004508 HAO:0000217 TGMA:0000024 uberon Facettenauge Komplexauge adult compound eye faceted eye insect eye zusammengesetztes Auge UBERON:0000018 compound eye https://github.com/obophenotype/uberon/issues/457 A light sensing organ composed of ommatidia FB:gg The term compound eye is sometimes used for the multi-unit eyes of annelids, bivalves, echinoderms. We follow Richter et al and restrict this class to the arthropod structure for these structures Facettenauge BTO:0001921 Komplexauge BTO:0001921 zusammengesetztes Auge BTO:0001921 An organ of sight that includes the camera-type eyeball and supporting structures such as the lacrimal apparatus, the conjunctiva, the eyelid. A cavitated compound organ that transduces light waves into neural signals.[TAO] The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] FMA distinguishes Eye (subdivision of face) which has its parts an Eyeball (organ), as well as other structures, and the orbit of skull. MA includes eyelid, conjunctiva and lacrimal apparatus as part of MA:eye - consistent with FMA - so we can infer that MA:eye is more like FMA:eye than FMA:eyeball. For other AOs this distinction is less meaningful - e.g. ZFA has no eyelid; XAO has no eyelid, but it has conjuctiva, which is considered part of the xao:eye. GO considers eyelid development part of eye development. See also notes on optic nerve - XAO, AAO and BTO consider this part of the eye. MA considers the eye muscles part of the eye, whereas FMA has a class 'orbital content' for this eye AAO:0010340 BIRNLEX:1169 BTO:0004688 EHDAA2:0000484 EHDAA:936 EMAPA:16198 FMA:54448 MA:0000261 NCIT:C12401 OpenCyc:Mx8Ngx4rwKSh9pwpEbGdrcN5Y29ycB4rvVil5pwpEbGdrcN5Y29ycB4rvViTvpwpEbGdrcN5Y29ycA TAO:0000107 UMLS:C0015392 UMLS:C1280202 VHOG:0000275 XAO:0000179 ZFA:0000107 regio orbitalis vertebrate eye uberon camera-type eye plus associated structures eyes orbital part of face orbital region UBERON:0000019 camera-type eye definitional An organ of sight that includes the camera-type eyeball and supporting structures such as the lacrimal apparatus, the conjunctiva, the eyelid. GO:0043010 A cavitated compound organ that transduces light waves into neural signals.[TAO] 2012-08-14 TAO:0000107 TAO TAO:wd The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] 2012-09-17 VHOG:0000275 VHOG DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007) FMA distinguishes Eye (subdivision of face) which has its parts an Eyeball (organ), as well as other structures, and the orbit of skull. MA includes eyelid, conjunctiva and lacrimal apparatus as part of MA:eye - consistent with FMA - so we can infer that MA:eye is more like FMA:eye than FMA:eyeball. For other AOs this distinction is less meaningful - e.g. ZFA has no eyelid; XAO has no eyelid, but it has conjuctiva, which is considered part of the xao:eye. GO considers eyelid development part of eye development. See also notes on optic nerve - XAO, AAO and BTO consider this part of the eye. MA considers the eye muscles part of the eye, whereas FMA has a class 'orbital content' for this FMA eye FMA:54448 UMLS:C0015392 BIRNLEX:1169 UMLS:C0015392 ncithesaurus:Eye UMLS:C1280202 BIRNLEX:1169 regio orbitalis FMA:54448 FMA:TA eyes TAO:0000107 orbital part of face FMA:54448 orbital region FMA:54448 An organ that is capable of transducing sensory stimulus to the nervous system. AEO:0000094 BSA:0000121 BTO:0000202 CALOHA:TS-2043 EHDAA2:0001824 EHDAA:500 EMAPA:35955 FBbt:00005155 GAID:63 HAO:0000930 MA:0000017 MESH:D012679 NCIT:C33224 UMLS:C0935626 VHOG:0001407 WBbt:0006929 organ of sense organ system organ of sensory organ system organ of sensory system sense organ system organ sensory organ sensory organ system organ sensory system organ sensillum uberon Sinnesorgan sensor UBERON:0000020 sense organ http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png An organ that is capable of transducing sensory stimulus to the nervous system. UMLS:C0935626 ncithesaurus:Organ_of_the_Special_Sense organ of sense organ system OBOL:accepted organ of sensory organ system OBOL:accepted organ of sensory system OBOL:accepted sense organ system organ OBOL:automatic sensory organ system organ OBOL:automatic sensory system organ OBOL:accepted sensillum WBbt:0006929 Sinnesorgan BTO:0000202 Anatomical projection that protrudes from the skin. Examples: hair, nail, feather, claw, hoof, horn, wattle, spur, beak, antler, bristle and some scales. Mammary glands develop by similar mechanisms, and there is an argument for including them here (e.g. http://www.ncbi.nlm.nih.gov/pubmed/20484386), but these structures do not fit the current definition (lactiferous glands are part of the integumentary system in FMA). Note the FMA class is a subdivision of epidermis, which may be too restrictive for our purposes here. CALOHA:TS-0051 FMA:71012 skin appendage epidermal appendage uberon epidermal growth UBERON:0000021 cutaneous appendage Anatomical projection that protrudes from the skin. Examples: hair, nail, feather, claw, hoof, horn, wattle, spur, beak, antler, bristle and some scales. skin appendage FMA:71012 one of the epidermal growths that form the distinctive outer covering, or plumage, on birds. Feathers are formed in tiny follicles in the epidermis, or outer skin layer, that produce keratin proteins. Among the characteristics that distinguish the extant Aves from other living groups. Feathers have also been noticed in those Theropoda which have been termed feathered dinosaurs. Although feathers cover most parts of the body of birds, they arise only from certain well-defined tracts on the skin. They aid in flight, thermal insulation, waterproofing and coloration that helps in communication and protection The beta-keratins in feathers, beaks and claws - and the claws, scales and shells of reptiles - are composed of protein strands hydrogen-bonded into beta-pleated sheets, which are then further twisted and crosslinked by disulfide bridges into structures even tougher than the alpha-keratins of mammalian hair, horns and hoof. BTO:0000447 EFO:0000955 GAID:1214 MAT:0000156 MESH:D005241 OpenCyc:Mx4rvVjW-5wpEbGdrcN5Y29ycA uberon UBERON:0000022 feather http://xkcd.com/1104/ http://upload.wikimedia.org/wikipedia/commons/4/41/Parts_of_feather_modified.jpg one of the epidermal growths that form the distinctive outer covering, or plumage, on birds. Feathers are formed in tiny follicles in the epidermis, or outer skin layer, that produce keratin proteins. Appendage that is shaped in order to produce lift for flight through the air. alar This class is not monophyletic. See also: GO:0007629 BTO:0001463 EFO:0000885 GAID:1217 MAT:0000202 MESH:D014921 MIAA:0000202 aliform appendage uberon UBERON:0000023 wing Appendage that is shaped in order to produce lift for flight through the air. aliform appendage Forelimb that is used to produce lift for flight through the air. uberon UBERON:0000024 Examples: bat wing, bird wing forelimb wing Forelimb that is used to produce lift for flight through the air. Any hollow cylindrical anatomical structure containing a lumen through which substances are transported. not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts) tubular galen:Tube anatomical tube duct uberon UBERON:0000025 tube Any hollow cylindrical anatomical structure containing a lumen through which substances are transported. Major subdivision of an organism that protrudes from the body[DOS, CARO]. An appendage is an external body part, or natural prolongation, that protrudes from an organism's body, such as a vertebrate's limbs[BILA][BILA:0000018]. Organ or organ part that is attached to the body of an organism. For example a limb[GO, modified][GO:0048736]. appendicular this is currently a subtype of organism subdivision - which would exclude feathers AEO:0000193 BILA:0000018 BTO:0001492 CARO:0010003 EFO:0000799 EHDAA2:0003193 EMAPA:37283 EV:0100155 FBbt:00007000 HAO:0000144 MAT:0000023 MESH:D005121 MIAA:0000023 NCIT:C61460 OpenCyc:Mx4rvViC-JwpEbGdrcN5Y29ycA UMLS:C0598782 VSAO:0000075 XAO:0000218 uberon appendages extremitaet extremity limbs/digits/tail UBERON:0000026 appendage Major subdivision of an organism that protrudes from the body[DOS, CARO]. CARO:DOS An appendage is an external body part, or natural prolongation, that protrudes from an organism's body, such as a vertebrate's limbs[BILA][BILA:0000018]. BILA:0000018 Organ or organ part that is attached to the body of an organism. For example a limb[GO, modified][GO:0048736]. GO:0048736 EMAPA:37283 MA:th UMLS:C0598782 ncithesaurus:Appendage appendages XAO:0000218 extremitaet BTO:0001492 limbs/digits/tail MP:0000001 true true Any of the rounded masses of lymphoid tissue that are surrounded by a capsule of connective tissue, are distributed along the lymphatic vessels, and contain numerous lymphocytes which filter the flow of lymph. Lymph nodes that are associated with the lymphatic system have evolved in mammals.[well established][VHOG] BTO:0000784 CALOHA:TS-0579 EFO:0000872 EMAPA:35523 EV:0100050 FMA:5034 GAID:947 MA:0000139 MAT:0000442 MESH:D008198 NCIT:C12745 NCIT:C33027 OpenCyc:Mx4rwLPqLpwpEbGdrcN5Y29ycA TAO_RETIRED:0005318 UMLS:C0024204 VHOG:0001273 ZFA_RETIRED:0005318 galen:Lymphnode uberon lymph gland nodus lymphaticus UBERON:0000029 lymph node https://github.com/obophenotype/uberon/issues/650 http://upload.wikimedia.org/wikipedia/commons/b/b8/Illu_lymph_node_structure.png Any of the rounded masses of lymphoid tissue that are surrounded by a capsule of connective tissue, are distributed along the lymphatic vessels, and contain numerous lymphocytes which filter the flow of lymph. BTO:0000784 Lymph nodes that are associated with the lymphatic system have evolved in mammals.[well established][VHOG] 2012-09-17 VHOG:0001273 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.630 UMLS:C0024204 ncithesaurus:Lymph_Node lymph gland VHOG:0001273 nodus lymphaticus A thin layer of loose connective tissue which lies beneath the epithelium and together with the epithelium constitutes the mucosa[WP]. The lamina propria contains capillaries and a central lacteal (lymph vessel) in the small intestine, as well as lymphoid tissue. Lamina propria also contains glands with the ducts opening on to the mucosal epithelium, that secrete mucus and serous secretions. BTO:0002330 FMA:62517 NCIT:C32918 UMLS:C1179187 lamina propria mucosa lamina propria mucosae uberon tunica propria UBERON:0000030 lamina propria GI:Organization.svg A thin layer of loose connective tissue which lies beneath the epithelium and together with the epithelium constitutes the mucosa[WP]. The lamina propria contains capillaries and a central lacteal (lymph vessel) in the small intestine, as well as lymphoid tissue. Lamina propria also contains glands with the ducts opening on to the mucosal epithelium, that secrete mucus and serous secretions. UMLS:C1179187 ncithesaurus:Lamina_Propria tunica propria BTO:0002330 A lamina propria that is part of a respiratory airway. EMAPA:35877 FMA:265157 MA:0001858 NCIT:C49305 UMLS:C1710457 lamina propria mucosa of trachea lamina propria mucosa of windpipe lamina propria mucosae of trachea lamina propria mucosae of windpipe lamina propria of windpipe trachea lamina propria trachea lamina propria mucosa trachea lamina propria mucosae tracheal lamina propria windpipe lamina propria windpipe lamina propria mucosa windpipe lamina propria mucosae uberon UBERON:0000031 lamina propria of trachea true A lamina propria that is part of a respiratory airway. OBOL:automatic UMLS:C1710457 ncithesaurus:Trachea_Lamina_Propria lamina propria mucosa of trachea OBOL:automatic lamina propria mucosa of windpipe OBOL:automatic lamina propria mucosae of trachea OBOL:automatic lamina propria mucosae of windpipe OBOL:automatic lamina propria of windpipe OBOL:automatic trachea lamina propria mucosa OBOL:automatic trachea lamina propria mucosae OBOL:automatic windpipe lamina propria OBOL:automatic windpipe lamina propria mucosa OBOL:automatic windpipe lamina propria mucosae OBOL:automatic uberon UBERON:0000032 obsoleted as it was a grouping class that served no purpose obsolete cranial structure true The head is the anterior-most division of the body [GO]. Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO] Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO] Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG] AAO:0010335 AEO:0000106 BILA:0000115 BIRNLEX:1230 BTO:0000282 CALOHA:TS-0436 EFO:0000964 EHDAA2:0003106 EMAPA:31858 FBbt:00000004 FMA:7154 GAID:61 HAO:0000397 MA:0000023 MAT:0000294 MESH:D006257 MIAA:0000294 NCIT:C12419 OpenCyc:Mx4rEOLm4rgPEdmAAAACs6hRjg OpenCyc:Mx4rvVi6YJwpEbGdrcN5Y29ycA SPD:0000016 TAO:0001114 TGMA:0000002 UMLS:C0018670 VHOG:0001644 WBbt:0005739 XAO:0003024 ZFA:0001114 galen:Head head (volume) adult head uberon cephalic area UBERON:0000033 head The head is the anterior-most division of the body [GO]. GO:0060322 Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO] 2012-06-20 AAO:0010335 AAO AAO:BJB Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO] 2012-08-14 TAO:0001114 TAO ZFIN:curator Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG] 2012-09-17 VHOG:0001644 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.82 UMLS:C0018670 BIRNLEX:1230 UMLS:C0018670 ncithesaurus:Head head (volume) FMA:7154 cephalic area SPD:0000016 1 1 An ovarian follicle that has one layer of granulosa cells. BTO:0000410 EMAPA:35631 FMA:18634 MA:0002907 folliculus ovaricus primarius ovary primary follicle primary follicle of ovary primary ovarian follicle uberon preantral follicle of ovary primary egg follicle primary follicle UBERON:0000035 primary ovarian follicle An ovarian follicle that has one layer of granulosa cells. GO:0001545 GOC:mtg_mpo folliculus ovaricus primarius FMA:18634 ovary primary follicle EMAPA:35631 ovary primary follicle MA:0002907 primary follicle of ovary FMA:18634 primary ovarian follicle FMA:18634 primary follicle EMAPA:35631 2 A maturing ovarian follicle that has two more more layers of granulosa cells, up to the onset of antrum formation. consider adopting distinction in MA EMAPA:35632 FMA:18637 MA:0002908 folliculus ovaricus secondarius ovary secondary follicle pre-antral follicle preantral follicle secondary follicle of ovary uberon antral follicle of ovary pre-ovulatory follicle secondary egg follicle secondary follicle UBERON:0000036 secondary ovarian follicle A maturing ovarian follicle that has two more more layers of granulosa cells, up to the onset of antrum formation. GO:0001546 ovary secondary follicle MA:0002908 pre-antral follicle GO:0001546 preantral follicle GO:0001546 antral follicle of ovary FMA:18637 pre-ovulatory follicle EMAPA:30777 secondary follicle EMAPA:35632 2 A follicle that has reached the most mature stage of folliculogenesis, characterized by the presence of the antrum antral follicle EMAPA:30763 FMA:18641 MA:0002909 NCIT:C32692 UMLS:C0600225 Graafian follicle antral ovarian follicle folliculi ovarici vesiculosi folliculus ovaricus tertiarius folliculus ovaricus tertiarius (vesiculosus) folliculus ovaricus tertiarius (vesiculous) ovary antral follicle tertiary follicle of ovary vesicular follicle of ovary vesicular ovarian follicle uberon tertiary egg follicle UBERON:0000037 tertiary ovarian follicle Primary:follicle-4.JPG A follicle that has reached the most mature stage of folliculogenesis, characterized by the presence of the antrum UMLS:C0600225 ncithesaurus:Graafian_Follicle Graafian follicle antral ovarian follicle GO:0001547 folliculi ovarici vesiculosi FMA:18641 FMA:TA folliculus ovaricus tertiarius (vesiculosus) FMA:18641 ovary antral follicle MA:0002909 tertiary follicle of ovary FMA:18641 vesicular follicle of ovary FMA:18641 vesicular ovarian follicle FMA:18641 The fluid surrounding the ovum and granulosa cells in the ovarian follicle. Generally, larger species such as ovine, equine, porcine, human, and bovine have larger follicles, with the fluid comprising a substantial proportion of the volume of the follicles at ovulation (estimated at >95% in bovine [3]). Smaller species such as rats and mice have smaller follicles with fractionally less follicular fluid[20164441] The follicular fluid contains sex steroids, glycoprotein hormones, plasma proteins, mucopolysaccharides, and enzymes and is rich in hyaluronic acid. BTO:0004383 CALOHA:TS-0728 FMA:18665 GAID:372 MA:0002511 MESH:D015571 NCIT:C52556 UMLS:C1709369 liquor follicularis liquor folliculi ovary follicle fluid uberon antral fluid, ovarian follicle liquor folliculi ovarian follicular fluid ovary follicular fluid UBERON:0000038 follicular fluid http://upload.wikimedia.org/wikipedia/commons/8/81/Gray3.png The fluid surrounding the ovum and granulosa cells in the ovarian follicle. ISBN:145114847X MESH:D015571 UMLS:C1709369 ncithesaurus:Ovarian_Follicle_Fluid liquor follicularis FMA:18665 liquor folliculi ovary follicle fluid MA:0002511 liquor folliculi ovarian follicular fluid BTO:0004383 ovary follicular fluid BTO:0004383 Region of ovarian follicle filled with follicular fluid. EMAPA:37867 FMA:18675 antral cavity antrum folliculare ovarian follicle antrum uberon antrum follicularum UBERON:0000039 follicular antrum Region of ovarian follicle filled with follicular fluid. EMAPA:37867 MA:th antral cavity FMA:18675 antrum folliculare FMA:18675 ovarian follicle antrum GO:0001548 antrum follicularum A hemopoietic organ found in elasmobranchs. Along with the spleen and special tissue around the gonads, this structure produces red blood cells and it is nestled along the top and bottom of the esophagus. Found in elasmobranchs (sharks and rays) but with some exceptions. uberon UBERON:0000040 Phenotype notes: Leydig's organ can be quite large - a 1.6-kilogram (3.5-pound) one was reported from a 1.8-metre (6-foot) long Bluntnose Sixgill Shark (Hexanchus griseus). Structure notes: divided into dorsal and ventral patches, gradation varies between species. Lacks erythroblasts and fat cells[Honma 1983] Leydig's organ Wikipedia Honma1983 A hemopoietic organ found in elasmobranchs. Along with the spleen and special tissue around the gonads, this structure produces red blood cells and it is nestled along the top and bottom of the esophagus. Multi-tissue structure composed of enameloid, dentine surrounding a pulp cavity, and bone of attachment anchoring the element into the dermis[VSAO]. TODO check dentin def Small outgrowths which cover the skin of many cartilaginous fish including sharks. They are similar in structure to teeth, and teeth may have evolved from denticle-like structures in primitive fish.[citation needed] The placoid scales in sharks are formed of dentine with dermal papillae located in the core. These scales develop from the dermal layer of the skin, which is in contrast to the epidermal development seen the in the elasmoid scales of tetrapods. The shape of denticle varies from species to species and can be used in identification. Studies have found that the denticles create tiny vortices that reduce drag to make swimming more efficient. Denticles also allow sharks to swim silently compared to other fish that generate considerable noise when they ply the water[WP][Wikipedia:Dermal_denticle]. Scales and teeth of sharks are examples of dermal skeletal elements that are still composed of the three ancient components-enamel, dentine, and bone. VSAO:0000079 dermal denticle odontode scale placoid scale uberon UBERON:0000041 odontode scale VSAO Multi-tissue structure composed of enameloid, dentine surrounding a pulp cavity, and bone of attachment anchoring the element into the dermis[VSAO]. GO_REF:0000034 VSAO:0000079 Small outgrowths which cover the skin of many cartilaginous fish including sharks. They are similar in structure to teeth, and teeth may have evolved from denticle-like structures in primitive fish.[citation needed] The placoid scales in sharks are formed of dentine with dermal papillae located in the core. These scales develop from the dermal layer of the skin, which is in contrast to the epidermal development seen the in the elasmoid scales of tetrapods. The shape of denticle varies from species to species and can be used in identification. Studies have found that the denticles create tiny vortices that reduce drag to make swimming more efficient. Denticles also allow sharks to swim silently compared to other fish that generate considerable noise when they ply the water[WP][Wikipedia:Dermal_denticle]. dermal denticle odontode scale VSAO:0000079 placoid scale VSAO:curator multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer. A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO] a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP] in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA. FMA:9581 GAID:19 MESH:D012704 NCIT:C13169 TAO:0005425 UMLS:C0036760 ZFA:0005425 tunica serosa wall of serous sac uberon serosa UBERON:0000042 serous membrane http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer. A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO] 2012-08-14 TAO:0005425 TAO a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP] in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA. FMA UMLS:C0036760 ncithesaurus:Serosa tunica serosa FMA:9581 wall of serous sac FMA:9581 serosa Dense regular connective tissue that connects muscle to bone[VSAO]. Dense regular connective tissue that connects muscle to bone.[VSAO] Phylogenetically, tendinous tissue first appears in the invertebrate chordate Branchiostoma as myosepta. This two-dimensional array of collagen fibers is highly organized, with fibers running along two primary axes. In hagfish the first linear tendons appear and the myosepta have developed specialized regions with unidirectional fiber orientation - a linear tendon within the flat sheet of myoseptum.[well established][VHOG] in FMA, tendon is an organ component that with parts dense-irregular-connective-tissue of tendon and dense-irregular-connective-tissue of tendon sheath; we follow VSAO in making it a subtype of the former. In VSAO tendons connect muscle to bone; in WP the def states integument (e.g. auricular muscles) - but JB confirms this is not actually tendon but aponeurosis AEO:0000091 BTO:0001356 CALOHA:TS-1021 EHDAA2:0003091 EMAPA:35854 EV:0100149 FMA:9721 GAID:276 MA:0000115 MESH:D013710 NCIT:C13045 OpenCyc:Mx4rvVjefJwpEbGdrcN5Y29ycA UMLS:C0039508 VHOG:0001286 VSAO:0000073 XAO:0000173 ZFA:0005647 galen:Tendon uberon sinew tendo UBERON:0000043 tendon http://upload.wikimedia.org/wikipedia/commons/3/3c/Achilles-tendon.jpg VSAO OG AEO Dense regular connective tissue that connects muscle to bone[VSAO]. GO_REF:0000034 VSAO:0000073 Dense regular connective tissue that connects muscle to bone.[VSAO] 2012-08-14 VSAO:0000073 VSAO PSPUB:0000170 Phylogenetically, tendinous tissue first appears in the invertebrate chordate Branchiostoma as myosepta. This two-dimensional array of collagen fibers is highly organized, with fibers running along two primary axes. In hagfish the first linear tendons appear and the myosepta have developed specialized regions with unidirectional fiber orientation - a linear tendon within the flat sheet of myoseptum.[well established][VHOG] 2012-09-17 VHOG:0001286 VHOG DOI:10.1016/S1095-6433(02)00241-6 Summers AP, Koob TJ, The evolution of tendon - morphology and material properties. Comparative Biochemistry and Physiology-Part A: Molecular and Integrative Physiology (2002) in FMA, tendon is an organ component that with parts dense-irregular-connective-tissue of tendon and dense-irregular-connective-tissue of tendon sheath; we follow VSAO in making it a subtype of the former. In VSAO tendons connect muscle to bone; in WP the def states integument (e.g. auricular muscles) - but JB confirms this is not actually tendon but aponeurosis FMA UMLS:C0039508 ncithesaurus:Tendon sinew tendo Sensory ganglia located on the dorsal spinal roots within the vertebral column. The spinal ganglion cells are pseudounipolar. The single primary branch bifurcates sending a peripheral process to carry sensory information from the periphery and a central branch which relays that information to the spinal cord or brain. (MSH) * ganglion found on the posterior root of each spinal nerve, composed of the unipolar nerve cell bodies of the sensory neurons of the nerve. (CSP) Trunk ganglion which is located adjacent to the spine on a dorsal root and contains the cell bodies of afferent sensory nerves.[TAO] 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] The sensory ganglia of spinal nerves arise only from the neural crest, whereas many sensory ganglia of the 'dorsal' cranial nerves arise from epibranchial placodes as well as the neural crest[DOI:10.1093/icb/icn065] MA and EMAPA introduce distinct classes for what appears to be the same thing UBERON:0026602 AAO:0011032 BIRNLEX:2596 BIRNLEX:2598 BTO:0001264 CALOHA:TS-0954 EFO:0000900 EHDAA2:0000418 EHDAA2:0001897 EHDAA:2899 EMAPA:16667 EMAPA:16668 EMAPA:18372 EV:0100373 FMA:5888 MA:0000231 MA:0000232 MAT:0000162 MIAA:0000162 NCIT:C12462 TAO:0000200 UMLS:C0017070 VHOG:0000222 XAO:0000210 ZFA:0000200 dorsal root ganglion ganglion of dorsal root ganglion spinalis spinal ganglion spinal ganglion part of peripheral nervous system uberon DRG dorsal root ganglia ganglion sensorium nervi spinalis ganglion spinale posterior root ganglion UBERON:0000044 dorsal root ganglion http://upload.wikimedia.org/wikipedia/commons/7/71/DRG_Chicken_e7.jpg MA ZFA Sensory ganglia located on the dorsal spinal roots within the vertebral column. The spinal ganglion cells are pseudounipolar. The single primary branch bifurcates sending a peripheral process to carry sensory information from the periphery and a central branch which relays that information to the spinal cord or brain. (MSH) * ganglion found on the posterior root of each spinal nerve, composed of the unipolar nerve cell bodies of the sensory neurons of the nerve. (CSP) BIRNLEX:2596 Trunk ganglion which is located adjacent to the spine on a dorsal root and contains the cell bodies of afferent sensory nerves.[TAO] 2012-08-14 TAO:0000200 TAO ZFIN:curator From comparative analyses of craniate brains, a morphotype of the brain in the earliest craniate stock can be constructed. In marked contrast to cephalochordates, the ancestral craniate morphotype had a plethora of unique features, which included a telencephalon with pallial and subpallial parts, paired olfactory bulbs with substantial projections to most or all of the telencephalic pallium, paired lateral eyes and ears, a lateral line system for both electroreception and mechanoreception, spinal cord dorsal root ganglia, and an autonomic nervous system.[well established][VHOG] 2012-09-17 VHOG:0000222 VHOG DOI:10.1002/1097-0185(20000615)261:3<111::AID-AR6>3.0.CO;2-F Butler AB, Chordate evolution and the origin of craniates: An old brain in a new head. AnaT Rec (New Anat) (2000) MA and EMAPA introduce distinct classes for what appears to be the same thing FMA UMLS:C0017070 BIRNLEX:2596 UMLS:C0017070 ncithesaurus:Dorsal_Root_Ganglion dorsal root ganglion BTO:0001264 ganglion of dorsal root OBOL:automatic ganglion spinalis FMA:5888 spinal ganglion FMA:5888 spinal ganglion part of peripheral nervous system BIRNLEX:2598 DRG dorsal root ganglia ganglion sensorium nervi spinalis ganglion sensorium nervi spinalis BTO:0001264 ganglion spinale BTO:0001264 posterior root ganglion EMAPA:16668 A biological tissue mass, most commonly a mass of nerve cell bodies. TODO - check vert vs invert. Other species: Any of a number of aggregations of neurons, glial cells and their processes, surrounded by a glial cell and connective tissue sheath (plural: ganglia). // Subdivision of neural tree (organ) which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord); together with a nucleus and its associated nerve, it constitutes a neural tree (organ). Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion. // a cluster of nerve cells and associated glial cells (nuclear location) // Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system. A ganglion is a cluster of neurons. It is part of a nervous system. It may include glial cells. The neurons are arranged in a specific constellation: neuronal somata are concentrated at the surface, thus forming a cell cortex, and neurites are concentrated in the centre of the ganglion to form the neuropil. A ganglion is a distinct unit but several ganglia may be anterio-posteriorly joined by connectives or transversally by commissures Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system.[AAO] Structures containing a collection of nerve cell bodies. (Source: BioGlossary, www.Biology-Text.com)[TAO] Subdivision of nervous system which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord. Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion (adapted from Foundational Model of Anatomy)[NLXANAT:100302]. Cranial sensory placodes are focused areas of the head ectoderm of vertebrates that contribute to the development of the cranial sense organs and their associated ganglia. Placodes have long been considered a key character of vertebrates, and their evolution is proposed to have been essential for the evolution of an active predatory lifestyle by early vertebrates.[well established][VHOG] ganglionic AAO:0010426 AEO:0000135 BAMS:G BTO:0000497 CALOHA:TS-0397 EFO:0000899 EHDAA2:0003135 EHDAA:2897 EHDAA:4662 EHDAA:5621 EHDAA:918 EMAPA:32846 EV:0100372 FBbt:00005137 FMA:5884 MA:0002406 MAT:0000207 MAT:0000343 MESH:D005724 MIAA:0000207 MIAA:0000343 NCIT:C12719 NLXANAT:100302 TAO:0000190 TGMA:0001016 UMLS:C0017067 VHOG:0000156 WBbt:0005189 XAO:0000209 ZFA:0000190 uberon ganglia neural ganglion UBERON:0000045 ganglion EHDAA2 Bgee:AN BTO 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 Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system.[AAO] 2012-06-20 AAO:0010426 AAO AAO:EJS Structures containing a collection of nerve cell bodies. (Source: BioGlossary, www.Biology-Text.com)[TAO] 2012-08-14 TAO:0000190 TAO ZFIN:curator Subdivision of nervous system which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord. Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion (adapted from Foundational Model of Anatomy)[NLXANAT:100302]. NLXANAT:100302 Cranial sensory placodes are focused areas of the head ectoderm of vertebrates that contribute to the development of the cranial sense organs and their associated ganglia. Placodes have long been considered a key character of vertebrates, and their evolution is proposed to have been essential for the evolution of an active predatory lifestyle by early vertebrates.[well established][VHOG] 2012-09-17 VHOG:0000156 VHOG DOI:10.1016/j.ydbio.2005.02.021 Mazet F, Hutt JA, Milloz J, Millard J, Graham A, Shimeld SM, Molecular evidence from Ciona intestinalis for the evolutionary origin of vertebrate sensory placodes. Developmental Biology (2005) UMLS:C0017067 ncithesaurus:Ganglion neural ganglion BTO:0000497 eye-spots which may be set into a pit to reduce the angles of light that enters and affects the eyespot, to allow the organism to deduce the angle of incoming light pit eye uberon UBERON:0000046 stemma eye-spots which may be set into a pit to reduce the angles of light that enters and affects the eyespot, to allow the organism to deduce the angle of incoming light pit eye An eye with one concave chamber. Note that 'simple' does not imply a reduced level of complexity or acuity. TGMA:0000729 uberon UBERON:0000047 simple eye An eye with one concave chamber. Note that 'simple' does not imply a reduced level of complexity or acuity. Simple eye that has a small aperture (which may be adjustable) and deep pit. It is only found in the nautiloids. uberon UBERON:0000048 pinhole eye Simple eye that has a small aperture (which may be adjustable) and deep pit. It is only found in the nautiloids. simple eye that consists of a lens of one refractive index uberon UBERON:0000049 spherical lensed eye simple eye that consists of a lens of one refractive index simple eye that has two or more lenses. Some marine organisms bear more than one lens; for instance the copeopod Pontella has three. The outer has a parabolic surface, countering the effects of spherical aberration while allowing a sharp image to be formed. Copilla's eyes have two lenses, which move in and out like a telescope uberon UBERON:0000050 simple eye with multiple lenses 2 simple eye that has two or more lenses. Some marine organisms bear more than one lens; for instance the copeopod Pontella has three. The outer has a parabolic surface, countering the effects of spherical aberration while allowing a sharp image to be formed. Copilla's eyes have two lenses, which move in and out like a telescope The deepest portions of the vagina, extending into the recesses created by the vaginal portion of cervix[WP,unvetted]. fornix FMA:19985 NCIT:C33848 UMLS:C0227794 fornix vaginae vaginal fornix uberon vaginal fornices UBERON:0000051 fornix of vagina Female:anatomy.png The deepest portions of the vagina, extending into the recesses created by the vaginal portion of cervix[WP,unvetted]. UMLS:C0227794 ncithesaurus:Vaginal_Fornix fornix vaginae FMA:19985 FMA:TA vaginal fornices A C-shaped bundle of fibres (axons) in the brain, and carries signals from the hippocampus to the mammillary bodies and septal nuclei. It is typically divided into the columns (crus), body, commissure and the pre-commissural and post-commissural fornix (MM). fornix BAMS:f BIRNLEX:705 DHBA:10576 DMBA:17767 EMAPA:35352 FMA:61965 FMA:83865 HBA:9249 MA:0002747 NCIT:C32289 UMLS:C0152334 UMLS:C0458370 http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=268 brain fornix cerebral fornix forebrain fornix fornix of neuraxis neuraxis fornix uberon fornix (column and body of fornix) fornix cerebri fornix hippocampus hippocampus fornix UBERON:0000052 fornix of brain http://upload.wikimedia.org/wikipedia/commons/2/21/Gray747.png NIFSTD A C-shaped bundle of fibres (axons) in the brain, and carries signals from the hippocampus to the mammillary bodies and septal nuclei. It is typically divided into the columns (crus), body, commissure and the pre-commissural and post-commissural fornix (MM). BIRNLEX:705 FMA:61965 inferred UMLS:C0152334 BIRNLEX:705 UMLS:C0458370 ncithesaurus:Cerebral_Fornix http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=268 BIRNLEX:705 forebrain fornix FMA:61965 fornix of neuraxis FMA:83865 neuraxis fornix FMA:83865 fornix (column and body of fornix) FMA:61965 fornix cerebri NeuroNames:268 An oval area in the retina, usually located temporal to the posterior pole of the eye and slightly below the level of the optic disk. It is characterized by the presence of a yellow pigment diffusely permeating the inner layers, contains the fovea centralis in its center, and provides the best phototopic visual acuity. It is devoid of retinal blood vessels, except in its periphery, and receives nourishment from the choriocapillaris of the choroid. (From Cline et al., Dictionary of Visual Science, 4th ed) BIRNLEX:2540 BTO:0003015 EMAPA:36516 EV:0100349 FMA:58637 GAID:909 MA:0001306 MESH:D008266 NCIT:C26464 NCIT:C33044 UMLS:C0450295 UMLS:C1284755 uberon macula macula flava retinae macula retinae maculae UBERON:0000053 macula lutea http://upload.wikimedia.org/wikipedia/commons/e/ed/Human_eye_cross-sectional_view_grayscale.png An oval area in the retina, usually located temporal to the posterior pole of the eye and slightly below the level of the optic disk. It is characterized by the presence of a yellow pigment diffusely permeating the inner layers, contains the fovea centralis in its center, and provides the best phototopic visual acuity. It is devoid of retinal blood vessels, except in its periphery, and receives nourishment from the choriocapillaris of the choroid. (From Cline et al., Dictionary of Visual Science, 4th ed) MESH:A09.371.729.522 UMLS:C0450295 BIRNLEX:2540 UMLS:C0450295 ncithesaurus:Macula_Lutea UMLS:C1284755 BIRNLEX:2540 macula flava retinae BTO:0003015 macula retinae BTO:0003015 Thickened areas of the saccule or utricle where the termination of the vestibular nerve occurs[MESH,modified]. 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 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] macular GAID:777 MESH:D008267 TAO:0000386 ZFA:0000386 macula maculae sensory macula sensory patch uberon acoustic macula acoustic maculae UBERON:0000054 macula Thickened areas of the saccule or utricle where the termination of the vestibular nerve occurs[MESH,modified]. MESH:A09.246.631.909.625.125 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] 2012-08-14 TAO:0000386 TAO ZFIN:curator maculae sensory macula ZFA:0000386 sensory patch ZFA:0000386 acoustic macula MESH:A09.246.631.909.625.125 acoustic maculae MESH:A09.246.631.909.625.125 A tubular structure that contains, conveys body fluid, such as blood or lymph. uberon UBERON:0000055 vessel A tubular structure that contains, conveys body fluid, such as blood or lymph. Muscular duct that propels urine from the kidneys to the urinary bladder, or related organs. Anatomical structure consisting of long narrow duct which carries urine from the kidney to the urinary bladder.[AAO] 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] ureteral ureteric in humans, consists of adventitial, muscular and mucoa layers AAO:0010254 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 NCIT:C12416 OpenCyc:Mx4rvhmm6JwpEbGdrcN5Y29ycA UMLS:C0041951 VHOG:0000605 XAO:0000144 galen:Ureter uberon metanephric duct UBERON:0000056 ureter Urinary:system.svg GO Muscular duct that propels urine from the kidneys to the urinary bladder, or related organs. GO:0090189 Anatomical structure consisting of long narrow duct which carries urine from the kidney to the urinary bladder.[AAO] 2012-06-20 AAO:0010254 AAO AAO:BJB 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] 2012-09-17 VHOG:0000605 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] 2012-09-17 VHOG:0000605 VHOG ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543 UMLS:C0041951 ncithesaurus:Ureter metanephric duct ISBN:0073040584 VHOG:0000605 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 urethral 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. BTO:0001426 CALOHA:TS-1132 EFO:0000931 EMAPA:30901 EV:0100099 FMA:19667 GAID:390 MA:0000379 MAT:0000121 MESH:D014521 MIAA:0000121 NCIT:C12417 OpenCyc:Mx4rvVjkypwpEbGdrcN5Y29ycA UMLS:C0041967 VHOG:0001264 XAO:0000153 galen:Urethra uberon UBERON:0000057 urethra Female:anatomy.png pelvic part of UG sinus gives rise to prostatic and membranous parts of urethra Wikipedia Wikipedia 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 MGI:anna MP:0000537 UMLS:C0041967 ncithesaurus:Urethra A tubular structure that transports secreted or excreted substances. A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171]. Most ducts, but not all, are exocrine gland ducts. Some ontologies classify structures such as the oviduct here. AAO:0011123 FBbt:00100314 FMA:30320 NCIT:C12948 TAO:0005171 UMLS:C0687028 XAO:0004000 ZFA:0005171 galen:Duct anatomical duct exocrine duct exocrine gland duct uberon ducts UBERON:0000058 duct A tubular structure that transports secreted or excreted substances. A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171]. ZFA:0005171 UMLS:C0687028 ncithesaurus:Duct ducts XAO:0004000 A subdivision of the digestive tract that connects the small intestine to the cloaca or anus. Lacks or has few villi[Kardong]. Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG] AAO:0010396 BTO:0000706 CALOHA:TS-1306 EFO:0000840 EMAPA:19252 EV:0100077 FMA:7201 GAID:306 MA:0000333 MESH:A03.492.411.495 MIAA:0000046 NCIT:C12379 OpenCyc:Mx4rvVkF5pwpEbGdrcN5Y29ycA UMLS:C0021851 VHOG:0000054 XAO:0000131 galen:LargeIntestine uberon intestinum crassum UBERON:0000059 large intestine cjm A subdivision of the digestive tract that connects the small intestine to the cloaca or anus. Lacks or has few villi[Kardong]. ISBN:0073040584 Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG] 2012-09-17 VHOG:0000054 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.566 UMLS:C0021851 ncithesaurus:Large_Intestine intestinum crassum BTO:0000706 Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers. in FMA, serosa is a wall UBERON:0009915 wall EMAPA:25036 FMA:82482 galen:Wall wall of organ uberon organ wall UBERON:0000060 anatomical wall Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers. FMA:82482 in FMA, serosa is a wall FMA wall of organ FMA:82482 organ wall FMA:82482 Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. AAO:0010825 AEO:0000003 BILA:0000003 CARO:0000003 EHDAA2:0003003 EMAPA:0 FBbt:00007001 FMA:305751 FMA:67135 GAID:781 HAO:0000003 MA:0003000 MESH:D000825 TAO:0000037 TGMA:0001823 VHOG:0001759 XAO:0003000 ZFA:0000037 biological structure connected biological structure uberon UBERON:0000061 anatomical structure Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. CARO:0000003 connected biological structure CARO:0000003 Anatomical structure that performs a specific function or group of functions [WP]. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4 BIRNLEX:4 CARO:0020004 EFO:0000634 EMAPA:35949 ENVO:01000162 FMA:67498 MA:0003001 NCIT:C13018 OpenCyc:Mx4rv5XMb5wpEbGdrcN5Y29ycA OpenCyc:Mx4rwP3iWpwpEbGdrcN5Y29ycA UMLS:C0178784 WBbt:0003760 uberon anatomical unit body organ element UBERON:0000062 organ Anatomical structure that performs a specific function or group of functions [WP]. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. GO:0048513 UMLS:C0178784 ncithesaurus:Organ element A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity. FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball. Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal. FMA:86140 uberon organ region with fixed fiat boundary organ segment segment of organ UBERON:0000063 organ subunit A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity. Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball. FMA:86140 3 Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal. FMA:86140 1 organ region with fixed fiat boundary FMA:86140 organ segment FMA:86140 segment of organ FMA:86140 A multicellular structure that is a part of an organ. currently defined in a very broad sense, may be replaced by more specific classes in the future AAO:0011124 BIRNLEX:16 EFO:0000635 FMA:82472 cardinal organ part uberon regional part of organ UBERON:0000064 organ part A multicellular structure that is a part of an organ. cardinal organ part FMA:82472 regional part of organ BIRNLEX:16 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 VHOG:0000393 uberon UBERON:0000065 respiratory tract NCBIBook:NBK10107 Anatomical structure that is part of the respiratory system. In mammals consists of upper and lower tracts The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage. adult stage BTO:0001043 BilaDO:0000004 EFO:0001272 FBdv:00005369 WBls:0000041 XtroDO:0000084 fully formed animal stage juvenile-adult stage uberon UBERON:0000066 fully formed stage https://github.com/obophenotype/uberon/issues/566 The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage. A stage that is part of the embryo stage. embryonic stage part uberon UBERON:0000067 obsolete embryo stage part true A stage that is part of the 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 WBls:0000003 WBls:0000092 WBls:0000102 XAO:1000012 embryonic stage uberon embryogenesis UBERON:0000068 embryo stage A life cycle stage that starts with fertilization and ends with the fully formed embryo. A distinct juvenile stage many animals undergo before metamorphosis into adults. Animals with indirect development such as insects, amphibians, or cnidarians typically have a larval phase of their life cycle. Uberon includes clade-specific subclasses, e.g. nematod larva It is a misunderstanding that the larval form always reflects the group's evolutionary history. It could be the case, but often the larval stage has evolved secondarily, as in insects. In these cases the larval form might differ more from the group's common origin than the adult form BTO:0000915 BTO:0000954 EFO:0001303 FBdv:00005336 MIAA:0000400 OGES:000008 ZFS:0000048 larva stage ammocoete ammocoete stage bipinnaria bipinnaria stage caterpillar caterpillar stage glochidium glochidium stage grub grub stage leptocephalus leptocephalus stage maggot maggot stage metacestode naiad, nymph naiad, nymph stage nauplius nauplius stage nymph nymph stage planula planula stage tornaria trochophore trochophore stage veliger veliger stage wriggler wriggler stage zoea zoea stage uberon larva UBERON:0000069 larval stage A distinct juvenile stage many animals undergo before metamorphosis into adults. Animals with indirect development such as insects, amphibians, or cnidarians typically have a larval phase of their life cycle. It is a misunderstanding that the larval form always reflects the group's evolutionary history. It could be the case, but often the larval stage has evolved secondarily, as in insects. In these cases the larval form might differ more from the group's common origin than the adult form WP ammocoete ammocoete stage bipinnaria bipinnaria stage caterpillar caterpillar stage glochidium glochidium stage grub grub stage leptocephalus leptocephalus stage maggot maggot stage metacestode BTO:0000859 naiad, nymph naiad, nymph stage nauplius nauplius stage nymph nymph stage planula planula stage tornaria NCBITaxon:10219 trochophore trochophore stage veliger veliger stage wriggler wriggler stage zoea zoea stage A life cycle stage of holometabolous insects in which the organism is a pupa and starts with the larval-pupal apolysis and ends with pupal-adult apolysis. The pupal stage is found only in holometabolous insects, those that undergo a complete metamorphosis, going through four life stages; embryo, larva, pupa and imago FBdv:00005349 pupa stage aurelia stage chrysalides stage chrysalis stage uberon UBERON:0000070 pupal stage https://github.com/obophenotype/uberon/issues/562 may be better to model pupal development as including the pre-pupal stage A life cycle stage of holometabolous insects in which the organism is a pupa and starts with the larval-pupal apolysis and ends with pupal-adult apolysis. aurelia stage NCBITaxon:37572 chrysalides stage NCBITaxon:37572 chrysalis stage NCBITaxon:37572 End of the life of an organism. ncit:Death is an outcome XAO:0000437 XtroDO:0000085 uberon death UBERON:0000071 death stage End of the life of an organism. XAO:0000437 ncit:Death is an outcome ncit An section of a respiratory tract. MA:0000434 has subclasses upper and lower, so it corresponds to a segment of the tract, rather than the tract as a whole EMAPA:16737 FMA:45660 MA:0000434 uberon respiratory tract subdivision of respiratory tract UBERON:0000072 proximo-distal subdivision of respiratory tract An section of a respiratory tract. MA:0000434 has subclasses upper and lower, so it corresponds to a segment of the tract, rather than the tract as a whole MA respiratory tract MA:0000434 Any part or collection of parts of the central or peripheral nervous system. Parts may span both CNS and PNS. Melissa Haendel 2009-06-18T09:00:04Z BIRNLEX:1157 NCIT:C13040 UMLS:C1518256 part of nervous system uberon UBERON:0000073 regional part of nervous system Any part or collection of parts of the central or peripheral nervous system. Parts may span both CNS and PNS. BIRNLEX:1157 UMLS:C1518256 ncithesaurus:Nervous_System_Part part of nervous system BIRNLEX:1157 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]. 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? Melissa Haendel 2009-06-18T09:26:37Z glomerulus BTO:0000530 CALOHA:TS-0862 EFO:0003667 EMAPA:28329 EV:0100386 FMA:15624 MA:0001657 MESH:D007678 NCIT:C13250 TAO:0001288 UMLS:C0022663 ZFA:0001288 renal glomeruli uberon Malphigian glomerulus Malpighian glomerulus Malpighian tuft glomerular capillary tuft glomerular tuft glomerulus renis renal corpuscle UBERON:0000074 renal glomerulus Renal:corpuscle.svg http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg FMA MA 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]. MP:0005325 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 UMLS:C0022663 ncithesaurus:Glomerulus renal glomeruli TAO:0001288 Malphigian glomerulus BTO:0000530 Malpighian glomerulus Malpighian tuft glomerular capillary tuft ZFA:0001288 glomerular tuft glomerulus renis renal corpuscle Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism. UBERON:0010322 FMA:85544 NCIT:C34076 UMLS:C1519343 galen:ComplexSkeletalStructure skeletal system subdivision uberon skeletal system part UBERON:0000075 subdivision of skeletal system cjm Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism. UBERONREF:0000003 UMLS:C1519343 ncithesaurus:Skeletal_System_Part skeletal system subdivision FMA:85544 The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm. mer