2015-03-15 release
Cephalopods and comb jellies and sponges, oh my!
This release see the incorporation of 3 invertebrate ontologies into the Uberon composite-metazoan edition. The 3 ontologies are:
- PORO - porifera ontology (sponges)
- CTENO - ctenophore ontology (comb jellies)
- CEPH - cephalopod ontology (note this may later be generalized to MOLO)
Classes from these ontologies appear as children of generalized uberon classes such ‘nervous system’ in composite-metazoa. For more details, see the composite ontologies docs
Classes from these ontologies can therefore be used in making homology assertions - for example between the gastroderm of eumetazoa and the choanocyte chamber of sponges.
This release also incorporates a number of improvements from the Uberon community, see diffs below for details.
Ontology Diff Report
- Composite Metazoa
- Added PORO: Fixes 658
- Added CTENO
- Added CEPH
- Invertebrate and cyclostomes
- relabeled gut epithelium and added gastrodermis as a synonym. BGEE:ANN. Issue 578
- Fixed def of blastopore. BGEE:ANN. Fixes 660
- changed label for oral/aboral sides. Fixes 661
- Referencing BSPO in definition of spatial subdivisions
- NT: Pharyngeal bar
- NT: Mucocartilage tissue (as found in lampreys)
- NT: future piston
- Upper
- NTs: cell cluster, multi organ part structures. From CARO
- organ component layer review: reclassified many layered structures and ensured most has their composition defined
- removed some axioms from bone tissue and added them to mineralized child. Issue 27
- CARO: replacing clusters with multi organ part structures
- NT: external soft tissue zone
- Neuro
- Glands and integumentary system
- alignment with MP: mucuous glands. https://sourceforge.net/p/obo/mammalian-phenotype-requests/2036/
- NT: Weber gland. parts of ciliary body. https://sourceforge.net/p/obo/mammalian-phenotype-requests/2035/
- def-of-suprabasal
- Circulatory and duct systems
- Taxon constraint on retina vasculature (and hence all blood vessels) for Aves. Fixes 657
- various edits, incl elastic layers and blood vessel layers
- fixed confusion between arcuate veins
- Multiple improvements to representation of biliary system. Related to issue 653
- NT: biliary tree epithelium. Fixes 653
- Improved definitions of biliary structures using MP and sources provided by @cindyJax
- Other
- Stages and development
Original Ontology
- IRI: http://purl.obolibrary.org/obo/uberon.owl
- VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2015-02-14/uberon.owl
New Ontology
- IRI: http://purl.obolibrary.org/obo/uberon.owl
- VersionIRI: http://purl.obolibrary.org/obo/uberon/releases/2015-03-15/uberon.owl
Report for classes
Class objects lost from source: 1
Class objects new in target: 21
New Class : pars plicata of ciliary body
- pars plicata of ciliary body database cross reference http://www.snomedbrowser.com/Codes/Details/280859006
- pars plicata of ciliary body SubClassOf organ part
- pars plicata of ciliary body definition Corrugated anterior region of ciliary body where ciliary processes arise { database cross reference=UBERON:cjm }
- pars plicata of ciliary body label pars plicata of ciliary body
- pars plicata of ciliary body has exact synonym ciliary crown { database cross reference=FMA:58431 }
- pars plicata of ciliary body has obo namespace uberon
- pars plicata of ciliary body has exact synonym corona ciliaris { database cross reference=FMA:58431 }
- pars plicata of ciliary body SubClassOf ectoderm-derived structure
- pars plicata of ciliary body database cross reference FMA:58431
- pars plicata of ciliary body SubClassOf part of some ciliary body
- pars plicata of ciliary body id UBERON:0034935
New Class : Weber’s gland
- Weber’s gland has exact synonym gland of Weber
- Weber’s gland definition One of the lingual glands located on the lateral margins of the tongue, at the level of the foliate papillae and in the root of the tongue behind the circumvallate papillae. { database cross reference=http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2667924/ , database cross reference=MGI:anna }
- Weber’s gland label Weber’s gland
- Weber’s gland has obo namespace uberon
- Weber’s gland taxon notes in humans, the ducts of posterior superficial lingual glands open into the crypts of lingual tonsils; mucous supplied by these glands may help to cleanse the crypts and aid in deglutition
- Weber’s gland SubClassOf minor salivary gland
- Weber’s gland id UBERON:0034934
- Weber’s gland has exact synonym posterior superficial lingual gland { database cross reference=MGI:anna }
New Class : pharyngeal bar
- pharyngeal bar has related synonym gill bar
- pharyngeal bar taxon notes Haikouella possessed a small number of pharyngeal bars that may have been composed of mucocartilage, as in modern lampreys (Holland and Chen, 2001). the pharyngeal bars of Haikouella were probably derived from neural crest, as were the sensory components of the cranial nerves that innervated its pharyngeal muscles[http://icb.oxfordjournals.org/content/42/4/743.full]
- pharyngeal bar label pharyngeal bar
- pharyngeal bar has related synonym branchial bar
- pharyngeal bar id UBERON:0034937
- pharyngeal bar present in taxon http://purl.obolibrary.org/obo/NCBITaxon_117569
- pharyngeal bar SubClassOf multi-tissue structure
- pharyngeal bar SubClassOf part of some chordate pharynx
- pharyngeal bar present in taxon http://purl.obolibrary.org/obo/NCBITaxon_7737
- pharyngeal bar has obo namespace uberon
- pharyngeal bar SubClassOf endoderm-derived structure
New Class : pars plana of ciliary body
- pars plana of ciliary body definition Flattened posterior region of ciliary body { database cross reference=UBERON:cjm }
- pars plana of ciliary body has exact synonym ciliary ring { database cross reference=FMA:58480 }
- pars plana of ciliary body has exact synonym orbiculus ciliaris { database cross reference=FMA:58480 }
- pars plana of ciliary body database cross reference http://www.snomedbrowser.com/Codes/Details/368830002
- pars plana of ciliary body has obo namespace uberon
- pars plana of ciliary body id UBERON:0034936
- pars plana of ciliary body label pars plana of ciliary body
- pars plana of ciliary body SubClassOf organ part
- pars plana of ciliary body SubClassOf ectoderm-derived structure
- pars plana of ciliary body database cross reference FMA:58480
- pars plana of ciliary body SubClassOf part of some ciliary body
New Class : perforant path
- perforant path SubClassOf part of some forebrain ipsilateral fiber tracts
- perforant path SubClassOf extends fibers into some layer of dentate gyrus
- perforant path database cross reference MESH:A08.612.600
- perforant path has related synonym perforant path { database cross reference=MESH:A08.612.600 }
- perforant path has related synonym perf { database cross reference=DHBA:12080 , has synonym type=abbreviation }
- perforant path database cross reference http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=2686
- perforant path has related synonym perforant pathway { database cross reference=MESH:A08.612.600 }
- perforant path database cross reference http://ncicb.nci.nih.gov/xml/owl/EVS/Perforant_Pathway
- perforant path database cross reference http://linkedlifedata.com/resource/umls/id/C0524810
- perforant path database cross reference DHBA:12080
- perforant path database cross reference MBA:713
- perforant path has related synonym perforating fasciculus { database cross reference=MESH:A08.612.600 }
- perforant path SubClassOf part of some white matter of telencephalon
- perforant path definition A pathway of fibers originating in the lateral part of the entorhinal area, perforating the subiculum of the hippocampus, and running into the stratum moleculare of the hippocampus, where these fibers synapse with others that go to the dentate gyrus. (Dorland, 28th ed) { database cross reference=MESH:A08.612.600 }
- perforant path EquivalentTo axon tract and extends fibers into some layer of dentate gyrus and extends fibers into some entorhinal cortex and extends fibers into some hippocampal field
- perforant path has related synonym tractus perforans { database cross reference=http://en.wikipedia.org/wiki/Perforant_path , has synonym type=latin term }
- perforant path has obo namespace uberon
- perforant path id UBERON:0034931
- perforant path SubClassOf tract of brain
- perforant path database cross reference HBA:265505250
- perforant path database cross reference http://en.wikipedia.org/wiki/Perforant_path
- perforant path SubClassOf extends fibers into some hippocampal field
- perforant path label perforant path
- perforant path SubClassOf extends fibers into some entorhinal cortex
New Class : auricular feather
- auricular feather EquivalentTo feather and surrounds some external ear
- auricular feather SubClassOf surrounds some external ear
- auricular feather id UBERON:0034930
- auricular feather SubClassOf feather
- auricular feather label auricular feather
- auricular feather has obo namespace uberon
- auricular feather function notes the auricular feathers play a role in hearing by reflecting and funneling sound into the external acoustic meatus
New Class : layer of smooth muscle tissue
- layer of smooth muscle tissue has obo namespace uberon
- layer of smooth muscle tissue id UBERON:0034933
- layer of smooth muscle tissue definition Any organ component layer that consists of smooth muscle tissue. { database cross reference=UBERON:cjm }
- layer of smooth muscle tissue EquivalentTo organ component layer and composed primarily of some smooth muscle tissue
- layer of smooth muscle tissue SubClassOf composed primarily of some smooth muscle tissue
- layer of smooth muscle tissue label layer of smooth muscle tissue
- layer of smooth muscle tissue SubClassOf layer of muscle tissue
New Class : epithelium of biliary system
- epithelium of biliary system SubClassOf epithelium
- epithelium of biliary system definition The epithelial layer covering the biliary system. This includes the epithelium of the gallbladder (when present) as well as the intrahepatic and extrahepatic bile ducts. { database cross reference=BTO:0001513 , database cross reference=MGI:cs , database cross reference=UBERON:cjm }
- epithelium of biliary system has exact synonym biliary system epithelium { database cross reference=UBERON:cjm }
- epithelium of biliary system id UBERON:0034932
- epithelium of biliary system has obo namespace uberon
- epithelium of biliary system database cross reference BTO:0001513
- epithelium of biliary system has related synonym biliary tract epithelium { database cross reference=UBERON:cjm }
- epithelium of biliary system label epithelium of biliary system
- epithelium of biliary system SubClassOf part of some biliary system
- epithelium of biliary system has related synonym biliary epithelium { database cross reference=BTO:0001513 }
- epithelium of biliary system EquivalentTo epithelium and part of some biliary system
New Class : future piston
- future piston has related synonym future lamprey tongue { database cross reference=UBERON:0010896 }
- future piston has exact synonym future lingual cartilage { database cross reference=UBERON:0010896 }
- future piston SubClassOf cartilage element
- future piston label future piston
- future piston development notes the mucocartilage dedifferentiaes to mesenchyme creating a blastema which differentiates to chondroblasts secreting proteoglycans resulting in the piston cartilage
- future piston in subset cyclostome subset
- future piston has related synonym future piston { database cross reference=UBERON:0010896 }
- future piston has related synonym piston mucocartilage
- future piston id UBERON:0034939
- future piston has obo namespace uberon
- future piston SubClassOf composed primarily of some mucocartilage tissue
- future piston SubClassOf part of some head
New Class : mucocartilage tissue
- mucocartilage tissue definition A temporary avascular cartilage found in the heads of ammocoete larvae and surrounded by perichondrium. Contains a few fibroblasts scattered throughout ECM containing elastic-like microfibrils. { database cross reference=ISBN:0124166857 }
- mucocartilage tissue SubClassOf part of some ammocoete
- mucocartilage tissue id UBERON:0034938
- mucocartilage tissue has exact synonym mucocartilaginous tissue
- mucocartilage tissue SubClassOf cartilage tissue
- mucocartilage tissue label mucocartilage tissue
- mucocartilage tissue has obo namespace uberon
- mucocartilage tissue has exact synonym mucocartilage
New Class : external soft tissue zone
- external soft tissue zone SubClassOf has part some vasculature
- external soft tissue zone SubClassOf part of some organism subdivision
- external soft tissue zone SubClassOf has part some nerve
- external soft tissue zone SubClassOf has part some musculature
- external soft tissue zone label external soft tissue zone
- external soft tissue zone id UBERON:0034929
- external soft tissue zone SubClassOf has part some zone of skin
- external soft tissue zone has obo namespace uberon
- external soft tissue zone SubClassOf multicellular anatomical structure
- external soft tissue zone definition A region or zone on the surface of an organism that encompasses skin and any adnexa, down through muscles and bounded by underlying skeletal support structures. { database cross reference=UBERON:cjm }
New Class : arcuate artery of foot
- arcuate artery of foot id UBERON:0034927
- arcuate artery of foot SubClassOf pes blood vessel
- arcuate artery of foot database cross reference FMA:44594
- arcuate artery of foot SubClassOf branching part of some anterior tibial artery
- arcuate artery of foot label arcuate artery of foot
- arcuate artery of foot SubClassOf artery
- arcuate artery of foot has obo namespace uberon
- arcuate artery of foot database cross reference http://en.wikipedia.org/wiki/Arcuate_artery_of_the_foot
- arcuate artery of foot database cross reference http://www.snomedbrowser.com/Codes/Details/244331005
- arcuate artery of foot SubClassOf part of some pes
New Class : dorsal surface of penis
- dorsal surface of penis SubClassOf part of some penis
- dorsal surface of penis has exact synonym dorsum of penis { database cross reference=FMA:19623 }
- dorsal surface of penis has exact synonym dorsum penis { database cross reference=FMA:TA }
- dorsal surface of penis label dorsal surface of penis
- dorsal surface of penis database cross reference FMA:19623
- dorsal surface of penis EquivalentTo anatomical surface and in dorsal side of some penis
- dorsal surface of penis has obo namespace uberon
- dorsal surface of penis SubClassOf anatomical surface
- dorsal surface of penis SubClassOf in dorsal side of some penis
- dorsal surface of penis id UBERON:0034928
New Class : multi organ part structure
- multi organ part structure definition An multicellular anatomical structure that has subparts of multiple organs as a part. { database cross reference=CARO:0020001 }
- multi organ part structure SubClassOf composed primarily of some organ part
- multi organ part structure database cross reference CARO:0020001
- multi organ part structure has obo namespace uberon
- multi organ part structure label multi organ part structure
- multi organ part structure has related synonym anatomical cluster { database cross reference=CARO:0020001 }
- multi organ part structure id UBERON:0034921
- multi organ part structure SubClassOf multicellular anatomical structure
New Class : cell cluster
- cell cluster has obo namespace uberon
- cell cluster SubClassOf surrounded by some anatomical boundary
- cell cluster id UBERON:0034922
- cell cluster SubClassOf multicellular anatomical structure
- cell cluster definition A cluster of cells, largely surrounded by a morphological boundary. { database cross reference=CARO:0020002 }
- cell cluster database cross reference FMA:62807
- cell cluster database cross reference CARO:0020002
- cell cluster label cell cluster
New Class : infant stage
- infant stage has obo namespace uberon
- infant stage SubClassOf part of some nursing stage
- infant stage SubClassOf immediately preceded by some neonate stage
- infant stage SubClassOf life cycle stage
- infant stage definition Nursing stage that follows the neonate stage in mammals and ends at weaning. { database cross reference=https://github.com/obophenotype/uberon/issues/644 , database cross reference=Bgee:AN }
- infant stage id UBERON:0034920
- infant stage label infant stage
New Class : anatomical collection
- anatomical collection SubClassOf has member some anatomical structure
- anatomical collection has obo namespace uberon
- anatomical collection definition A collection of anatomical structures that are alike in terms of their morphology or developmental origin. { database cross reference=UBERON:cjm }
- anatomical collection SubClassOf material anatomical entity
- anatomical collection editor note resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected
- anatomical collection id UBERON:0034925
- anatomical collection label anatomical collection
New Class : anatomical row
- anatomical row definition An anatomical collection that is arranged in a line. { database cross reference=UBERON:cjm }
- anatomical row id UBERON:0034926
- anatomical row editor note resolve if this should be a subclass of or merged with aligned anatomical group.
- anatomical row has obo namespace uberon
- anatomical row SubClassOf anatomical collection
- anatomical row label anatomical row
New Class : disconnected anatomical group
- disconnected anatomical group SubClassOf ObjectMinCardinality( has component anatomical structure )
- disconnected anatomical group SubClassOf composed primarily of some anatomical structure
- disconnected anatomical group SubClassOf material anatomical entity
- disconnected anatomical group label disconnected anatomical group
- disconnected anatomical group definition Material anatomical entity consisting of multiple anatomical structures that are not connected to each other. { database cross reference=CARO:0020000 }
- disconnected anatomical group database cross reference CARO:0020000
- disconnected anatomical group has obo namespace uberon
- disconnected anatomical group id UBERON:0034923
New Class : aligned anatomical group
- aligned anatomical group id UBERON:0034924
- aligned anatomical group label aligned anatomical group
- aligned anatomical group database cross reference CARO:0002002
- aligned anatomical group definition An anatomical group whose members are arranged in a line. { database cross reference=CARO:0002002 }
- aligned anatomical group comment Examples include the rows of sense organs commonly found in the cuticles of insects.
- aligned anatomical group SubClassOf disconnected anatomical group
- aligned anatomical group has obo namespace uberon
New Class : juvenile stage
- juvenile stage definition The stage of being no more dependent of the nest and/or from caregivers for subsistence while having not reach sexual maturity. { database cross reference=https://github.com/obophenotype/uberon/issues/645 , database cross reference=Bgee:AN }
- juvenile stage id UBERON:0034919
- juvenile stage has obo namespace uberon
- juvenile stage label juvenile stage
- juvenile stage SubClassOf part of some sexually immature stage
- juvenile stage SubClassOf life cycle stage
Changed Class objects: 727
Changes for: mycetome
- Deleted
- Added
- + mycetome SubClassOf cell cluster organ
Changes for: cephalodorsosubpharyngeus
- Deleted
- - cephalodorsosubpharyngeus SubClassOf innervated by some vagus nerve { source=cjm }
Changes for: buttock
- Deleted
- - buttock SubClassOf organism subdivision
- - buttock definition The buttocks are rounded portions of the anatomy located on the posterior of the pelvic region of apes and humans, including many other bipeds or quadrupeds. { database cross reference=http://en.wikipedia.org/wiki/Buttocks }
- Added
- + buttock SubClassOf external soft tissue zone
- + buttock SubClassOf has part some gluteal muscle
- + buttock definition A zone of soft tissue located on the posterior of the lateral side of the pelvic region corresponding to the gluteal muscles. { database cross reference=http://en.wikipedia.org/wiki/Buttocks , database cross reference=UBERON:cjm }
Changes for: cerebral cortex neuropil
- Deleted
Changes for: aproctal bone of priapium
- Deleted
- - aproctal bone of priapium definition he ventral element in the priapium of the Phallostethidae on which articulate the ctenactinia (q.v.). Also called aproctal or pelvic bone { database cross reference=http://en.academic.ru/dic.nsf/en_ichthyology/1032/axial }
- Added
- + aproctal bone of priapium definition The ventral element in the priapium of the Phallostethidae on which articulate the ctenactinia (q.v.). Also called aproctal or pelvic bone { database cross reference=http://en.academic.ru/dic.nsf/en_ichthyology/1032/axial }
Changes for: velar skeleton
- Deleted
- - velar skeleton SubClassOf endoderm-derived structure
- - velar skeleton SubClassOf structure with developmental contribution from neural crest
Changes for: dilatator laryngis
- Deleted
- - dilatator laryngis SubClassOf innervated by some vagus nerve { source=cjm }
Changes for: zeugopodial skeleton
- Deleted
- - zeugopodial skeleton SubClassOf mesoderm-derived structure
Changes for: paired limb/fin skeleton
- Deleted
- - paired limb/fin skeleton SubClassOf mesoderm-derived structure
Changes for: stylopodial skeleton
- Deleted
- - stylopodial skeleton SubClassOf mesoderm-derived structure
Changes for: dorsal fin distal radial element
- Deleted
- - dorsal fin distal radial element EquivalentTo dorsal fin radial element and part of some dorsal fin pterygiophore and connected to some lepidotrichium
- - dorsal fin distal radial element SubClassOf connected to some lepidotrichium
- - dorsal fin distal radial element SubClassOf distally connected to some dorsal fin lepidotrichium
Changes for: paired fin radial skeleton
- Deleted
- - paired fin radial skeleton SubClassOf mesoderm-derived structure
Changes for: temporal cortex cingulum
- Deleted
Changes for: cingulate cortex cingulum
- Deleted
Changes for: pleural plate of carapace
- Deleted
- - pleural plate of carapace SubClassOf lateral structure
Changes for: hypoplastron
- Deleted
- - hypoplastron SubClassOf lateral structure
Changes for: xiphiplastron
- Deleted
- - xiphiplastron SubClassOf lateral structure
Changes for: pontocerebellar tract
- Deleted
Changes for: enameloid
- Added
- + enameloid SubClassOf mineralized skeletal tissue
Changes for: orbital part of frontal bone
- Deleted
- - orbital part of frontal bone SubClassOf lateral structure
Changes for: epiplastron
- Deleted
- - epiplastron SubClassOf lateral structure
Changes for: hippocampus cortex cingulum
- Deleted
Changes for: corticopontine fibers
- Deleted
Changes for: corticobulbar tract
- Deleted
Changes for: cerebral nerve fasciculus
- Deleted
Changes for: entorhinal cortex layer 4
- Deleted
- Added
- + entorhinal cortex layer 4 SubClassOf composed primarily of some nerve fiber
Changes for: dorsal cochlear nucleus pyramidal cell layer
- Deleted
Changes for: entorhinal cortex layer 3
- Deleted
Changes for: entorhinal cortex layer 5
- Deleted
Changes for: entorhinal cortex layer 6
- Deleted
Changes for: superior colliculus stratum zonale
- Deleted
- Added
Changes for: primary motor cortex layer 6
- Deleted
- Added
- + primary motor cortex layer 6 SubClassOf layer of neocortex
Changes for: primary motor cortex layer 5
- Deleted
- Added
- + primary motor cortex layer 5 SubClassOf layer of neocortex
Changes for: olfactory cortex layer 2
- Deleted
Changes for: olfactory cortex layer 1
- Deleted
Changes for: piriform cortex layer 2a
- Deleted
Changes for: piriform cortex layer 2b
- Deleted
Changes for: dentate gyrus granule cell layer outer blade
- Deleted
Changes for: dentate gyrus granule cell layer inner blade
- Deleted
Changes for: dentate gyrus molecular layer inner
- Deleted
Changes for: dentate gyrus molecular layer middle
- Deleted
Changes for: entorhinal cortex layer 1
- Deleted
- Added
- + entorhinal cortex layer 1 SubClassOf composed primarily of some nerve fiber
Changes for: entorhinal cortex layer 2
- Deleted
Changes for: short ciliary nerve
- Deleted
- - short ciliary nerve SubClassOf neural crest-derived structure
Changes for: nervous system cell part layer
- Added
- + nervous system cell part layer editor note this is currently used to group some cellular layers that may not strictly conform to the CARO definition of cell-part layer. Consider genericisizing and introducing subtypes for cellular layer, fibrous layer and cell soma layer
Changes for: collection of feathers
- Deleted
- - collection of feathers EquivalentTo anatomical cluster and has member some feather
- - collection of feathers SubClassOf anatomical cluster
- Added
- + collection of feathers EquivalentTo anatomical collection and has member some feather
- + collection of feathers SubClassOf anatomical collection
Changes for: acinus of parotid gland
- Added
- + acinus of parotid gland SubClassOf serous acinus
Changes for: anterior uvea
- Deleted
- - anterior uvea SubClassOf neural crest-derived structure
- Added
- + anterior uvea SubClassOf ectoderm-derived structure
Changes for: palatoquadrate arch
- Deleted
- - palatoquadrate arch SubClassOf endoderm-derived structure
- - palatoquadrate arch SubClassOf neural crest-derived structure
Changes for: left pelvic girdle region
- Added
- + left pelvic girdle region SubClassOf lateral structure
Changes for: right pelvic girdle region
- Added
- + right pelvic girdle region SubClassOf lateral structure
Changes for: angular bone
- Deleted
- - angular bone SubClassOf lateral structure
Changes for: articular cartilage element
- Added
- + articular cartilage element definition Cartilage of the lower jaw that give rise to a portion of the anguloarticular compound bone. { database cross reference=ZFA:0001644 }
Changes for: mammary lobe
- Deleted
- - mammary lobe SubClassOf anatomical cluster
- Added
- + mammary lobe SubClassOf anatomical lobe
Changes for: hindbrain commissure
- Deleted
Changes for: margin of eyelid
- Deleted
- - margin of eyelid SubClassOf anatomical cluster
- Added
- + margin of eyelid SubClassOf multi organ part structure
Changes for: ventricular musculature
- Deleted
- - ventricular musculature SubClassOf mesoderm-derived structure
Changes for: hindbrain marginal layer
- Deleted
Changes for: cranial neuron projection bundle
- Deleted
- - cranial neuron projection bundle SubClassOf lateral structure
Changes for: upper urinary tract
- Deleted
- - upper urinary tract SubClassOf lateral structure
Changes for: facial skeleton
- Deleted
- - facial skeleton SubClassOf neural crest-derived structure
Changes for: pretectal region
- Deleted
- - pretectal region comment AO notes: part of diencephalon in ZFA - modify to adjacent here, supported by pub. Note there is some inconsistency in resources between the region vs nuclei - sometimes they are treated equivalent, sometimes separate (e.g. MP)
- Added
- + pretectal region external ontology notes part of diencephalon in ZFA - modify to adjacent here, supported by pub. Note there is some inconsistency in resources between the region vs nuclei - sometimes they are treated equivalent, sometimes separate (e.g. MP) { external ontology=ZFA }
Changes for: bile
- Deleted
- - bile definition A bodily fluid that is produced by the liver and aids the process of digestion of lipids in the small intestine[WP, modified]. { database cross reference=http://en.wikipedia.org/wiki/Bile }
- Added
- + bile SubClassOf bodily fluid
- + bile definition vital aqueous secretion of the liver that is formed by hepatocytes and modified down stream by absorptive and secretory properties of the bile duct epithelium. { database cross reference=http://dx.doi.org/10.1002/cphy.c120027 , database cross reference=http://en.wikipedia.org/wiki/Bile }
- + bile function notes aids the process of digestion of lipids in the small intestine
- + bile function notes bile salts function to emulsify dietary fats and facilitate their intestinal absorption
- + bile function notes elimination of cholesterol
- + bile function notes major excretory route for potentially harmful exogenous lipophilic substances
- + bile function notes many hormones and pheromones are excreted in bile, and contribute to growth and development of the intestine in some species and provide attractants for the weaning of non-human vertebrates
- + bile function notes protects the organism from enteric infections by excreting immune globulin A (IgA), inflammatory cytokines, and stimulating the innate immune system in the intestine
Changes for: periarterial lymphatic sheath
- Deleted
- - periarterial lymphatic sheath SubClassOf mesoderm-derived structure
- Added
- + periarterial lymphatic sheath SubClassOf abdomen element
- + periarterial lymphatic sheath SubClassOf digestive system element
- + periarterial lymphatic sheath SubClassOf hemopoietic organ
Changes for: post-cranial axial skeletal system
- Deleted
Changes for: type 1 adrenal tissue
- Deleted
- - type 1 adrenal tissue definition Adrenal tissue dispersed in clusters, found in periphery and center of adranal gland in turtles (Yadav, 2008). { database cross reference=PHENOSCAPE:nizar }
- Added
- + type 1 adrenal tissue definition Adrenal tissue dispersed in clusters, found in periphery and center of adrenal gland in turtles (Yadav, 2008). { database cross reference=PHENOSCAPE:nizar }
Changes for: skeletal musculature
- Deleted
- - skeletal musculature SubClassOf anatomical group
- Added
- + skeletal musculature SubClassOf anatomical structure
Changes for: central nervous system cell part cluster
- Deleted
Changes for: pulmonary part of lymphatic system
- Deleted
- - pulmonary part of lymphatic system EquivalentTo anatomical cluster and part of some lung and part of some lymphatic part of lymphoid system
- - pulmonary part of lymphatic system SubClassOf anatomical cluster
- - pulmonary part of lymphatic system SubClassOf endoderm-derived structure
- Added
- + pulmonary part of lymphatic system EquivalentTo organ system subdivision and part of some lung and part of some lymphatic part of lymphoid system
- + pulmonary part of lymphatic system SubClassOf organ system subdivision
Changes for: pulmonary lymphatic vessel
- Deleted
- Added
- + pulmonary lymphatic vessel SubClassOf endoderm-derived structure
Changes for: renin-angiotensin system
- Deleted
- - renin-angiotensin system SubClassOf anatomical cluster
- Added
- + renin-angiotensin system SubClassOf organ system subdivision
Changes for: accessory articulation
- Deleted
- - accessory articulation SubClassOf mesoderm-derived structure
Changes for: subserosa
- Added
- + subserosa EquivalentTo organ component layer and adjacent to some serous membrane and composed primarily of some areolar connective tissue
- + subserosa SubClassOf adjacent to some serous membrane
- + subserosa SubClassOf composed primarily of some areolar connective tissue
- + subserosa comment Contains nerves, blood vessels, lymphatics and lymph nodes
Changes for: sensory ganglion
- Deleted
- - sensory ganglion editor note This class was created automatically from a combination of ontologies
- - sensory ganglion has exact synonym ganglion sensorium
- Added
- + sensory ganglion EquivalentTo ganglion and extends fibers into some sensory nerve
- + sensory ganglion SubClassOf extends fibers into some sensory nerve
- + sensory ganglion has exact synonym ganglion sensorium { has synonym type=latin term }
Changes for: circular muscle layer of muscular coat
- Deleted
- Added
Changes for: longitudinal muscle layer of muscular coat
- Deleted
- Added
Changes for: holocrine gland
- Deleted
- - holocrine gland definition A gland whose discharged secretion contains entire secreting cells. { database cross reference=http://en.wikipedia.org/wiki/Holocrine , database cross reference=http://en.wikipedia.org/wiki/Holocrine_glands , database cross reference=BTO:0002325 }
- Added
- + holocrine gland definition any exocrine gland whose secretion consists of its own disintegrated secretory cells along with its secretory product; holocrine secretions are produced in the cytoplasm of the cell and released by the rupture of the plasma membrane, which destroys the cell and results in the secretion of the product into the lumen. { database cross reference=MP:0013543 }
Changes for: ethmoid region
- Deleted
- - ethmoid region SubClassOf anatomical cluster
- Added
- + ethmoid region SubClassOf multi organ part structure
Changes for: dentate gyrus of hippocampal formation
- Deleted
- - dentate gyrus of hippocampal formation SubClassOf ectoderm-derived structure
- - dentate gyrus of hippocampal formation SubClassOf organ part
- Added
Changes for: mastoid process of temporal bone
- Deleted
Changes for: cartilaginous external acoustic tube
- Deleted
- Added
- + cartilaginous external acoustic tube SubClassOf composed primarily of some cartilage tissue
Changes for: lobule of pinna
- Deleted
- - lobule of pinna SubClassOf subdivision of head
- Added
- + lobule of pinna SubClassOf external soft tissue zone
Changes for: internal ear
- Deleted
- - internal ear SubClassOf anatomical cluster
- Added
- + internal ear SubClassOf multi organ part structure
Changes for: cochlea
- Deleted
- - cochlea SubClassOf anatomical cluster
- Added
- + cochlea SubClassOf multi organ part structure
Changes for: white matter of telencephalon
- Deleted
Changes for: parotid gland
- Added
- + parotid gland SubClassOf serous gland
Changes for: bony labyrinth
- Deleted
- - bony labyrinth SubClassOf anatomical cluster
- Added
- + bony labyrinth SubClassOf multi organ part structure
Changes for: superior laryngeal nerve
- Deleted
Changes for: cranial nerve
- Deleted
Changes for: layer of retina
- Deleted
- - layer of retina SubClassOf ectoderm-derived structure
- - layer of retina SubClassOf organ component layer
- Added
- + layer of retina SubClassOf nervous system cell part layer
Changes for: pigmented layer of retina
- Added
- + pigmented layer of retina SubClassOf lamina
Changes for: gray matter of telencephalon
- Deleted
Changes for: inner limiting layer of retina
- Deleted
Changes for: nerve fiber layer of retina
- Deleted
- - nerve fiber layer of retina SubClassOf structure with developmental contribution from neural crest
- - nerve fiber layer of retina definition Fiber layer adjacent the retinal ganglion cell layer which is comprised of their axons as they traverse to the optic nerve[ZFA]. The retinal nerve fiber layer (nerve fiber layer, stratum opticum, RNFL) is formed by the expansion of the fibers of the optic nerve; it is thickest near the porus opticus, gradually diminishing toward the ora serrata. As the nerve fibers pass through the lamina cribrosa sclerae they lose their medullary sheaths and are continued onward through the choroid and retina as simple axis-cylinders. When they reach the internal surface of the retina they radiate from their point of entrance over this surface grouped in bundles, and in many places arranged in plexuses. Most of the fibers are centripetal, and are the direct continuations of the axis-cylinder processes of the cells of the ganglionic layer, but a few of them are centrifugal and ramify in the inner plexiform and inner nuclear layers, where they end in enlarged extremities. { database cross reference=http://en.wikipedia.org/wiki/Nervous_system_fiber_layer , database cross reference=ZFA:0001619 }
- - nerve fiber layer of retina editor note This class was created automatically from a combination of ontologies
- Added
- + nerve fiber layer of retina definition layer of the retina formed by expansion of the fibers of the optic nerve { database cross reference=ISBN:0-914294-08-3 , database cross reference=MGI:smb }
Changes for: proximal convoluted tubule brush border
- Deleted
- - proximal convoluted tubule brush border SubClassOf mesoderm-derived structure
- - proximal convoluted tubule brush border definition A brush border layer that is part of a proximal convoluted tubule. { database cross reference=OBOL:automatic }
- Added
- + proximal convoluted tubule brush border definition A brush border layer that is part of a proximal tubule in the kidney. { database cross reference=Function , database cross reference=UBERON:cjm }
- + proximal convoluted tubule brush border function notes the microvilli in this layer can act as mechanosensors. They sense the fluid flow in the tubule lumen and convert this information via biochemical responses into reabsorption
- + proximal convoluted tubule brush border has broad synonym kidney brush border layer
- + proximal convoluted tubule brush border has broad synonym proximal tubule brush border layer
Changes for: intestinal brush border layer
- Deleted
- - intestinal brush border has exact synonym brush border microvillus later of intestine
- - intestinal brush border label intestinal brush border
- Added
- + intestinal brush border layer comment Consider merging into UBERON:0012425
- + intestinal brush border layer has exact synonym brush border microvillus layer of intestine
- + intestinal brush border layer has exact synonym intestinal brush border
- + intestinal brush border layer label intestinal brush border layer
Changes for: short microvillus layer
- Added
- + short microvillus layer definition A layer of microvilli covering lymphocytes. { database cross reference=UBERON:cjm }
- + short microvillus layer editor note consider ceding to GO
Changes for: striated border microvillus layer
- Added
- + striated border microvillus layer SubClassOf part of some intestine
- + striated border microvillus layer definition A microvillus layer that is striated and found in the intestine. { database cross reference=http://medical-dictionary.thefreedictionary.com/striated+border , database cross reference=UBERON:cjm }
Changes for: layer of microvilli
- Added
- + layer of microvilli function notes a wide variety of physiological and cellular functions including absorption, secretion, cellular adhesion, and mechanotransduction
- + layer of microvilli function notes increases the surface area of a cell lining whilst minimizing increase in volume
Changes for: taenia coli
- Deleted
- - taenia coli SubClassOf large intestine smooth muscle
- Added
- + taenia coli SubClassOf composed primarily of some smooth muscle tissue
- + taenia coli SubClassOf layer of smooth muscle tissue
Changes for: midbody melanophore spot
- Deleted
- - midbody melanophore spot definition distinct colored area on the midbody region of an organism, similar in shapre to a spot, i.e. circular. { database cross reference=PHENOSCAPE:alex }
- Added
- + midbody melanophore spot definition distinct colored area on the midbody region of an organism, similar in shape to a spot, i.e. circular. { database cross reference=PHENOSCAPE:alex }
Changes for: prehallux skeleton
- Deleted
- - prehallux skeleton SubClassOf mesoderm-derived structure
Changes for: palatine process of premaxilla
- Deleted
- - palatine process of premaxilla comment Taxon notes: A posterior extension of the premaxilla that lies along the palatine and fuses to some extent with it. In the Passeres it may be fused, unfused, free or a lateral flange. Evolved multiple times in Passerines [http://www.biodiversitylibrary.org/part/29066]
- Added
- + palatine process of premaxilla taxon notes A posterior extension of the premaxilla that lies along the palatine and fuses to some extent with it. In the Passeres it may be fused, unfused, free or a lateral flange. Evolved multiple times in Passerines [http://www.biodiversitylibrary.org/part/29066]
Changes for: caudal melanophore spot
- Deleted
- - caudal melanophore spot definition distinct colored area on the caudal region of an organism, similar in shapre to a spot, i.e. circular. { database cross reference=PHENOSCAPE:Nizar }
- Added
- + caudal melanophore spot definition distinct colored area on the caudal region of an organism, similar in shape to a spot, i.e. circular. { database cross reference=PHENOSCAPE:Nizar }
Changes for: cloacal villus
- Deleted
- - cloacal villus SubClassOf mesoderm-derived structure
- - cloacal villus SubClassOf organ component layer
- Added
- + cloacal villus EquivalentTo layer of microvilli and part of some cloaca
- + cloacal villus SubClassOf layer of microvilli
Changes for: tunica fibrosa of eyeball
- Added
- + tunica fibrosa of eyeball SubClassOf has part some cornea
- + tunica fibrosa of eyeball SubClassOf has part some sclera
- + tunica fibrosa of eyeball SubClassOf structure with developmental contribution from neural crest
- + tunica fibrosa of eyeball database cross reference http://en.wikipedia.org/wiki/Fibrous_tunic_of_eyeball
- + tunica fibrosa of eyeball definition The sclera and cornea form the fibrous tunic of the bulb of the eye; the sclera is opaque, and constitutes the posterior five-sixths of the tunic; the cornea is transparent, and forms the anterior sixth. { database cross reference=http://en.wikipedia.org/wiki/Fibrous_tunic_of_eyeball }
- + tunica fibrosa of eyeball has related synonym corneosclera { database cross reference=http://en.wikipedia.org/wiki/Fibrous_tunic_of_eyeball }
- + tunica fibrosa of eyeball has related synonym fibrous tunic { database cross reference=http://en.wikipedia.org/wiki/Fibrous_tunic_of_eyeball }
Changes for: row of scales
- Deleted
- - row of scales SubClassOf anatomical cluster
- - row of scales SubClassOf composed primarily of some scale
- Added
- + row of scales EquivalentTo anatomical row and has member some scale
- + row of scales SubClassOf anatomical row
- + row of scales SubClassOf has member some scale
Changes for: Merkel nerve ending
- Deleted
- - Merkel nerve ending SubClassOf cell part
- - Merkel nerve ending SubClassOf neural crest-derived structure
Changes for: nerve ending
- Deleted
- - nerve ending SubClassOf anatomical cluster
- Added
- + nerve ending SubClassOf multi cell part structure
Changes for: dentine
- Deleted
- - dentine SubClassOf develops from some pre-dentine
- - dentine comment Dentine is found in the fossil record as early as the late Cambrian, in fish, where it may have had a role in electrochemical sensing of the environment as well as assisting in defense[WP]. Editors note: note the asserted dual is_a parentage, as dentine is both skeletal tissue and a substance
- Added
- + dentine SubClassOf mineralized skeletal tissue
- + dentine SubClassOf transformation of some pre-dentine
- + dentine comment .
- + dentine taxon notes Dentine is found in the fossil record as early as the late Cambrian, in fish, where it may have had a role in electrochemical sensing of the environment as well as assisting in defense[WP]
Changes for: lacrimal apparatus
- Deleted
- - lacrimal apparatus SubClassOf anatomical cluster
- Added
- + lacrimal apparatus SubClassOf anatomical system
Changes for: enamel
- Added
- + enamel SubClassOf mineralized skeletal tissue
Changes for: middle ear
- Deleted
- - middle ear SubClassOf anatomical cluster
- Added
- + middle ear SubClassOf multi organ part structure
Changes for: arytenoid cartilage
- Deleted
- - arytenoid cartilage SubClassOf lateral structure
Changes for: ciliary body
- Deleted
- - ciliary body SubClassOf neural crest-derived structure
- Added
- + ciliary body SubClassOf ectoderm-derived structure
- + ciliary body SubClassOf has part some ciliary muscle
- + ciliary body SubClassOf has part some ciliary processes
Changes for: ciliary epithelium
- Deleted
- - ciliary epithelium SubClassOf neural crest-derived structure
Changes for: iris stroma
- Deleted
- - iris stroma SubClassOf neural crest-derived structure
- Added
- + iris stroma SubClassOf ectoderm-derived structure
Changes for: iris
- Deleted
- - iris SubClassOf neural crest-derived structure
- Added
- + iris SubClassOf ectoderm-derived structure
Changes for: uvea
- Deleted
- - uvea SubClassOf vasculature of eye
- Added
- + uvea SubClassOf ectoderm-derived structure
- + uvea SubClassOf has part some ciliary body
- + uvea SubClassOf has part some iris
- + uvea SubClassOf has part some optic choroid
- + uvea SubClassOf organ component layer
- + uvea SubClassOf structure with developmental contribution from neural crest
Changes for: jaw skeleton
- Deleted
- - jaw skeleton SubClassOf neural crest-derived structure
Changes for: pudendal nerve
- Deleted
- - pudendal nerve SubClassOf lateral structure
Changes for: blood vessel internal elastic membrane
- Deleted
- - internal elastic membrane SubClassOf acellular anatomical structure
- - internal elastic membrane label internal elastic membrane
- Added
- + blood vessel internal elastic membrane external definition A stretchable connective tissue membrane that is the outermost component of the tunica intima, delineating the border between the tunica media and the tunica intima. { source=ncithesaurus:Internal_Elastic_Membrane }
- + blood vessel internal elastic membrane external ontology notes in FMA this is classified as an acellular membrane, which is inconsistent with our classification as a tissue layer. Requires further investigation { external ontology=FMA }
- + blood vessel internal elastic membrane has exact synonym internal elastic membrane { database cross reference=MA:0002863 }
- + blood vessel internal elastic membrane label blood vessel internal elastic membrane
Changes for: nail
- Deleted
- - nail SubClassOf part of some skin of body
Changes for: neurocranium
- Deleted
- - neurocranium SubClassOf mesoderm-derived structure
Changes for: larynx
- Deleted
- - larynx SubClassOf endoderm-derived structure
Changes for: soft palate
- Deleted
- - soft palate SubClassOf endoderm-derived structure
- - soft palate SubClassOf neural crest-derived structure
Changes for: palatine uvula
- Deleted
- - palatine uvula SubClassOf anatomical cluster
- Added
- + palatine uvula SubClassOf anatomical projection
Changes for: oropharynx
- Deleted
- - oropharynx SubClassOf endoderm-derived structure
Changes for: nasopharynx
- Deleted
- - nasopharynx SubClassOf endoderm-derived structure
Changes for: primary motor cortex layer 1
- Deleted
- Added
- + primary motor cortex layer 1 SubClassOf layer of neocortex
Changes for: temporal bone
- Deleted
- - temporal bone SubClassOf lateral structure
Changes for: lacrimal bone
- Deleted
- - lacrimal bone SubClassOf lateral structure
Changes for: nasal bone
- Deleted
- - nasal bone SubClassOf lateral structure
Changes for: palatine bone
- Deleted
- - palatine bone SubClassOf lateral structure
Changes for: jugal bone
- Deleted
- - jugal bone SubClassOf lateral structure
Changes for: sensory root of facial nerve
- Deleted
Changes for: external ear
- Deleted
- - external ear definition Part of the ear external to the tympanum (eardrum). It consists of a tube (the external auditory meatus) that directs sound waves on to the tympanum, and may also include the external pinna, which extends beyond the skull[GO]. { database cross reference=http://en.wikipedia.org/wiki/External_ear , database cross reference=GO:0042473 }
- - external ear editor note This class was created automatically from a combination of ontologies
- Added
- + external ear definition Part of the ear external to the tympanum (eardrum). It typically consists of a tube (the external auditory meatus) that directs sound waves on to the tympanum, and may also include the external pinna, which extends beyond the skull[GO]. { database cross reference=http://en.wikipedia.org/wiki/External_ear , database cross reference=GO:0042473 }
- + external ear external ontology notes in XAO this includes and is only the tympanum { external ontology=XAO }
Changes for: orbit of skull
- Deleted
- - orbit of skull SubClassOf lateral structure
- - orbit of skull SubClassOf neural crest-derived structure
Changes for: articulation
- Deleted
- - articulation SubClassOf anatomical cluster
- Added
- + articulation SubClassOf multi organ part structure
Changes for: organ component layer
- Deleted
- - organ component layer definition Organ component which is a part of a wall of an organ. { database cross reference=FMA:82485 }
- Added
- + organ component layer definition A part of a wall of an organ that forms a layer. { database cross reference=UBERON:cjm }
Changes for: postnatal subventricular zone
- Deleted
- - postnatal subventricular zone SubClassOf ectoderm-derived structure
- - postnatal subventricular zone SubClassOf organ component layer
- Added
Changes for: biliary bud
- Deleted
- - biliary bud SubClassOf epithelial tube
- Added
- + biliary bud SubClassOf digestive tract diverticulum
- + biliary bud SubClassOf endodermal part of digestive tract
- + biliary bud SubClassOf epithelial sac
- + biliary bud SubClassOf part of some hepatobiliary system
Changes for: hepatopancreatic ampulla
- Deleted
- - hepatopancreatic ampulla SubClassOf digestive system duct
- - hepatopancreatic ampulla SubClassOf endoderm-derived structure
- Added
- + hepatopancreatic ampulla SubClassOf bile duct
Changes for: dorsolateral fasciculus of medulla
- Deleted
Changes for: dorsal longitudinal fasciculus of medulla
- Deleted
Changes for: cuneate fasciculus of medulla
- Deleted
Changes for: decussation of medial lemniscus
- Deleted
Changes for: cuneocerebellar tract
- Deleted
Changes for: cerebral crus
- Deleted
- - cerebral crus SubClassOf lateral structure
Changes for: periamygdaloid area
- Deleted
- - periamygdaloid area comment Editor note: consider splitting
- Added
- + periamygdaloid area editor note consider splitting
Changes for: gracile fasciculus of medulla
- Deleted
Changes for: kidney arcuate artery
- Deleted
- - kidney arcuate artery database cross reference FMA:44594
- - kidney arcuate artery database cross reference http://en.wikipedia.org/wiki/Arcuate_artery_of_the_foot
- - kidney arcuate artery database cross reference http://www.snomedbrowser.com/Codes/Details/244331005
- - kidney arcuate artery editor note This class was created automatically from a combination of ontologies
- - kidney arcuate artery has exact synonym arcuate artery { database cross reference=MA:0002583 }
- Added
- + kidney arcuate artery SubClassOf branching part of some interlobar artery
- + kidney arcuate artery database cross reference http://en.wikipedia.org/wiki/Arcuate_arteries_of_the_kidney
- + kidney arcuate artery has broad synonym arcuate artery { database cross reference=MA:0002583 }
Changes for: popliteal vein
- Added
- + popliteal vein SubClassOf hindlimb blood vessel
Changes for: granular cell layer of dorsal cochlear nucleus
- Deleted
Changes for: pineal complex
- Deleted
- - pineal complex SubClassOf ectoderm-derived structure
- Added
Changes for: septal olfactory organ
- Deleted
- - septal olfactory organ SubClassOf organ
- Added
- + septal olfactory organ SubClassOf cell cluster organ
Changes for: olfactory nerve
- Deleted
- - olfactory nerve SubClassOf ectoderm-derived structure
Changes for: cheek
- Deleted
- - cheek SubClassOf subdivision of head
- Added
- + cheek SubClassOf external soft tissue zone
Changes for: temporalis muscle
- Deleted
- - temporalis muscle SubClassOf part of some subdivision of head
- Added
- + temporalis muscle SubClassOf part of some head
Changes for: extrastriate cortex
- Deleted
Changes for: aryepiglottic fold
- Deleted
- - aryepiglottic fold SubClassOf lateral structure
Changes for: vestibular nerve
- Deleted
Changes for: collection of basal ganglia
- Deleted
Changes for: skeleton of digitopodium
- Deleted
- - skeleton of digitopodium SubClassOf mesoderm-derived structure
Changes for: coccygeal nerve
- Deleted
- - coccygeal nerve SubClassOf lateral structure
Changes for: ciliary muscle
- Deleted
- - ciliary muscle SubClassOf neural crest-derived structure
- Added
Changes for: muscle of iris
- Deleted
- - muscle of iris SubClassOf neural crest-derived structure
Changes for: nephron tubule basement membrane
- Added
- + nephron tubule basement membrane database cross reference http://www.snomedbrowser.com/Codes/Details/245251000
- + nephron tubule basement membrane has exact synonym renal tubular basement membrane
Changes for: bronchus basement membrane
- Deleted
- - bronchus basement membrane SubClassOf bronchus connective tissue
- Added
- + bronchus basement membrane SubClassOf endoderm-derived structure
- + bronchus basement membrane external ontology notes MA classifies as type of connective tissue: https://sourceforge.net/p/obo/mouse-anatomy-requests/94/ { external ontology=MA }
- + bronchus basement membrane has exact synonym bronchial basement membrane { database cross reference=UBERON:cjm }
Changes for: central tegmental tract
- Deleted
Changes for: carotid body
- Deleted
- - carotid body SubClassOf organ
- Added
- + carotid body SubClassOf cell cluster organ
Changes for: echolocation organ
- Added
- + echolocation organ definition Any organ that plays a role in the process of echolocation. { database cross reference=UBERON:cjm }
Changes for: future common hepatic duct
- Added
- + future common hepatic duct SubClassOf epithelium of biliary system
Changes for: vestibulocochlear nerve
- Deleted
- - vestibulocochlear nerve SubClassOf ectoderm-derived structure
Changes for: abducens nerve
- Deleted
- - abducens nerve SubClassOf ectoderm-derived structure
Changes for: oculomotor nerve
- Deleted
- - oculomotor nerve SubClassOf ectoderm-derived structure
Changes for: chromaffin system
- Deleted
- - chromaffin system SubClassOf anatomical group
- - chromaffin system SubClassOf neural crest-derived structure
- Added
- + chromaffin system SubClassOf organ system subdivision
Changes for: rubrospinal tract
- Deleted
Changes for: spinal trigeminal tract of medulla
- Deleted
Changes for: solitary tract
- Deleted
Changes for: spino-olivary tract
- Deleted
Changes for: future hindbrain meninges
- Added
- + future hindbrain meninges SubClassOf neural tissue
Changes for: vestibulocochlear nerve root
- Deleted
Changes for: longitudinal pontine fibers
- Deleted
Changes for: transverse pontine fibers
- Deleted
Changes for: lamina of septum pellucidum
- Deleted
Changes for: eponychium
- Deleted
- - eponychium SubClassOf ectoderm-derived structure
- - eponychium SubClassOf integumentary system layer
- Added
- + eponychium SubClassOf ecto-epithelium
- + eponychium taxon notes In hoofed animals, the eponychium is the deciduous hoof capsule in fetuses and newborn foals, and is a part of the permanent hoof in older animals
Changes for: diagonal band of Broca
- Deleted
Changes for: medial lemniscus of medulla
- Deleted
Changes for: ventral amygdalofugal projection
- Deleted
Changes for: hilum of dentate nucleus
- Deleted
Changes for: set of lower jaw teeth
- Deleted
- - set of lower jaw teeth SubClassOf endoderm-derived structure
- - set of lower jaw teeth SubClassOf neural crest-derived structure
Changes for: tooth row
- Added
- + tooth row EquivalentTo anatomical row and has member some calcareous tooth
- + tooth row SubClassOf anatomical row
- + tooth row SubClassOf has member some calcareous tooth
Changes for: bile duct epithelium
- Deleted
- - bile duct epithelium database cross reference BTO:0001513
- - bile duct epithelium definition Epithelium of the gallbladder and the intrahepatic and extrahepatic bile ducts. { database cross reference=BTO:0001513 }
- - bile duct epithelium editor note TODO - check if BTO terms need merged
- - bile duct epithelium has exact synonym bile duct epithelial tissue { database cross reference=OBOL:automatic }
- - bile duct epithelium has exact synonym biliary duct epithelial tissue { database cross reference=OBOL:automatic }
- - bile duct epithelium has exact synonym biliary epithelium { database cross reference=BTO:0001513 }
- - bile duct epithelium has exact synonym epithelial tissue of bile duct { database cross reference=OBOL:automatic }
- - bile duct epithelium has exact synonym epithelial tissue of biliary duct { database cross reference=OBOL:automatic }
- Added
- + bile duct epithelium SubClassOf epithelium of biliary system
- + bile duct epithelium definition Any epithelium that lines one of the bile ducts. { database cross reference=UBERON:cjm }
- + bile duct epithelium external definition The irregularly shaped proliferating bile ducts are lined by normal cuboidal epithelium. { source=BTO:0000417 }
Changes for: extrahepatic bile duct epithelium
- Added
- + extrahepatic bile duct epithelium database cross reference EHDAA2:0000742
- + extrahepatic bile duct epithelium database cross reference EHDAA:3051
Changes for: telencephalic nucleus
- Deleted
Changes for: hindbrain nucleus
- Deleted
Changes for: intrahepatic bile duct epithelium
- Added
- + intrahepatic bile duct epithelium database cross reference EHDAA2:0000743
- + intrahepatic bile duct epithelium database cross reference EHDAA:3053
Changes for: esophagus skeletal muscle
- Deleted
- - esophagus skeletal muscle has exact synonym gullet skeletal muscle tissue { database cross reference=OBOL:automatic }
- - esophagus skeletal muscle has exact synonym gullet skeletal muscle { database cross reference=OBOL:automatic }
- - esophagus skeletal muscle has exact synonym oesophagus skeletal muscle tissue { database cross reference=OBOL:automatic }
- - esophagus skeletal muscle has exact synonym oesophagus skeletal muscle { database cross reference=OBOL:automatic }
- - esophagus skeletal muscle has exact synonym skeletal muscle of gullet { database cross reference=OBOL:automatic }
- - esophagus skeletal muscle has exact synonym skeletal muscle of oesophagus { database cross reference=OBOL:automatic }
- - esophagus skeletal muscle has exact synonym skeletal muscle tissue of esophagus { database cross reference=OBOL:automatic }
- - esophagus skeletal muscle has exact synonym skeletal muscle tissue of gullet { database cross reference=OBOL:automatic }
- - esophagus skeletal muscle has exact synonym skeletal muscle tissue of oesophagus { database cross reference=OBOL:automatic }
- Added
- + esophagus skeletal muscle comment Most muscle tissue lining the digestive tract is smooth, but part of the externa of the esophagus is skeletal
Changes for: hepatic duct smooth muscle
- Deleted
- - hepatic duct smooth muscle definition A smooth muscle tissue that is part of a hepatic duct. { database cross reference=OBOL:automatic }
- Added
- + hepatic duct smooth muscle definition Smooth muscle tissue in all or part of a hepatic duct. { database cross reference=UBERON:cjm }
Changes for: set of upper jaw teeth
- Deleted
- - set of upper jaw teeth SubClassOf neural crest-derived structure
Changes for: prepollex skeleton
- Deleted
- - prepollex skeleton SubClassOf mesoderm-derived structure
Changes for: lateral corticospinal tract
- Deleted
Changes for: heart vasculature
- Deleted
- - heart vasculature SubClassOf mesoderm-derived structure
Changes for: nursing stage
- Deleted
- - nursing stage SubClassOf has part some part of some neonate stage
- Added
- + nursing stage SubClassOf has part some neonate stage
Changes for: basal part of pons
- Deleted
- - basal part of pons SubClassOf anatomical cluster
- - basal part of pons SubClassOf ectoderm-derived structure
- Added
- + basal part of pons SubClassOf regional part of brain
Changes for: temporal operculum
- Deleted
- - temporal operculum SubClassOf anatomical cluster
- - temporal operculum SubClassOf ectoderm-derived structure
- Added
- + temporal operculum SubClassOf regional part of brain
Changes for: intermediate hypothalamic region
- Deleted
- - intermediate hypothalamic region SubClassOf anatomical cluster
- - intermediate hypothalamic region SubClassOf ectoderm-derived structure
- Added
- + intermediate hypothalamic region SubClassOf regional part of brain
Changes for: vestibulocerebellar tract
- Deleted
Changes for: anterior hypothalamic region
- Deleted
- - anterior hypothalamic region SubClassOf anatomical cluster
- - anterior hypothalamic region SubClassOf ectoderm-derived structure
- Added
- + anterior hypothalamic region SubClassOf regional part of brain
Changes for: ventral trigeminal tract
- Deleted
Changes for: gland
- Added
- + gland database cross reference FMA:7146
- + gland has exact synonym glandular organ { database cross reference=UBERON:cjm }
Changes for: limb segment
- Added
- + limb segment SubClassOf has part some skeletal muscle organ
Changes for: dorsal side of post-anal tail
- Deleted
- - dorsal side of post-anal tail EquivalentTo organism subdivision and in dorsal side of some post-anal tail
- - dorsal side of post-anal tail SubClassOf organism subdivision
- Added
- + dorsal side of post-anal tail EquivalentTo external soft tissue zone and in dorsal side of some post-anal tail
- + dorsal side of post-anal tail SubClassOf external soft tissue zone
Changes for: ventral side of post-anal tail
- Deleted
- - ventral side of post-anal tail EquivalentTo organism subdivision and in ventral side of some post-anal tail
- - ventral side of post-anal tail SubClassOf organism subdivision
- Added
- + ventral side of post-anal tail EquivalentTo external soft tissue zone and in ventral side of some post-anal tail
- + ventral side of post-anal tail SubClassOf external soft tissue zone
Changes for: elastic tissue
- Deleted
- - elastic tissue has exact synonym textus connectivus elasticus
- Added
- + elastic tissue has exact synonym textus connectivus elasticus { has synonym type=latin term }
Changes for: tunica intima
- Deleted
- - tunica intima SubClassOf has part some endothelium
- Added
- + tunica intima SubClassOf blood vessel endothelium
Changes for: basicranium
- Deleted
- - basicranium SubClassOf mesoderm-derived structure
Changes for: thoracic skeleton
- Deleted
- - thoracic skeleton SubClassOf mesoderm-derived structure
Changes for: subdivision of head
- Deleted
- - subdivision of head editor note This class was created automatically from a combination of ontologies
- - subdivision of head has exact synonym head region
- - subdivision of head has exact synonym region of head
- Added
- + subdivision of head has related synonym head region
- + subdivision of head has related synonym region of head
Changes for: Pacinian corpuscle
- Deleted
- - Pacinian corpuscle SubClassOf ectoderm-derived structure
- - Pacinian corpuscle SubClassOf mesoderm-derived structure
Changes for: recurrent laryngeal nerve
- Deleted
Changes for: neural tissue
- Deleted
- - neural tissue definition Portion of tissue which consists of neurons, neuroglia and vasculature. Examples: Neural tissue of brain, neural tissue of peripheral ganglion, neural tissue of nerve[FMA]. { database cross reference=FMA:9642 }
- Added
- + neural tissue definition Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature. { database cross reference=FMA:9642 }
Changes for: aggregate regional part of brain
- Deleted
- - aggregate regional part of brain SubClassOf regional part of brain
- - aggregate regional part of brain comment May be obsoleted. The FMA class is more specific
- - aggregate regional part of brain has exact synonym set of nuclei of neuraxis { database cross reference=FMA:256381 }
- Added
- + aggregate regional part of brain EquivalentTo disconnected anatomical group and part of some brain and has member some regional part of brain
- + aggregate regional part of brain SubClassOf disconnected anatomical group
- + aggregate regional part of brain SubClassOf has member some regional part of brain
- + aggregate regional part of brain editor note May be obsoleted.
- + aggregate regional part of brain has related synonym set of nuclei of neuraxis { database cross reference=FMA:256381 }
Changes for: laryngeal vocal fold
- Deleted
- - laryngeal vocal fold SubClassOf lateral structure
Changes for: cell cluster organ
- Deleted
- - cell cluster organ definition A multicellular anatomical strucure consisting of a few cells of various types which forms a discrete structure with a largely bona fide boundary. { database cross reference=CARO:0010001 }
- Added
- + cell cluster organ SubClassOf cell cluster
- + cell cluster organ comment Examples include arthropod sensilla.
- + cell cluster organ definition A small cluster of cells of various types which form a discrete structure, largely delimited by a morphological boundary and whose components work together to make the whole structure capable of a specific function. { database cross reference=CARO:0010001 }
Changes for: intrahepatic bile duct
- Added
- + intrahepatic bile duct editor note includes the hepatic duct of the caudate lobe, and the intra- and inter- lobar bile ducts
Changes for: extrahepatic bile duct
- Added
- + extrahepatic bile duct editor note includes all the cystic duct, all the common bile duct and the extrahapetic part of the hepatic duct
Changes for: vaginal venous plexus
- Deleted
- - vaginal venous plexus SubClassOf reproductive structure
Changes for: orbital operculum
- Deleted
- - orbital operculum SubClassOf anatomical cluster
- - orbital operculum SubClassOf ectoderm-derived structure
- Added
- + orbital operculum SubClassOf regional part of brain
Changes for: spermaceti organ
- Deleted
- - spermaceti organ EquivalentTo organ and produces some spermaceti
- - spermaceti organ SubClassOf produces some spermaceti
- - spermaceti organ definition An organ that secretes a spermaceti. { database cross reference=OBOL:automatic }
- Added
- + spermaceti organ EquivalentTo organ and contains some spermaceti
- + spermaceti organ SubClassOf contains some spermaceti
- + spermaceti organ database cross reference http://en.wikipedia.org/wiki/Spermaceti_organ
- + spermaceti organ definition An organ that contains spermaceti. { database cross reference=http://en.wikipedia.org/wiki/Spermaceti_organ }
Changes for: paraganglion
- Deleted
- - paraganglion SubClassOf anatomical group
- - paraganglion SubClassOf structure with developmental contribution from neural crest
- Added
- + paraganglion SubClassOf organ system subdivision
Changes for: aorta tunica intima
- Added
- + aorta tunica intima SubClassOf aorta endothelium
Changes for: blood vessel elastic tissue
- Deleted
- - blood vessel elastic tissue definition A tissue that is found in the tunica media of the vessels wall and allows vessels to stretch. { database cross reference=MP:0006083 }
- Added
- + blood vessel elastic tissue definition Elastic tissue layer that lines a blood vessel layer. { database cross reference=https://sourceforge.net/p/obo/mammalian-phenotype-requests/2026/ , database cross reference=UBERON:cjm }
- + blood vessel elastic tissue has broad synonym elastic lamina { database cross reference=MP:0006083 }
- + blood vessel elastic tissue has broad synonym elastic laminae { database cross reference=MP:0006083 , has synonym type=plural term }
Changes for: border between sublaminar layers
- Deleted
- - border between sublaminar layers SubClassOf ectoderm-derived structure
- - border between sublaminar layers SubClassOf organ component layer
- Added
Changes for: blood vessel layer
- Deleted
- - blood vessel layer definition An organ component layer that is part of a blood vessel. { database cross reference=OBOL:automatic }
- Added
- + blood vessel layer definition Any of the tissue layers that comprise a blood vessel. Examples: tunica media, tunica adventitia. { database cross reference=UBERON:cjm }
- + blood vessel layer depicted by http://upload.wikimedia.org/wikipedia/commons/thumb/6/61/Blood_vessels.svg/500px-Blood_vessels.svg.png
Changes for: mouth floor
- Added
- + mouth floor editor note reclassify after CARO2 overhaul
Changes for: dentition
- Deleted
- - dentition SubClassOf anatomical cluster
- - dentition SubClassOf has part some calcareous tooth
- - dentition SubClassOf structure with developmental contribution from neural crest
- Added
- + dentition EquivalentTo anatomical collection and has member some calcareous tooth
- + dentition SubClassOf has member some calcareous tooth
- + dentition SubClassOf skeleton
Changes for: pars superior ear
- Deleted
Changes for: articular system
- Deleted
- - articular system EquivalentTo anatomical cluster and has member some skeletal joint
- - articular system SubClassOf anatomical cluster
- - articular system SubClassOf anatomical system
- Added
- + articular system EquivalentTo anatomical collection and has member some skeletal joint
- + articular system SubClassOf anatomical collection
Changes for: pars inferior ear
- Deleted
Changes for: skeletal tissue
- Deleted
- - skeletal tissue has narrow synonym mineralized tissue
Changes for: regional part of brain
- Added
- + regional part of brain SubClassOf composed primarily of some neural tissue
- + regional part of brain has exact synonym neuroanatomical region
Changes for: cartilaginous neurocranium
- Deleted
- - cartilaginous neurocranium SubClassOf mesoderm-derived structure
Changes for: tuber cinereum
- Deleted
- - tuber cinereum SubClassOf anatomical cluster
- - tuber cinereum SubClassOf ectoderm-derived structure
- Added
- + tuber cinereum SubClassOf regional part of brain
Changes for: skeletal element
- Deleted
- - skeletal element editor note TODO - add more general class for other kinds of mineralized tissue
Changes for: metanephric juxtaglomerular apparatus
- Deleted
Changes for: dentary
- Deleted
- - dentary SubClassOf lateral structure
Changes for: fused sacrum
- Added
- + fused sacrum SubClassOf mesoderm-derived structure
Changes for: precentral operculum
- Deleted
- - precentral operculum SubClassOf anatomical cluster
- - precentral operculum SubClassOf ectoderm-derived structure
- Added
- + precentral operculum SubClassOf regional part of brain
Changes for: incisor region of dentition
- Deleted
- - incisor region of dentition EquivalentTo anatomical group and part of some dentition and composed primarily of some incisor tooth
- - incisor region of dentition SubClassOf anatomical group
- Added
- + incisor region of dentition EquivalentTo anatomical structure and part of some dentition and composed primarily of some incisor tooth
Changes for: conceptus
- Deleted
- - conceptus SubClassOf anatomical group
- Added
- + conceptus SubClassOf anatomical structure
Changes for: septum pellucidum
- Deleted
- - septum pellucidum SubClassOf anatomical cluster
- Added
- + septum pellucidum SubClassOf cell layer
Changes for: cochlear nerve
- Deleted
- - cochlear nerve SubClassOf ectoderm-derived structure
- - cochlear nerve SubClassOf structure with developmental contribution from neural crest
Changes for: digestive syncytial vacuole
- Deleted
- - digestive syncytial vacuole SubClassOf cell part
Changes for: cervical gland
- Deleted
- - cervical gland SubClassOf mucous gland
Changes for: urinary bladder vasculature
- Deleted
- - urinary bladder vasculature SubClassOf mesoderm-derived structure
Changes for: inner optic circle
- Deleted
- - inner optic circle SubClassOf mesoderm-derived structure
Changes for: coccyx
- Added
- + coccyx SubClassOf mesoderm-derived structure
Changes for: femoral vein
- Deleted
- - femoral vein SubClassOf part of some organism subdivision
- Added
- + femoral vein SubClassOf hindlimb blood vessel
- + femoral vein SubClassOf part of some hindlimb
Changes for: cumulus oophorus
- Deleted
- - cumulus oophorus SubClassOf organ part
- Added
- + cumulus oophorus SubClassOf cell cluster
Changes for: placentome of cotyledonary placenta
- Deleted
- - placentome of cotyledonary placenta SubClassOf anatomical cluster
- Added
Changes for: scrotum
- Deleted
- - scrotum SubClassOf organism subdivision
- Added
- + scrotum SubClassOf external soft tissue zone
Changes for: urethral gland
- Deleted
- - urethral gland SubClassOf exocrine gland
- Added
- + urethral gland SubClassOf mucous gland
- + urethral gland has exact synonym urethral mucuous gland
Changes for: brain gray matter
- Deleted
- - brain grey matter has exact synonym brain gray matter { database cross reference=OBOL:automatic }
- - brain grey matter label brain grey matter
- Added
- + brain gray matter has exact synonym brain grey matter { database cross reference=MA:0000810 }
- + brain gray matter label brain gray matter
Changes for: prostate epithelial cord
- Deleted
- - prostate epithelial cord EquivalentTo epithelial cord and part of some prostate gland
- - prostate epithelial cord SubClassOf part of some prostate gland
- - prostate epithelial cord SubClassOf prostate epithelium
- Added
- + prostate epithelial cord EquivalentTo epithelial cord and has potential to develop into some prostate gland
- + prostate epithelial cord SubClassOf developing epithelial placode
- + prostate epithelial cord SubClassOf has potential to develop into some prostate gland
Changes for: glandular acinus
- Deleted
- - acinus SubClassOf organ part
- - acinus definition An acinus refers to any cluster of cells that resembles a many-lobed ‘berry,’ such as a raspberry (acinus is Latin for berry). The berry-shaped termination of an exocrine gland, where the secretion is produced is acinar in form, as is the alveolar sac containing multiple alveoli in the lungs. { database cross reference=http://en.wikipedia.org/wiki/Acinus }
- - acinus has related synonym glandular acinus
- - acinus label acinus
- Added
- + glandular acinus SubClassOf cell cluster
- + glandular acinus SubClassOf part of some gland
- + glandular acinus definition The many-lobed berry cluster of cells that is the terminous of a gland where the secretion is produced is acinar in form. { database cross reference=http://en.wikipedia.org/wiki/Acinus }
- + glandular acinus has broad synonym acinus { database cross reference=FMA:55588 }
- + glandular acinus label glandular acinus
Changes for: mesopodial skeleton
- Deleted
- - mesopodial skeleton SubClassOf mesoderm-derived structure
Changes for: pole of cerebral hemisphere
- Deleted
Changes for: interlobar vein
- Added
- + interlobar vein EquivalentTo vein and drains some renal lobe
- + interlobar vein SubClassOf drains some renal lobe
Changes for: ciliary stroma
- Deleted
- - ciliary stroma SubClassOf neural crest-derived structure
- Added
- + ciliary stroma SubClassOf ectoderm-derived structure
Changes for: interlobar artery
- Deleted
- - interlobar artery definition One of a set of curved arteries at the corticomedullary border of the kidney that arise from the interlobar arteries and give rise to the interlobular arteries. { database cross reference=http://en.wikipedia.org/wiki/Interlobar_arteries , database cross reference=MP:0011315 }
- Added
- + interlobar artery EquivalentTo artery and supplies some renal lobe
- + interlobar artery SubClassOf supplies some renal lobe
- + interlobar artery definition An artery that supplies a renal lobe. { database cross reference=http://en.wikipedia.org/wiki/Interlobar_arteries , database cross reference=UBERON:cjm }
Changes for: parietal operculum
- Deleted
- - parietal operculum SubClassOf anatomical cluster
- - parietal operculum SubClassOf ectoderm-derived structure
- Added
- + parietal operculum SubClassOf regional part of brain
Changes for: dentate gyrus polymorphic layer
- Added
- + dentate gyrus polymorphic layer definition A cellular layer of the dentate gyrus enclosed by the granule cell layer. A number of cell types are located in the polymorphic layer but the most prominent is the mossy cell. { database cross reference=http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2492885/ , database cross reference=UBERON:cjm }
- + dentate gyrus polymorphic layer editor note TODO: add mossy cell
- + dentate gyrus polymorphic layer has related synonym CA4 { database cross reference=NCBI:PMC2492885 , has synonym type=dubious or contested synonym }
Changes for: terminal nerve
- Deleted
- - terminal nerve SubClassOf neural crest-derived structure
Changes for: tectopontine tract
- Deleted
Changes for: tectospinal tract
- Deleted
Changes for: frontal operculum
- Deleted
- - frontal operculum SubClassOf anatomical cluster
- - frontal operculum SubClassOf ectoderm-derived structure
- Added
- + frontal operculum SubClassOf regional part of brain
Changes for: spinothalamic tract of medulla
- Deleted
Changes for: dorsal hypothalamic area
- Deleted
- - dorsal hypothalamic area SubClassOf anatomical cluster
- - dorsal hypothalamic area SubClassOf ectoderm-derived structure
- Added
- + dorsal hypothalamic area SubClassOf regional part of brain
Changes for: medial lemniscus of pons
- Deleted
Changes for: anterior spinocerebellar tract
- Deleted
Changes for: central tegmental tract of pons
- Deleted
Changes for: decussation of trochlear nerve
- Deleted
Changes for: root of abducens nerve
- Deleted
Changes for: posterior hypothalamic region
- Deleted
- - posterior hypothalamic region SubClassOf anatomical cluster
- - posterior hypothalamic region SubClassOf ectoderm-derived structure
- Added
- + posterior hypothalamic region SubClassOf regional part of brain
Changes for: olivocochlear bundle
- Deleted
Changes for: vestibulospinal tract
- Deleted
Changes for: predorsal bundle
- Deleted
Changes for: olivocerebellar tract
- Deleted
Changes for: medial longitudinal fasciculus of medulla
- Deleted
Changes for: pyramidal decussation
- Deleted
Changes for: myometrium
- Deleted
- - myometrium SubClassOf layer of muscle tissue
- Added
- + myometrium SubClassOf layer of smooth muscle tissue
Changes for: core of melon organ
- Added
- + core of melon organ SubClassOf composed primarily of some adipose tissue
- + core of melon organ definition The core component of the ovoid-shaped, fatty organ found in the forehead of all toothed whales. { database cross reference=http://en.wikipedia.org/wiki/Melon_(whale) }
Changes for: ampullary nerve
- Deleted
- - ampullary nerve SubClassOf ectoderm-derived structure
- - ampullary nerve SubClassOf structure with developmental contribution from neural crest
Changes for: bile canaliculus
- Deleted
- - bile canaliculus definition Fine tubular canals running between liver cells, throughout the parenchyma, usually occurring singly between each adjacent pair of cells, and forming a three-dimensional network of polyhedral meshes, with a single cell in each mesh[BTO]. A thin tube that collects bile secreted by hepatocytes. The bile canaliculi merge and form bile ductules, which eventually become common hepatic duct. Hepatocytes are polyhedral in shape, therefore having no set shape or design. They have surfaces facing the sinusoids, (called sinusoidal faces) and surfaces which contact other hepatocytes, (called lateral faces). Bile canaliculi are formed by grooves on some of the lateral faces of these hepatocytes. Microvilli are present in the canaliculi but are sparse. [WP,unvetted]. { database cross reference=http://en.wikipedia.org/wiki/Bile_canaliculus , database cross reference=BTO:0002841 }
- - bile canaliculus editor note This class was created automatically from a combination of ontologies
- Added
- + bile canaliculus definition An intercellular channel that takes up bile from hepatocytes, transporting it to the bile ducts. { database cross reference=MP:0008991 }
- + bile canaliculus function notes conducts the flow of bile countercurrent to the direction of portal blood flow and connects with the canal of Hering[doi:10.1002/cphy.c120027]
- + bile canaliculus structure notes The bile canaliculi merge and form bile ductules, which eventually become common hepatic duct. Hepatocytes are polyhedral in shape, therefore having no set shape or design. They have surfaces facing the sinusoids, (called sinusoidal faces) and surfaces which contact other hepatocytes, (called lateral faces). Bile canaliculi are formed by grooves on some of the lateral faces of these hepatocytes. Microvilli are present in the canaliculi but are sparse. [WP]
Changes for: ovarian medulla
- Deleted
- - ovarian medulla definition The medulla of ovary (or Zona vasculosa of Waldeyer) is a highly vascular stroma in the center of the ovary. It forms from embryonic mesenchyme and contains blood vessels, lymphatic vessels, and nerves. This stroma forms the tissue of the hilum by which the ovarian ligament is attached, and through which the blood vessels enter: it does not contain any ovarian follicles. { database cross reference=http://en.wikipedia.org/wiki/Medulla_of_ovary }
- Added
- + ovarian medulla definition highly vascular stroma found in the center of the ovary that forms from embryonic mesenchyme and contains blood vessels, lymphatic vessels, and nerves; this stroma forms the tissue of the hilum by which the ovarian ligament is attached, and through which the blood vessels enter; it does not contain any ovarian follicles. { database cross reference=MGI:anna }
Changes for: ovarian cortex
- Deleted
- - ovarian cortex definition The outer layer of the ovary, composed of cellular connective tissue which contains the ovarian follicles { database cross reference=ncithesaurus:Ovarian_Cortex }
- Added
- + ovarian cortex SubClassOf part of some ovary stroma
- + ovarian cortex definition the layer of the ovarian stroma lying immediately beneath the tunica albuginea, composed of connective tissue cells and fibers, among which are scattered primary and secondary (antral) follicles in various stages of development; the cortex varies in thickness according to the age of the individual, becoming thinner with advancing years; included in the follicles are the cumulus oophorus, membrana granulosa (and the granulosa cells inside it), corona radiata, zona pellucida, and primary oocyte; the zona pellucida, theca of follicle, antrum and liquor folliculi are also contained in the follicle; also in the cortex is the corpus luteum derived from the follicles. { database cross reference=MGI:anna }
Changes for: portal triad
- Deleted
- - portal triad SubClassOf organ part
- - portal triad definition the three vessels of the portal lobule including the bile duct, a terminal branch of the hepatic artery and portal vein, and may also include a lymphatic vessel { database cross reference=MP:0008993,ISBN:0-683-40008-8,MGI:csmith }
- Added
- + portal triad SubClassOf has part some hepatic artery
- + portal triad SubClassOf has part some intrahepatic bile duct
- + portal triad SubClassOf has part some portal vein
- + portal triad SubClassOf multi organ part structure
- + portal triad definition A multi-organ-part structure that consists of three vessels of the portal lobule including the bile duct, a terminal branch of the hepatic artery and portal vein, and may also include a lymphatic vessel { database cross reference=ISBN:0-683-40008-8 , database cross reference=MGI:csmith , database cross reference=MP:0008993 , database cross reference=UBERON:cjm }
Changes for: pubis
- Deleted
- - pubis SubClassOf lateral structure
Changes for: ischium
- Deleted
- - ischium SubClassOf lateral structure
Changes for: ilium
- Deleted
- - ilium SubClassOf lateral structure
Changes for: neurovascular bundle
- Deleted
- - neurovascular bundle SubClassOf anatomical cluster
- Added
- + neurovascular bundle SubClassOf multi organ part structure
Changes for: innominate bone
- Deleted
- - innominate bone SubClassOf lateral structure
Changes for: pelvic girdle region
- Deleted
- - pelvic girdle region SubClassOf lateral structure
Changes for: extrahepatic duct
- Deleted
- - extrahepatic duct SubClassOf digestive system duct
- - extrahepatic duct SubClassOf endoderm-derived structure
- Added
- + extrahepatic duct SubClassOf bile duct
Changes for: dorsal trigeminal tract
- Deleted
Changes for: spinothalamic tract of pons
- Deleted
Changes for: dorsal longitudinal fasciculus of pons
- Deleted
Changes for: medial longitudinal fasciculus of pons
- Deleted
Changes for: baleen feeding system
- Deleted
- - baleen feeding system SubClassOf anatomical group
- Added
- + baleen feeding system SubClassOf organ system subdivision
Changes for: auditory hillocks, pharyngeal arch 2 derived
- Deleted
Changes for: auditory hillocks, pharyngeal arch 1 derived
- Deleted
Changes for: branch of Y-shaped fibrocartilage skeleton of ventral pouch
- Deleted
Changes for: interlobular bile duct
- Deleted
- - interlobular bile duct editor note This class was created automatically from a combination of ontologies
- Added
- + interlobular bile duct SubClassOf connects some biliary ductule
- + interlobular bile duct SubClassOf connects some intralobular duct
- + interlobular bile duct has exact synonym interlobular ductule { database cross reference=MP:0009500 }
Changes for: lunge feeding vibrissa
- Deleted
- - lunge feeding vibrissa SubClassOf ectoderm-derived structure
- - lunge feeding vibrissa SubClassOf endoderm-derived structure
Changes for: subepicardial layer of epicardium
- Added
- + subepicardial layer of epicardium editor note consider merging into myocardial compact layer
Changes for: intestinal villus
- Deleted
- - intestinal villus editor note in mammals, villi are (largely?) absent from the large intestine, so we treat this as equivalent to small intestinal villus. small/large subdivision may not make sense for all speciesi for which this is present (see ZFA). Note that VHOG quotes ISBN:978-0030223693 as suggesting there are some villi in the large intestine
- Added
- + intestinal villus SubClassOf has part some blood vessel
- + intestinal villus SubClassOf has part some striated border microvillus layer
- + intestinal villus editor note in mammals, villi are (largely?) absent from the large intestine, so we treat this as equivalent to small intestinal villus. small/large subdivision may not make sense for all species for which this is present (see ZFA). Note that VHOG quotes ISBN:978-0030223693 as suggesting there are some villi in the large intestine
Changes for: connective tissue of prostate gland
- Deleted
- - connective tissue of prostate label connective tissue of prostate
- Added
- + connective tissue of prostate gland has exact synonym connective tissue of prostate { database cross reference=FMA:74165 }
- + connective tissue of prostate gland label connective tissue of prostate gland
Changes for: sensory root of trigeminal nerve
- Deleted
Changes for: renal lobule
- Added
- + renal lobule SubClassOf has part some medullary ray
- + renal lobule SubClassOf has part some nephron
Changes for: superior branch of oculomotor nerve
- Deleted
Changes for: inferior branch of oculomotor nerve
- Deleted
Changes for: gland of ocular region
- Deleted
- - gland of ocular region definition A gland that is typically found in or near the orbital region, in or around either the medial or lateral canthi, and is typically associated with secretions onto the eyeball or associated ducts. Includes the Harderian, nictitans and lacrimal glands. { database cross reference=UBERON:cjm }
- Added
- + gland of ocular region definition A gland that is typically found in or near the orbital region, in or around either the medial or lateral canthi, and is typically associated with secretions onto the eyeball or associated ducts. Includes the Harderian, nictitans and lacrimal glands. { database cross reference=https://github.com/obophenotype/uberon/issues/614 , database cross reference=UBERON:cjm }
Changes for: bony part of hard palate
- Deleted
- - bony part of hard palate SubClassOf endoderm-derived structure
- - bony part of hard palate SubClassOf neural crest-derived structure
Changes for: vomeronasal nerve
- Deleted
- - vomeronasal nerve SubClassOf ectoderm-derived structure
Changes for: right atrium endocardium
- Deleted
- - right atrium endocardium SubClassOf meso-epithelium
- - right atrium endocardium SubClassOf simple squamous epithelium
Changes for: branchial basket
- Deleted
- - branchial basket SubClassOf endoderm-derived structure
- - branchial basket SubClassOf neural crest-derived structure
Changes for: apex of cochlea
- Deleted
- - apex of cochlea SubClassOf anatomical cluster
- Added
- + apex of cochlea SubClassOf zone of bone organ
Changes for: spinal trigeminal tract of pons
- Deleted
Changes for: acropodial skeleton
- Deleted
- - acropodial skeleton SubClassOf mesoderm-derived structure
Changes for: metapodial skeleton
- Deleted
- - metapodial skeleton SubClassOf mesoderm-derived structure
Changes for: reticular formation
- Deleted
- - reticular formation SubClassOf anatomical cluster
- - reticular formation SubClassOf ectoderm-derived structure
- Added
- + reticular formation SubClassOf regional part of brain
Changes for: hyponychium
- Deleted
- - hyponychium SubClassOf adjacent to some nail
- - hyponychium SubClassOf ecto-epithelium
- Added
- + hyponychium SubClassOf immediately deep to some nail plate
- + hyponychium SubClassOf stratum corneum of epidermis
- + hyponychium function notes secures the nail to the finger tip
Changes for: primitive nephron
- Added
- + primitive nephron external ontology notes EHDAA2 treats this as already having a tubular structure, but in the ZFA representation this is a cluster of cells { external ontology=EHDAA2 }
Changes for: olfactory pathway
- Deleted
Changes for: choroid plexus of fourth ventricle
- Added
Changes for: biliary system
- Deleted
- - biliary system SubClassOf anatomical system
- - biliary system definition Anatomical system that consists of the organs and ducts (bile ducts, gallbladder, and associated structures) that are involved in the production and transportation of bile. { database cross reference=http://en.wikipedia.org/wiki/Biliary_system }
- - biliary system editor note This class was created automatically from a combination of ontologies
- - biliary system has exact synonym biliary apparatus
- Added
- + biliary system SubClassOf has part some biliary tree
- + biliary system SubClassOf organ system subdivision
- + biliary system database cross reference GAID:279
- + biliary system database cross reference MA:0001273
- + biliary system database cross reference MESH:A03.159
- + biliary system database cross reference http://ncicb.nci.nih.gov/xml/owl/EVS/Biliary_Tract
- + biliary system definition Organ system subdivision that consists of the organs and ducts that are involved in the production and transportation of bile. In most species this is the gallbladder and the bile ducts (biliary tree). { database cross reference=http://en.wikipedia.org/wiki/Biliary_system }
- + biliary system has exact synonym biliary apparatus { database cross reference=FMA:79646 }
- + biliary system has related synonym biliary tract { database cross reference=FMA:79646 , database cross reference=MA:0001273 }
Changes for: ventrum
- Deleted
- - ventrum definition The ventral part of an animal. [cjm]. { database cross reference=UBERONREF:0000006 }
- Added
- + ventrum definition A major organism subdivisionthat is the entire part of an anatomical structure ventral to a horizontal plane and bounded on one side by the same horizontal plane. { database cross reference=BSPO:0000068 , database cross reference=UBERONREF:0000006 }
Changes for: entire embryonic mesenchyme
- Deleted
- - entire embryonic mesenchyme SubClassOf developing mesenchymal structure
- - entire embryonic mesenchyme SubClassOf embryonic structure
Changes for: clavicle bone
- Deleted
- - clavicle bone SubClassOf lateral structure
Changes for: nuchal plate series
- Deleted
Changes for: dorsal horn of spinal cord
- Deleted
- - dorsal horn of spinal cord SubClassOf lateral structure
Changes for: ventral horn of spinal cord
- Deleted
- - ventral horn of spinal cord SubClassOf lateral structure
Changes for: dorsal funiculus of spinal cord
- Deleted
- - dorsal funiculus of spinal cord SubClassOf lateral structure
Changes for: olfactory tract
- Deleted
Changes for: vertebral column
- Deleted
- - vertebral column SubClassOf mesoderm-derived structure
Changes for: pupillary membrane
- Deleted
- - pupillary membrane SubClassOf neural crest-derived structure
- Added
- + pupillary membrane SubClassOf ectoderm-derived structure
Changes for: dorsum
- Deleted
- - dorsum definition The dorsal part of an animal, which in vertebrares includes the vertebral column. [cjm]. { database cross reference=http://en.wikipedia.org/wiki/Dorsum_(anatomy) , database cross reference=UBERONREF:0000006 }
- Added
- + dorsum definition A major subdivision of an organism that is the entire part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. In vertebrares this includes the vertebral column.. { database cross reference=http://en.wikipedia.org/wiki/Dorsum_(anatomy) , database cross reference=BSPO:0000063 , database cross reference=UBERONREF:0000006 }
Changes for: laterodorsal tegmental nucleus
- Deleted
Changes for: glossopharyngeal nerve root
- Deleted
Changes for: dorsal ventricular ridge of pallium
- Deleted
- - dorsal ventricular ridge of pallium definition Central region of the telencephalon, located in the pallium. Found in reptiles and birds { database cross reference=http://www.ncbi.nlm.nih.gov/pubmed/23027930 }
- Added
- + dorsal ventricular ridge of pallium definition A large expansion of the lateral wall of the telencephalon, located in the pallium. Found in reptiles and birds { database cross reference=http://icb.oxfordjournals.org/content/42/4/743.full , database cross reference=http://www.ncbi.nlm.nih.gov/pubmed/23027930 }
- + dorsal ventricular ridge of pallium taxon notes Because of the phyletic continuity of the DVR in living reptiles and birds, and its numerous similarities in topography, histology, and connections in these two groups, there is little question that the DVR of reptiles and birds is homologous as a telencephalic neural center. In contrast, the telencephalon in living mammals does not appear to have a DVR. It has been suggested, however, that their predecessors did have such a ridge, and that its cells migrated to the surface of the telencephalon during development to form part of the cerebral cortices which characterize all living mammals (Karten, 1969, 1991)[http://icb.oxfordjournals.org/content/42/4/743.full]
Changes for: compound cell cluster organ
- Added
- + compound cell cluster organ SubClassOf composed primarily of some cell cluster organ
Changes for: vasculature of eye
- Deleted
- - vasculature of eye SubClassOf neural crest-derived structure
Changes for: subfornical organ
- Added
Changes for: biliary tree
- Deleted
- - biliary tree database cross reference GAID:279
- - biliary tree database cross reference MA:0001273
- - biliary tree database cross reference MESH:A03.159
- - biliary tree database cross reference http://ncicb.nci.nih.gov/xml/owl/EVS/Biliary_Tract
- - biliary tree definition Hollow tree organ, the organ parts of which consists of the bile ducts[FMA]. { database cross reference=http://en.wikipedia.org/wiki/Biliary_tract , database cross reference=FMA:14665 }
- - biliary tree has exact synonym biliary tract
- Added
- + biliary tree EquivalentTo organ and part of some biliary system and composed primarily of some bile duct
- + biliary tree SubClassOf composed primarily of some bile duct
- + biliary tree SubClassOf has part some extrahepatic bile duct
- + biliary tree SubClassOf has part some interlobular bile duct
- + biliary tree SubClassOf has part some intralobular bile duct
- + biliary tree comment The path in many species is as follows: Bile canaliculi -> Canals of Hering (intralobar bile duct) -> interlobular bile ducts -> intrahepatic bile ducts -> left and right hepatic ducts merge to form -> common hepatic duct exits liver and joins -> cystic duct (from gall bladder) forming -> common bile duct -> joins with pancreatic duct -> forming ampulla of Vater -> enters duodenum [WP]
- + biliary tree definition A complex network of conduits that begins with the canals of Hering (intralobar bile duct) and progressively merges into a system of interlobular, septal, and major ducts which then coalesce to form the extrahepatic bile ducts, which finally deliver bile to the intestine, and in some species to the gallbladder. { database cross reference=http://dx.doi.org/10.1002/ar.20664 }
- + biliary tree has related synonym biliary tract { database cross reference=MA:0001273 }
Changes for: portal lobule
- Deleted
- - portal lobule SubClassOf organ part
- Added
- + portal lobule SubClassOf lobule
Changes for: fontanelle
- Deleted
- - fontanelle SubClassOf anatomical cluster
- Added
- + fontanelle SubClassOf anatomical junction
Changes for: cell group
- Deleted
- - cell group SubClassOf anatomical group
- Added
- + cell group SubClassOf anatomical structure
Changes for: caudal-fin organ
- Deleted
- - caudal-fin organ has exact synonym caudal organ { database cross reference=TAO:0002125 }
- - caudal-fin organ has exact synonym glandular organ { database cross reference=TAO:0002125 }
- Added
- + caudal-fin organ has broad synonym caudal organ { database cross reference=TAO:0002125 }
- + caudal-fin organ has broad synonym glandular organ { database cross reference=TAO:0002125 }
Changes for: branchiostegal ray series
- Deleted
Changes for: epibranchial series
- Deleted
Changes for: ceratobranchial series
- Deleted
Changes for: commissure of telencephalon
- Deleted
Changes for: ventral funiculus of spinal cord
- Deleted
- - ventral funiculus of spinal cord SubClassOf lateral structure
Changes for: ciliary processes
- Deleted
- - ciliary processes SubClassOf neural crest-derived structure
- Added
- + ciliary processes SubClassOf ectoderm-derived structure
Changes for: gray matter of hindbrain
- Deleted
Changes for: endocardium
- Added
- + endocardium SubClassOf heart endothelium
Changes for: white matter of hindbrain
- Deleted
Changes for: musculature
- Deleted
- - musculature SubClassOf anatomical group
- - musculature definition A subdivision of the muscular system. { database cross reference=http://en.wikipedia.org/wiki/Muscular_system , database cross reference=https://orcid.org/0000-0002-6601-2165 }
- Added
- + musculature SubClassOf composed primarily of some muscle organ
- + musculature SubClassOf organ system subdivision
- + musculature definition A subdivision of the muscular system corresponding to a subdisivision of an organism. { database cross reference=http://en.wikipedia.org/wiki/Muscular_system , database cross reference=https://orcid.org/0000-0002-6601-2165 }
Changes for: central nervous system
- Deleted
- - central nervous system SubClassOf ectoderm-derived structure
Changes for: gall bladder
- Deleted
- - gall bladder SubClassOf part of some biliary tree
- Added
- + gall bladder SubClassOf part of some hepatobiliary system
Changes for: thymus lobule
- Deleted
- - lobule of thymus SubClassOf organ part
- - lobule of thymus definition The basic structural unit of the thymus. { database cross reference=MP:0002367 }
- - lobule of thymus editor note This class was created automatically from a combination of ontologies
- - lobule of thymus label lobule of thymus
- Added
- + thymus lobule EquivalentTo lobule and part of some thymus
- + thymus lobule SubClassOf lobule
- + thymus lobule has exact synonym lobule of thymus { database cross reference=FMA:72215 }
- + thymus lobule label thymus lobule
Changes for: chordate pharynx
- Added
- + chordate pharynx comment Consider generalizing to deuterostome pharynx
Changes for: nail plate
- Deleted
- - nail plate SubClassOf acellular anatomical structure
- Added
- + nail plate SubClassOf integumentary system layer
- + nail plate SubClassOf part of some skin epidermis
Changes for: neural tube
- Deleted
- - neural tube SubClassOf developing epithelial placode
Changes for: liver
- Deleted
- Added
- + liver function notes secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO].
Changes for: pair of nares
- Deleted
- - pair of nares SubClassOf anatomical cluster
- - pair of nares SubClassOf ectoderm-derived structure
- Added
- + pair of nares SubClassOf anatomical collection
Changes for: mushroom body
- Deleted
- - mushroom body SubClassOf anatomical group
- - mushroom body SubClassOf ectoderm-derived structure
- Added
- + mushroom body SubClassOf anatomical cluster
Changes for: hypopharynx
- Deleted
- - hypopharynx SubClassOf endoderm-derived structure
Changes for: neuromuscular junction
- Deleted
- - neuromuscular junction SubClassOf anatomical cluster
- Added
- + neuromuscular junction SubClassOf cell part
Changes for: sheath of Schwann
- Deleted
- - neurilemma SubClassOf neural tissue
- - neurilemma SubClassOf part of some nervous system
- - neurilemma database cross reference FBbt:00005151
- - neurilemma definition thin membranous sheath around a nerve fiber[TFD]. { database cross reference=http://en.wikipedia.org/wiki/Neurilemma , database cross reference=http://www.thefreedictionary.com/neurolemma }
- - neurilemma label neurilemma
- Added
- + sheath of Schwann SubClassOf cell layer
- + sheath of Schwann SubClassOf part of some peripheral nervous system
- + sheath of Schwann SubClassOf structure with developmental contribution from neural crest
- + sheath of Schwann definition The outermost nucleated cytoplasmic layer of Schwann cells that surrounds the axon of the neuron. It forms the outermost layer of the nerve fiber in the peripheral nervous system. The neurolemma is underlain by the basal lamina (referred to as the medullary sheath in the included illustrations. In CNS, axons are myelinated by oligodendrocytes, thus lack neurolemma. { database cross reference=http://en.wikipedia.org/wiki/Neurolemma }
- + sheath of Schwann has exact synonym neurilemma { database cross reference=FMA:62976 }
- + sheath of Schwann label sheath of Schwann
Changes for: endocardium of ventricle
- Deleted
- - endocardium of ventricle SubClassOf meso-epithelium
- - endocardium of ventricle SubClassOf simple squamous epithelium
Changes for: epidermis suprabasal layer
- Deleted
- - epidermis suprabasal layer SubClassOf adjacent to some stratum basale of epidermis
- - epidermis suprabasal layer definition the suprabasal layer of the epidermis { database cross reference=MP:0001233,PMID:10469309 }
- Added
- + epidermis suprabasal layer EquivalentTo integumentary system layer and part of some skin epidermis and superficial to some stratum basale of epidermis
- + epidermis suprabasal layer SubClassOf superficial to some stratum basale of epidermis
- + epidermis suprabasal layer definition Any layer of the epidermis that is superior to the stratum basale { database cross reference=UBERON:cjm,MP:0001233,PMID:10469309 }
Changes for: meckelian bone
- Deleted
- - meckelian bone SubClassOf endoderm-derived structure
Changes for: ventral pancreatic duct
- Deleted
- - ventral pancreatic duct SubClassOf bile duct
Changes for: pedicle of vertebra
- Added
- + pedicle of vertebra SubClassOf part of some neural arch
Changes for: velar vocal fold
- Deleted
- - velar vocal fold SubClassOf lateral structure
Changes for: genu of facial nerve
- Deleted
Changes for: cerebellopontine angle
- Deleted
- - cerebellopontine angle SubClassOf ectoderm-derived structure
Changes for: feather vane
- Deleted
- - feather vane SubClassOf ectoderm-derived structure
Changes for: aboral subdivision of organism
- Deleted
- - aboral surface has exact synonym abactinal side
- - aboral surface has exact synonym abactinal surface
- - aboral surface label aboral surface
- Added
- + aboral subdivision of organism SubClassOf aboral to some oral subdivision of organism
- + aboral subdivision of organism definition A major subdivision of an organism that is the entire side of the organism aboral to the plane that divides the organism in two, perpendicular to the oral-aboral axiom. { database cross reference=BSPO:0000198 }
- + aboral subdivision of organism has related synonym abactinal side
- + aboral subdivision of organism has related synonym abactinal subdivision
- + aboral subdivision of organism has related synonym abactinal surface
- + aboral subdivision of organism has related synonym aboral side
- + aboral subdivision of organism has related synonym aboral side of organism
- + aboral subdivision of organism has related synonym aboral subdivision
- + aboral subdivision of organism label aboral subdivision of organism
- + aboral subdivision of organism present in taxon http://purl.obolibrary.org/obo/NCBITaxon_7588
Changes for: oral subdivision of organism
- Deleted
- - oral surface has exact synonym actinal side
- - oral surface has exact synonym actinal surface
- - oral surface label oral surface
- Added
- + oral subdivision of organism SubClassOf has part some oral opening
- + oral subdivision of organism definition A major subdivision of an organism that is the entire side of the organism oral to the plane that divides the organism in two, perpendicular to the oral-aboral axiom. { database cross reference=BSPO:0000198 }
- + oral subdivision of organism has related synonym actinal side
- + oral subdivision of organism has related synonym actinal subdivision
- + oral subdivision of organism has related synonym actinal surface
- + oral subdivision of organism has related synonym oral side
- + oral subdivision of organism has related synonym oral side of organism
- + oral subdivision of organism has related synonym oral subdivision
- + oral subdivision of organism label oral subdivision of organism
- + oral subdivision of organism present in taxon http://purl.obolibrary.org/obo/NCBITaxon_7588
Changes for: lymphocyte domain
- Deleted
- - lymphocyte domain SubClassOf anatomical cluster
- Added
- + lymphocyte domain SubClassOf cell cluster organ
- + lymphocyte domain SubClassOf immune organ
Changes for: enteric nerve
- Deleted
- - enteric nerve SubClassOf neural crest-derived structure
Changes for: Peyer’s patch T cell area
- Added
- + Peyer’s patch T cell area SubClassOf digestive system element
Changes for: dorsal nerve of clitoris
- Deleted
- - dorsal nerve of clitoris SubClassOf reproductive structure
Changes for: dorsal nerve of penis
- Deleted
- - dorsal nerve of penis SubClassOf reproductive structure
Changes for: orbitosphenoid
- Deleted
- - orbitosphenoid SubClassOf lateral structure
Changes for: cerebellar peduncular complex
- Deleted
- - cerebellar peduncular complex SubClassOf anatomical cluster
- - cerebellar peduncular complex SubClassOf ectoderm-derived structure
- Added
Changes for: epicranium
- Deleted
- - epicranium SubClassOf anatomical cluster
- Added
- + epicranium SubClassOf multi organ part structure
Changes for: helix
- Deleted
- Added
- + helix database cross reference http://en.wikipedia.org/wiki/Helix_(ear)
- + helix definition The helix is the prominent rim of the pinna. { database cross reference=http://en.wikipedia.org/wiki/Helix }
Changes for: glottis
- Deleted
- - glottis SubClassOf endoderm-derived structure
Changes for: trabecular bone tissue
- Added
- + trabecular bone tissue EquivalentTo bone tissue and has part some trabecular network of bone
- + trabecular bone tissue SubClassOf has part some trabecular network of bone
Changes for: bone tissue
- Added
- + bone tissue database cross reference XAO:0004040
- + bone tissue editor note see https://github.com/obophenotype/uberon/issues/27
- + bone tissue has narrow synonym mineralized bone tissue { database cross reference=XAO:0004040 }
Changes for: pulmonary lobule
- Added
- + pulmonary lobule SubClassOf has part some terminal bronchiole
Changes for: gustatory gland
- Added
- + gustatory gland function notes posterior deep lingual glands produce lingual lipase, which hydrolyzes triacylglycerols in the acidic gastric lumen, the first step in the digestion of dietary fat (Hamosh & Scow, 1973; Hamosh & Burns, 1977). In view of their close proximity to the lingual lymphatic tissues, the glands were also thought to be involved in antimicrobial action and local immune response (Nair & Schroeder, 1983)[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2667924/]
- + gustatory gland has exact synonym posterior deep lingual gland { database cross reference=http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2667924 }
- + gustatory gland structure notes a group of tubulo-acinar serous glands located beneath the circumvallate and foliate papillae of the tongue and their ducts open into the trough at the base of the papillae. The saliva from posterior deep lingual glands is known to modulate the microenvironment at taste reception sites, and affect chemoreception (Gurkan & Bradley, 1988) and it is an important source of growth factors for taste receptor cells (Morris-Wiman et al. 2000)[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2667924/]
Changes for: pyramidal layer of CA2
- Added
- + pyramidal layer of CA2 SubClassOf neural tissue
Changes for: white matter lamina of cerebellum
- Deleted
Changes for: white matter lamina of cerebral hemisphere
- Deleted
Changes for: superficial cervical fascia
- Added
- + superficial cervical fascia SubClassOf composed primarily of some connective tissue
Changes for: synarcual region of vertebral column
- Deleted
- - synarcual region of vertebral column EquivalentTo subdivision of vertebral column and subdivision of some synarcual region
- - synarcual region of vertebral column SubClassOf subdivision of some synarcual region
Changes for: layer of hippocampal field
- Deleted
- - layer of hippocampal field SubClassOf organ component layer
- Added
- + layer of hippocampal field SubClassOf cell layer
Changes for: integumental system
- Deleted
- - integumental system definition An organ system that protects the body from damage, forming the bounding layer of the organism and comprising the outer epithelial layer and any associated adnexa. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle. { database cross reference=http://orcid.org/0000-0002-6601-2165 }
- Added
- + integumental system definition Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle. { database cross reference=http://orcid.org/0000-0002-6601-2165 , database cross reference=CARO:0002001 }
Changes for: hepatobiliary system
- Deleted
- - hepatobiliary system SubClassOf anatomical system
- - hepatobiliary system definition The hepaticobiliary system is responsible for metabolic and catabolic processing of small molecules absorbed from the blood or gut, hormones and serum proteins, detoxification, storage of glycogen, triglycerides, metals and lipid soluble vitamins and excretion of bile. Included are the synthesis of albumin, blood coagulation factors, complement, and specific binding proteins. The parts are: liver, bile duct, gall bladder and hepatic duct { database cross reference=http://en.wikipedia.org/wiki/Hepatobiliary_system , database cross reference=GO:0061008 }
- Added
- + hepatobiliary system SubClassOf has part some biliary system
- + hepatobiliary system SubClassOf has part some liver
- + hepatobiliary system SubClassOf organ system subdivision
- + hepatobiliary system definition The part of the digestive system that contains the liver and the biliary system { database cross reference=UBERON:cjm }
- + hepatobiliary system function notes The hepaticobiliary system is responsible for metabolic and catabolic processing of small molecules absorbed from the blood or gut, hormones and serum proteins, detoxification, storage of glycogen, triglycerides, metals and lipid soluble vitamins and excretion of bile. Included are the synthesis of albumin, blood coagulation factors, complement, and specific binding proteins. The parts are: liver, bile duct, gall bladder and hepatic duct [GO:0061008]
Changes for: pituitary stalk
- Added
- + pituitary stalk database cross reference BAMS:InfS
- + pituitary stalk database cross reference DHBA:10643
- + pituitary stalk database cross reference HBA:9358
- + pituitary stalk database cross reference UMLS:C0175325 { source=NIFSTD:birnlex_1248 }
- + pituitary stalk database cross reference UMLS:C0447641 { source=NIFSTD:birnlex_1248 }
- + pituitary stalk database cross reference http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=405
- + pituitary stalk database cross reference http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=405 { source=NIFSTD:birnlex_1248 }
- + pituitary stalk database cross reference http://linkedlifedata.com/resource/umls/id/C0175325
- + pituitary stalk database cross reference http://uri.neuinfo.org/nif/nifstd/birnlex_1248
- + pituitary stalk database cross reference http://www.snomedbrowser.com/Codes/Details/425300001
- + pituitary stalk has alternative id UBERON:0014606
- + pituitary stalk has broad synonym InfS { database cross reference=http://uri.neuinfo.org/nif/nifstd/birnlex_1248 , database cross reference=NIFSTD:NeuroNames_abbrevSource , has synonym type=abbreviation }
- + pituitary stalk has exact synonym infundibular stalk { database cross reference=NIFSTD:birnlex_1248 }
- + pituitary stalk has exact synonym infundibular stem of neurohypophysis { database cross reference=NIFSTD:birnlex_1248 }
- + pituitary stalk has exact synonym infundibular stem { database cross reference=NIFSTD:birnlex_1248 , has synonym type=preferred term when talking about an instance of this class in Homo sapiens }
- + pituitary stalk has exact synonym pituitary infundibular stalk
- + pituitary stalk has related synonym hypophyseal infundibulum { database cross reference=NIFSTD:birnlex_1248 }
- + pituitary stalk has related synonym infundibulum of posterior lobe of pituitary gland { database cross reference=NIFSTD:birnlex_1248 }
Changes for: lateral hypothalamic area
- Deleted
- - lateral hypothalamic area SubClassOf anatomical cluster
- - lateral hypothalamic area SubClassOf ectoderm-derived structure
- Added
- + lateral hypothalamic area SubClassOf regional part of brain
Changes for: palatine gland
- Added
- + palatine gland SubClassOf mucous gland
- + palatine gland has exact synonym palatine mucuous gland
Changes for: endometrial gland
- Added
- + endometrial gland SubClassOf mucous gland
- + endometrial gland has exact synonym endometrial mucuous gland
Changes for: lymphoid system
- Deleted
- - lymphoid system SubClassOf anatomical cluster
- Added
- + lymphoid system SubClassOf organ system subdivision
Changes for: lamina of omasum
- Deleted
- - omasal lamina definition A muscular sheet of the omasum consisting of two lateral layers and an intermediate layer of smooth muscle covered with non-glandular stratified squamous epithelium
- - omasal lamina label omasal lamina
- Added
- + lamina of omasum EquivalentTo organ component layer and part of some omasum and has part some non-glandular epithelium and has part some layer of smooth muscle tissue
- + lamina of omasum SubClassOf has part some layer of smooth muscle tissue
- + lamina of omasum SubClassOf has part some non-glandular epithelium
- + lamina of omasum definition A muscular sheet of the omasum wall consisting of two lateral layers and an intermediate layer of smooth muscle covered with non-glandular stratified squamous epithelium { database cross reference=http://www.ncbi.nlm.nih.gov/pubmed/7978351 , database cross reference=UBERON:cjm }
- + lamina of omasum has exact synonym omasal lamina
- + lamina of omasum label lamina of omasum
Changes for: iris epithelium
- Deleted
- - iris epithelium SubClassOf neural crest-derived structure
Changes for: zygomatic arch
- Deleted
- - zygomatic arch SubClassOf lateral structure
Changes for: layer of sclera
- Deleted
- - layer of sclera SubClassOf organ part
- Added
- + layer of sclera SubClassOf organ component layer
Changes for: axilla
- Deleted
- - axilla SubClassOf organism subdivision
- Added
- + axilla SubClassOf external soft tissue zone
Changes for: placental labyrinth vasculature
- Deleted
- - placental labyrinth vasculature SubClassOf extraembryonic structure
- - placental labyrinth vasculature SubClassOf reproductive structure
Changes for: ventral surface of penis
- Deleted
- - ventral surface of penis SubClassOf organism subdivision
- - ventral surface of penis SubClassOf reproductive structure
- Added
- + ventral surface of penis EquivalentTo anatomical surface and in ventral side of some penis
- + ventral surface of penis SubClassOf anatomical surface
Changes for: operculum of brain
- Deleted
Changes for: hyoid apparatus
- Deleted
- - hyoid apparatus SubClassOf endoderm-derived structure
- - hyoid apparatus SubClassOf structure with developmental contribution from neural crest
Changes for: midbrain basal plate
- Deleted
- - midbrain basal plate SubClassOf embryonic structure
Changes for: Hassall’s corpuscle
- Deleted
- - Hassall’s corpuscle SubClassOf organ part
- Added
- + Hassall’s corpuscle SubClassOf cell cluster
- + Hassall’s corpuscle database cross reference http://en.wikipedia.org/wiki/Hassall’s_corpuscles
- + Hassall’s corpuscle has exact synonym capsule of Hassal’s corpuscle { database cross reference=UBERON:cjm }
- + Hassall’s corpuscle has exact synonym thymic corpuscle
Changes for: row of feathers
- Deleted
- - row of feathers SubClassOf anatomical cluster
- - row of feathers SubClassOf composed primarily of some feather
- Added
- + row of feathers EquivalentTo anatomical row and has member some feather
- + row of feathers SubClassOf anatomical row
- + row of feathers SubClassOf collection of feathers
- + row of feathers SubClassOf has member some feather
Changes for: merocrine gland
- Deleted
- - merocrine gland definition An exocrine gland whose secretions are excreted via exocytosis from secretory cells into an epithelial-walled duct or ducts and thence onto a bodily surface or into the lumen; the gland releases its product and no part of the gland is lost or damaged. { database cross reference=http://en.wikipedia.org/wiki/Merocrine , database cross reference=MGI:anna }
- Added
- + merocrine gland definition An exocrine gland whose secretions are excreted via exocytosis from secretory cells into an epithelial-walled duct or ducts and thence onto a bodily surface or into the lumen; the gland releases its product and no part of the gland is lost or damaged. { database cross reference=http://en.wikipedia.org/wiki/Merocrine , database cross reference=MGI:anna , database cross reference=MP:0013544 }
Changes for: aqueous drainage system
- Deleted
- - aqueous drainage system SubClassOf neural crest-derived structure
- Added
- + aqueous drainage system SubClassOf ectoderm-derived structure
Changes for: Bruch’s membrane
- Deleted
- - Bruch’s membrane SubClassOf cell layer
- - Bruch’s membrane definition A transparent, nearly structureless innermost layer of the choroid in contact with the pigmented layer of the retina. Bruch’s membrane consists of five layers (from inside to outside): 1. the basement membrane of the retinal pigment epithelium; 2. the inner collagenous zone; 3. a central band of elastic fibers; 4. the outer collagenous zone; 5. the basement membrane of the choriocapillaris. The retinal pigment epithelium transports metabolic waste from the photoreceptors across Bruch’s membrane to the choroid. { database cross reference=http://en.wikipedia.org/wiki/Bruch’s_membrane , database cross reference=MP:0005239 }
- - Bruch’s membrane has exact synonym basal lamina of choroid { database cross reference=FMA:58438 }
- Added
- + Bruch’s membrane SubClassOf acellular anatomical structure
- + Bruch’s membrane definition A transparent, nearly structureless innermost layer of the choroid in contact with the pigmented layer of the retina. { database cross reference=MP:0005239 }
- + Bruch’s membrane development notes Bruch’s membrane is present by midterm in fetal development as an elastic sheet.
- + Bruch’s membrane has related synonym basal lamina of choroid { database cross reference=FMA:58438 }
- + Bruch’s membrane structure notes Bruch’s membrane consists of five layers (from inside to outside): 1. the basement membrane of the retinal pigment epithelium; 2. the inner collagenous zone; 3. a central band of elastic fibers; 4. the outer collagenous zone; 5. the basement membrane of the choriocapillaris. The retinal pigment epithelium transports metabolic waste from the photoreceptors across Bruch’s membrane to the choroid[WP]
Changes for: caudal principal ray set
- Deleted
Changes for: photoreceptor inner segment layer
- Deleted
- - photoreceptor inner segment layer SubClassOf ectoderm-derived structure
- - photoreceptor inner segment layer SubClassOf tissue
- Added
- + photoreceptor inner segment layer SubClassOf layer of retina
Changes for: photoreceptor outer segment layer
- Deleted
- - photoreceptor outer segment layer SubClassOf ectoderm-derived structure
- - photoreceptor outer segment layer SubClassOf tissue
- Added
- + photoreceptor outer segment layer SubClassOf layer of retina
Changes for: digestive tract epithelium
- Deleted
- - gut epithelium definition An epithelium that is part of a digestive tract [Automatically generated definition]. { database cross reference=OBOL:automatic }
- - gut epithelium has exact synonym digestive tract epithelium { database cross reference=OBOL:automatic }
- - gut epithelium has exact synonym epithelial tissue of lower gastrointestinal tract { database cross reference=OBOL:automatic }
- - gut epithelium has exact synonym epithelium of lower gastrointestinal tract { database cross reference=OBOL:automatic }
- - gut epithelium has exact synonym lower gastrointestinal tract epithelial tissue { database cross reference=OBOL:automatic }
- - gut epithelium has exact synonym lower gastrointestinal tract epithelium { database cross reference=OBOL:automatic }
- - gut epithelium label gut epithelium
- Added
- + digestive tract epithelium comment Taxon notes:
- + digestive tract epithelium definition An epithelium that lines the lumen of the digestive tract. { database cross reference=UBERON:cjm }
- + digestive tract epithelium has exact synonym gastrodermis { database cross reference=BGEE:ANN , database cross reference=NCBITaxon:6073 , has synonym type=taxonomic disambiguation }
- + digestive tract epithelium has exact synonym gut epithelium { database cross reference=EHDAA2:0004567 , database cross reference=MA:0003201 , database cross reference=ZFA:0005123 }
- + digestive tract epithelium has related synonym alimentary tract epithelium { database cross reference=OBOL:automatic }
- + digestive tract epithelium label digestive tract epithelium
Changes for: laryngeal apparatus
- Deleted
- - laryngeal apparatus SubClassOf anatomical cluster
- Added
- + laryngeal apparatus SubClassOf multi organ part structure
Changes for: subdivision of tube
- Added
- + subdivision of tube SubClassOf has part some anatomical wall
Changes for: meninx
- Deleted
- - meninx editor note consider separate term for meninges aka collection of meninges. Note in EHDAA2 pia mater etc are part of the meninges. Also consider a new class for primary/primitive meninx.
- Added
- + meninx SubClassOf composed primarily of some connective tissue
Changes for: pia mater
- Added
- + pia mater SubClassOf composed primarily of some loose connective tissue
Changes for: atrioventricular canal endocardium
- Deleted
- - atrioventricular canal endocardium SubClassOf embryonic structure
- Added
- + atrioventricular canal endocardium SubClassOf embryonic tissue
Changes for: dura mater
- Deleted
- - dura mater external ontology notes in ncit this is divided into periosteal layer and meningeal layer { external ontology=ncit }
- Added
- + dura mater SubClassOf composed primarily of some dense connective tissue
Changes for: hyolaryngeal complex
- Deleted
Changes for: epithelial tube
- Deleted
- - epithelial tube external ontology notes In EHDAA2, the developing spinal cord is classified as an epithelial tube { external ontology=EHDAA2 }
Changes for: maxilla
- Deleted
- - maxilla SubClassOf lateral structure
Changes for: bile duct
- Deleted
- - bile duct EquivalentTo duct and channel for some bile
- - bile duct SubClassOf part of some biliary system
- - bile duct comment The path is as follows: Bile canaliculi → Canals of Hering → interlobular bile ducts → intrahepatic bile ducts → left and right hepatic ducts merge to form → common hepatic duct exits liver and joins → cystic duct (from gall bladder) forming → common bile duct → joins with pancreatic duct → forming ampulla of Vater → enters duodenum [WP]
- - bile duct definition Duct that carries bile from the liver to the small intestine. { database cross reference=http://en.wikipedia.org/wiki/Bile_duct , database cross reference=ZFA:0001100 }
- - bile duct has related synonym hepatic duct
- Added
- + bile duct EquivalentTo duct and part of some biliary tree
- + bile duct database cross reference TAO:0001100
- + bile duct database cross reference ZFA:0001100
- + bile duct definition Any of the ducts that form the biliary tree, carrying bile from the liver to the small intestine. { database cross reference=http://en.wikipedia.org/wiki/Bile_duct , database cross reference=UBERON:cjm }
- + bile duct external definition A duct that carries bile from the liver to the intestine. { source=ZFA:0001100, ZFA:curator }
- + bile duct external ontology notes we place the ZFA class here as this fits its textual definition and child nodes. We may recommend a label change for ZFA { external ontology=ZFA }
- + bile duct has related synonym hepatic duct { database cross reference=ZFA:0001100 , has synonym type=indicates that a synonym is used in an inconsistent or confusing way, typically between species }
Changes for: astragalus-calcaneum unit
- Deleted
- - astragalus-calcaneum unit SubClassOf mesoderm-derived structure
Changes for: layer of neocortex
- Deleted
- - layer of neocortex EquivalentTo organ component layer and part of some neocortex
- - layer of neocortex SubClassOf ectoderm-derived structure
- - layer of neocortex SubClassOf organ component layer
- - layer of neocortex SubClassOf structure with developmental contribution from neural crest
- - layer of neocortex definition A organ component layer that is part of a neocortex. { database cross reference=OBOL:automatic }
- Added
- + layer of neocortex EquivalentTo nervous system cell part layer and part of some neocortex
- + layer of neocortex SubClassOf central nervous system cell part cluster
- + layer of neocortex SubClassOf nervous system cell part layer
- + layer of neocortex definition One of the layers of the neocortex. { database cross reference=UBERON:cjm }
Changes for: layer of hippocampus
- Deleted
Changes for: layer of dentate gyrus
- Deleted
- - layer of dentate gyrus SubClassOf structure with developmental contribution from neural crest
- - layer of dentate gyrus definition A central nervous system gray matter layer that is part of a dentate gyrus of hippocampal formation. { database cross reference=OBOL:automatic }
- - layer of dentate gyrus editor note This class was created automatically from a combination of ontologies
- Added
- + layer of dentate gyrus definition One of the three layers of the dentate gyrus of the hippocampal formation. { database cross reference=http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2492885/ , database cross reference=UBERON:cjm }
- + layer of dentate gyrus has exact synonym dentate gyrus cell layer
- + layer of dentate gyrus taxon notes the basic trilaminar structure of the dentate gyrus is common across all species studied, with relatively minimal phylogenetic variation[PMC2492885]
Changes for: myocardium
- Added
- + myocardium EquivalentTo heart layer and composed primarily of some cardiac muscle tissue
Changes for: hippocampus fimbria
- Deleted
Changes for: white matter of cerebellum
- Deleted
Changes for: costal plate of carapace
- Deleted
- - costal plate of carapace SubClassOf lateral structure
Changes for: hyoplastron
- Deleted
- - hyoplastron SubClassOf lateral structure
Changes for: hypothenar eminence
- Deleted
- - hypothenar eminence SubClassOf organism subdivision
- Added
- + hypothenar eminence SubClassOf external soft tissue zone
Changes for: thenar eminence
- Deleted
- - thenar eminence SubClassOf organism subdivision
- Added
- + thenar eminence SubClassOf external soft tissue zone
Changes for: withers
- Deleted
- - withers SubClassOf organism subdivision
- - withers definition he ridge between the shoulder blades of a four-legged mammal. { database cross reference=http://en.wikipedia.org/wiki/Withers }
- Added
- + withers SubClassOf external soft tissue zone
- + withers definition The ridge between the shoulder blades of a four-legged mammal. { database cross reference=http://en.wikipedia.org/wiki/Withers }
Changes for: aortic system
- Deleted
- - aortic system SubClassOf anatomical group
- Added
- + aortic system SubClassOf organ system subdivision
Changes for: nutrient foramen artery
- Added
- + nutrient foramen artery SubClassOf supplies some bone element
Changes for: bulb of aorta
- Deleted
- - bulb of aorta SubClassOf anatomical cluster
- Added
- + bulb of aorta SubClassOf organ part
Changes for: sinotubular junction
- Deleted
- - sinotubular junction SubClassOf anatomical cluster
- Added
- + sinotubular junction SubClassOf anatomical junction
Changes for: nutrient foramen vein
- Added
- + nutrient foramen vein SubClassOf drains some bone element
Changes for: region of neural crest
- Deleted
- - region of neural crest SubClassOf anatomical group
- - region of neural crest SubClassOf ectoderm-derived structure
- - region of neural crest SubClassOf embryonic structure
- Added
- + region of neural crest SubClassOf anatomical cluster
Changes for: rumen papilla
- Deleted
- - rumen papilla SubClassOf stomach region
- Added
- + rumen papilla SubClassOf anatomical projection
Changes for: collection of hairs
- Deleted
- - collection of hairs EquivalentTo anatomical cluster and has member some strand of hair
- - collection of hairs SubClassOf anatomical cluster
- - collection of hairs SubClassOf structure with developmental contribution from neural crest
- Added
- + collection of hairs EquivalentTo anatomical collection and has member some strand of hair
- + collection of hairs SubClassOf anatomical collection
Changes for: neural tube lumen
- Added
- + neural tube lumen has narrow synonym prosencoel
- + neural tube lumen has related synonym central lumen
Changes for: pancreatic lobule
- Added
- + pancreatic lobule SubClassOf has part some intralobular duct
- + pancreatic lobule SubClassOf has part some pancreatic acinus
Changes for: infraorbital series
- Deleted
Changes for: stria vascularis vasculature
- Deleted
Changes for: pharyngeal vasculature
- Deleted
- - pharyngeal vasculature SubClassOf endoderm-derived structure
Changes for: auditory hillocks
- Deleted
- - auditory hillocks SubClassOf embryonic structure
Changes for: segmental spinal nerve
- Deleted
- - segmental spinal nerve SubClassOf neural crest-derived structure
Changes for: gall bladder primordium
- Deleted
- - gall bladder primordium SubClassOf part of some hepatobiliary system
- Added
- + gall bladder primordium EquivalentTo primordium and has potential to develop into some gall bladder
- + gall bladder primordium SubClassOf develops from some cystic duct
- + gall bladder primordium SubClassOf part of some biliary tree
- + gall bladder primordium definition A sac-like cavity ventral to the liver, lying in the sub-mesodermal space and closed by a thin sheet of ectodermal cells, from which the future gall bladder develops. { database cross reference=ISBN:0815318960 , database cross reference=XAO:0004205 }
Changes for: midline column
- Deleted
- - midline column SubClassOf ectoderm-derived structure
- - midline column SubClassOf structure with developmental contribution from neural crest
Changes for: scapula cartilage element
- Deleted
- - scapula cartilage element SubClassOf cartilaginous condensation
- - scapula cartilage element SubClassOf embryonic tissue
- Added
- + scapula cartilage element SubClassOf embryonic structure
Changes for: scapula pre-cartilage condensation
- Deleted
- - scapula pre-cartilage condensation SubClassOf developing mesenchymal structure
- - scapula pre-cartilage condensation SubClassOf part of some embryo
- - scapula pre-cartilage condensation SubClassOf pre-cartilage condensation
Changes for: hepatic duct
- Deleted
- - hepatic duct SubClassOf continuous with some liver
- - hepatic duct database cross reference EMAPA:18672
- - hepatic duct database cross reference TAO:0001100
- - hepatic duct database cross reference ZFA:0001100
- - hepatic duct definition The hepatic duct is the duct that leads from the liver to the bile duct[GO]. A duct that carries bile from the liver to the small intestine[ZFA]. { database cross reference=GO:0061011 }
- Added
- + hepatic duct SubClassOf connects some common bile duct
- + hepatic duct SubClassOf connects some liver
- + hepatic duct database cross reference FMA:71891
- + hepatic duct definition Any portion of the ducts that carry bile from the liver to the common bile duct. This may include both intrahapetic components (parts of left and right hepatic ducts) and extrahapetic components (common hepatic duct, plus hilar portion). { database cross reference=UBERON:cjm }
- + hepatic duct external definition A duct that carries bile from the liver to the small intestine[ZFA]. { source=ZFA:0001100 }
- + hepatic duct external definition The hepatic duct is the duct that leads from the liver to the bile duct[GO]. { source=GO:0061011 }
Changes for: late embryonic stage
- Deleted
- - late embryonic stage definition Am embryo stage that covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching. { database cross reference=BGEE:ANiknejad }
- Added
- + late embryonic stage definition An embryo stage that covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching. { database cross reference=BGEE:ANiknejad }
Changes for: osseus cochlea
- Deleted
- - osseus cochlea SubClassOf mesoderm-derived structure
- - osseus cochlea SubClassOf neural crest-derived structure
Changes for: hilum of inferior olivary complex
- Deleted
Changes for: olfactory bulb layer
- Deleted
Changes for: nuclear complex of neuraxis
- Deleted
- - nuclear complex of neuraxis definition Internal gray matter component which consists of an assemblage of nuclei of neuraxis. Example: cerebellar nuclear complex, Vestibular nuclear complex.[FMA] { database cross reference=FMA:84059 , database cross reference=FMA:FMA }
- - nuclear complex of neuraxis editor note TODO - move existing complex classes currently under nucleus to be under this class
- Added
- + nuclear complex of neuraxis EquivalentTo gray matter and composed primarily of some neural nucleus
- + nuclear complex of neuraxis database cross reference FMA:256381
- + nuclear complex of neuraxis definition Gray matter of the central nervous system which is a collection of clustered nuclei. { database cross reference=UBERON:cjm }
Changes for: tunica intima of vein
- Added
- + tunica intima of vein SubClassOf endothelium of vein
Changes for: superior colliculus superficial gray layer
- Added
Changes for: accessory nerve fiber bundle
- Deleted
Changes for: posterior column of fornix
- Deleted
Changes for: vagal nerve fiber bundle
- Deleted
Changes for: aqueous vein
- Deleted
- - aqueous vein SubClassOf neural crest-derived structure
- Added
- + aqueous vein SubClassOf ectoderm-derived structure
Changes for: mucosa of gallbladder
- Deleted
- - mucosa of gallbladder SubClassOf mucosa of biliary tree
- Added
- + mucosa of gallbladder SubClassOf endoderm-derived structure
- + mucosa of gallbladder SubClassOf mucosa
Changes for: canal of Schlemm
- Deleted
- - canal of Schlemm SubClassOf neural crest-derived structure
- Added
- + canal of Schlemm SubClassOf ectoderm-derived structure
Changes for: Weberian ossicle set
- Deleted
- - Weberian ossicle set SubClassOf mesoderm-derived structure
Changes for: periorbital region
- Deleted
- - periorbital region SubClassOf anatomical cluster
- Added
- + periorbital region SubClassOf multi organ part structure
Changes for: neural tube marginal layer
- Deleted
- - neural tube marginal layer SubClassOf ectoderm-derived structure
- - neural tube marginal layer SubClassOf embryonic structure
Changes for: biliary ductule
- Added
- + biliary ductule has related synonym terminal cholangiole { database cross reference=UBERON:cjm }
Changes for: subungual region
- Deleted
- - subungual region SubClassOf ectoderm-derived structure
Changes for: anatomical conduit
- Deleted
- - anatomical conduit SubClassOf anatomical cluster
- Added
- + anatomical conduit SubClassOf multicellular anatomical structure
Changes for: myocardial layer
- Deleted
- - myocardial layer definition An organ component layer that is part of a myocardium. { database cross reference=OBOL:automatic }
- Added
- + myocardial layer definition Any of the layers of the myocardium. Example: compact layer, trabecular layer. { database cross reference=UBERON:cjm }
- + myocardial layer in subset non informative
Changes for: myocardium trabecular layer
- Added
- + myocardium trabecular layer SubClassOf adjacent to some endocardium
Changes for: myocardial compact layer
- Added
- + myocardial compact layer has exact synonym compact subepicardial layer { database cross reference=MP:0004056 }
- + myocardial compact layer has exact synonym heart compact layer { database cross reference=MP:0004056 }
- + myocardial compact layer has exact synonym myocardial compact layer { database cross reference=MP:0004056 }
- + myocardial compact layer has exact synonym subepicardial layer { database cross reference=MP:0004056 }
- + myocardial compact layer has exact synonym subepicardium { database cross reference=MP:0004056 }
- + myocardial compact layer has related synonym compact subepicardial myocardium { database cross reference=MP:0004056 }
- + myocardial compact layer has related synonym subepicardium layer { database cross reference=MP:0004056 }
Changes for: stroma of bone marrow
- Deleted
- - stroma of bone marrow SubClassOf connective tissue
- Added
- + stroma of bone marrow EquivalentTo stroma and part of some bone marrow
- + stroma of bone marrow SubClassOf has part some sinusoid
- + stroma of bone marrow SubClassOf has part some yellow bone marrow
- + stroma of bone marrow SubClassOf stroma
Changes for: external acoustic meatus osseus part
- Deleted
- - external acoustic meatus osseus part SubClassOf anatomical cluster
- Added
Changes for: renal glomerulus vasculature
- Deleted
- - renal glomerulus vasculature SubClassOf mesoderm-derived structure
Changes for: mammary gland cord
- Added
- + mammary gland cord SubClassOf develops from some mammary bud
- + mammary gland cord has exact synonym lactiferous gland cord
- + mammary gland cord has exact synonym mammary cord
- + mammary gland cord has related synonym mammary sprout
Changes for: prostate glandular acinus
- Deleted
- - prostate glandular acinus comment Concurrent with branching morphogenesis, the solid cords of epithelium formed by budding arborize and differentiate postnatally into glandular acin. The basic prostate architecture is established by puberty and acquires secretory function thereafter[PMID:18977204]
- Added
- + prostate glandular acinus development notes Concurrent with branching morphogenesis, the solid cords of epithelium formed by budding arborize and differentiate postnatally into glandular acin. The basic prostate architecture is established by puberty and acquires secretory function thereafter[PMID:18977204]
- + prostate glandular acinus editor note the muscle layer is implicitly treated as outside the acinus
Changes for: medulla reticulospinal tract
- Deleted
Changes for: pons reticulospinal tract
- Deleted
Changes for: cerebellar layer
- Deleted
Changes for: branchiomeric muscle
- Added
- + branchiomeric muscle has exact synonym branchial head muscle { database cross reference=XAO:0004325 }
- + branchiomeric muscle taxon notes It has been hypothesized that Haikouella must have been powered by branchiomeric muscles, as in living craniates, rather than by water moving through the pharynx via ciliary currents, as in lancelets[http://icb.oxfordjournals.org/content/42/4/743.full]
Changes for: iris smooth muscle
- Deleted
- - iris smooth muscle SubClassOf neural crest-derived structure
Changes for: muscular coat of vas deferens
- Added
Changes for: postcranial axial skeleton
- Deleted
- - postcranial axial skeleton SubClassOf mesoderm-derived structure
Changes for: skin of body
- Deleted
- - skin of body SubClassOf has part some dermis
- - skin of body SubClassOf has part some skin epidermis
Changes for: stratum lucidum of epidermis
- Deleted
- - stratum lucidum of epidermis SubClassOf adjacent to some stratum corneum of epidermis
- - stratum lucidum of epidermis SubClassOf adjacent to some stratum granulosum of epidermis
- Added
- + stratum lucidum of epidermis SubClassOf immediately deep to some stratum corneum of epidermis
- + stratum lucidum of epidermis SubClassOf immediately superficial to some stratum granulosum of epidermis
Changes for: levator veli palatini
- Deleted
- - levator veli palatini SubClassOf lateral structure
Changes for: tensor veli palatini
- Deleted
- - tensor veli palatini SubClassOf lateral structure
Changes for: external ear margin
- Deleted
- - external ear margin SubClassOf subdivision of head
- - external ear margin definition Subdivision of the head consisting of the area along the edge of the external ear. { database cross reference=UBERON:EJS }
- Added
- + external ear margin SubClassOf anatomical junction
- + external ear margin definition Anatomical junction consisting of the area along the edge of the external ear. { database cross reference=UBERON:EJS }
Changes for: labial commissure
- Deleted
- - labial commissure SubClassOf subdivision of head
- Added
- + labial commissure SubClassOf external soft tissue zone
Changes for: nose anterior margin
- Deleted
- - nose anterior margin SubClassOf subdivision of head
- Added
- + nose anterior margin SubClassOf external soft tissue zone
Changes for: nose vertex
- Deleted
- - nose vertex SubClassOf subdivision of head
- Added
- + nose vertex SubClassOf external soft tissue zone
Changes for: tip of snout
- Deleted
- - tip of snout SubClassOf subdivision of head
- Added
- + tip of snout SubClassOf external soft tissue zone
Changes for: tip of external ear
- Deleted
- - tip of external ear SubClassOf subdivision of head
- Added
- + tip of external ear SubClassOf external soft tissue zone
Changes for: root of nail
- Added
- + root of nail definition The part of the nail plate that extends into the dermis (nail matrix) { database cross reference=http://www.histology.leeds.ac.uk/skin/nails.php }
- + root of nail has exact synonym nail groove
Changes for: medial column
- Deleted
- - medial column SubClassOf ectoderm-derived structure
- - medial column SubClassOf structure with developmental contribution from neural crest
Changes for: anterior lingual gland
- Added
- + anterior lingual gland SubClassOf mucous gland
Changes for: nucleus lateralis valvulae
- Added
- + nucleus lateralis valvulae database cross reference TAO:0000551
- + nucleus lateralis valvulae definition Hindbrain nucleus in the tegmental region of rhombomere 1. The cells of the nucleus are granular and lie at the ventral border of the cerebellum and brain stem. { database cross reference=ZFA:0000551 , database cross reference=ZFIN:ZDB-PUB-100601-20 , database cross reference=ZFIN:ZDB-PUB-961014-1280 }
- + nucleus lateralis valvulae has obo namespace uberon
- + nucleus lateralis valvulae id UBERON:2000551
Changes for: ocular refractive media
- Added
- + ocular refractive media definition Body substance in a liquid or semi-solid state in the eyeball which serves to refract light. { database cross reference=UBERON:cjm }
- + ocular refractive media function notes ocular refraction
Changes for: stratum granulosum of epidermis
- Deleted
- - stratum granulosum of epidermis SubClassOf adjacent to some stratum spinosum of epidermis
- Added
Changes for: adrenal gland capsule
- Deleted
- - adrenal gland capsule definition the thick capsule of dense irregular connective tissue that surrounds each adrenal gland and contains scattered elastic fibers; the capsule contains a rich plexus of blood vessels (mainly small arteries) and numerous nerve fibers; some blood vessels and nerves enter the substance of the gland in the trabeculae that extend inward from the capsule and then leave the trabeculae to enter the cortex. { database cross reference=MGI:anna }
- Added
- + adrenal gland capsule definition the thick capsule of dense irregular connective tissue that surrounds each adrenal gland and contains scattered elastic fibers; the capsule contains a rich plexus of blood vessels (mainly small arteries) and numerous nerve fibers; some blood vessels and nerves enter the substance of the gland in the trabeculae that extend inward from the capsule and then leave the trabeculae to enter the cortex. { database cross reference=MP:0013565 }
Changes for: areola
- Deleted
- - areola SubClassOf organism subdivision
- Added
- + areola SubClassOf external soft tissue zone
Changes for: substantia nigra
- Deleted
- - substantia nigra SubClassOf lateral structure
Changes for: cerebellum
- Added
- + cerebellum dubious for taxon http://purl.obolibrary.org/obo/NCBITaxon_117569 { source=http://icb.oxfordjournals.org/content/42/4/743.full }
- + cerebellum present in taxon http://purl.obolibrary.org/obo/NCBITaxon_117569 { source=ISBN10:0471888893 }
- + cerebellum taxon notes The absence of a cerebellum in hagfishes and lampreys appears to be the only exception [to the rule that vertebrates possess the same number of brain divisions]. Both hagfishes and lampreys do possess a thin band of cells located medial to the lateral line centers of the medulla (Ronan and Northcutt, 1998), which has been interpreted as a primitive cerebellum (Larsell, 1967), but more recent experimental studies (Kishida et al., 1987; Weigle and Northcutt, 1998) fail to support Larsell’s claim[http://icb.oxfordjournals.org/content/42/4/743.full]
Changes for: stratum basale of epidermis
- Added
- + stratum basale of epidermis SubClassOf structure with developmental contribution from neural crest
- + stratum basale of epidermis function notes replaced damaged cells on outside of body
- + stratum basale of epidermis has broad synonym stratum germinosum
- + stratum basale of epidermis has exact synonym stratum germinosum of epidermis
- + stratum basale of epidermis has related synonym basal layer of epidermis
Changes for: skeleton
- Deleted
- - skeleton EquivalentTo anatomical cluster and has member some skeletal element
- - skeleton SubClassOf anatomical cluster
- Added
- + skeleton EquivalentTo anatomical collection and has member some skeletal element
- + skeleton SubClassOf anatomical collection
Changes for: stratum corneum of epidermis
- Added
- + stratum corneum of epidermis SubClassOf superficial to some stratum granulosum of epidermis
- + stratum corneum of epidermis has broad synonym keratinized squame layer
- + stratum corneum of epidermis has exact synonym keratinized squame layer of epidermis
Changes for: gray matter
- Deleted
- - gray matter definition Heterogeneous cluster of neural somas in the brain and the spinal cord. { database cross reference=http://en.wikipedia.org/wiki/Gray_matter , database cross reference=FMA:67242 }
- Added
- + gray matter definition A nervous system structure composed primarily of nerve cell bodies (somas). May also include dendrites and the initial unmyelinated portion of axons. { database cross reference=http://en.wikipedia.org/wiki/Gray_matter , database cross reference=UBERON:cjm }
Changes for: enteric nervous system
- Deleted
- - enteric nervous system SubClassOf neural crest-derived structure
Changes for: enamel knot
- Deleted
- - enamel knot SubClassOf anatomical cluster
- Added
- + enamel knot SubClassOf cell cluster
Changes for: thoracic rib cage
- Deleted
- - thoracic rib cage SubClassOf mesoderm-derived structure
Changes for: pyloric gastric gland
- Added
- + pyloric gastric gland has exact synonym pyloric mucuous gland
Changes for: stomach smooth muscle inner oblique layer
- Deleted
- Added
Changes for: stomach muscularis externa
- Added
- + stomach muscularis externa SubClassOf layer of smooth muscle tissue
Changes for: cardiac gastric gland
- Added
- + cardiac gastric gland has exact synonym gastric cardiac mucuous gland
Changes for: vesical venous plexus
- Deleted
- - vesical venous plexus SubClassOf mesoderm-derived structure
Changes for: skeleton of lower jaw
- Deleted
- - skeleton of lower jaw SubClassOf endoderm-derived structure
- - skeleton of lower jaw SubClassOf neural crest-derived structure
Changes for: skeleton of upper jaw
- Deleted
- - skeleton of upper jaw SubClassOf neural crest-derived structure
Changes for: hard palate
- Deleted
- - hard palate SubClassOf endoderm-derived structure
- - hard palate SubClassOf neural crest-derived structure
Changes for: splanchnocranium
- Deleted
Changes for: vault of skull
- Deleted
- - vault of skull SubClassOf mesoderm-derived structure
Changes for: ventral part of telencephalon
- Deleted
- - ventral part of telencephalon SubClassOf adjacent to some pallium
- Added
- + ventral part of telencephalon SubClassOf dorsal to some pallium
Changes for: lung vasculature
- Deleted
- - lung vasculature SubClassOf endoderm-derived structure
Changes for: blastopore
- Deleted
- - blastopore definition Structure around the opening into the archenteron during the embryonic stages of an organism. The distinction between protostomes and deuterostomes is based on the direction in which the mouth (stoma) develops in relation to the blastopore. { database cross reference=http://en.wikipedia.org/wiki/Blastopore }
- Added
- + blastopore definition the orifice of invagination of the endomesodermal cells during the embryonic stages of an organism. { database cross reference=http://www.ncbi.nlm.nih.gov/pubmed/23103190 , database cross reference=https://github.com/obophenotype/uberon/issues/660 , database cross reference=BGEE:ANN }
Changes for: sexually immature stage
- Deleted
- - sexually immature stage database cross reference TS28
- - sexually immature stage has exact synonym juvenile stage { database cross reference=XAO:1000010 }
- Added
- + sexually immature stage has narrow synonym juvenile stage { database cross reference=XAO:1000010 }
Changes for: membranous layer
- Added
- + membranous layer SubClassOf bounding layer of some organ part
- + membranous layer database cross reference FMA:30322
- + membranous layer database cross reference MESH:A10.615
- + membranous layer database cross reference http://ncicb.nci.nih.gov/xml/owl/EVS/Membrane
- + membranous layer external definition A thin sheet or layer of pliable tissue, serving as a covering or envelope of a part, as the lining of a cavity, as a partition or septum, or to connect two structures. { source=ncithesaurus:Membrane }
- + membranous layer has broad synonym membrane
Changes for: pair of lungs
- Deleted
- - pair of lungs SubClassOf anatomical cluster
- - pair of lungs SubClassOf endoderm-derived structure
- - pair of lungs SubClassOf has part some left lung
- - pair of lungs SubClassOf has part some right lung
- Added
- + pair of lungs EquivalentTo anatomical collection and has member some right lung and has member some left lung
- + pair of lungs SubClassOf ObjectMinCardinality( has member left lung ) and ObjectMaxCardinality( has member left lung )
- + pair of lungs SubClassOf ObjectMinCardinality( has member right lung ) and ObjectMaxCardinality( has member right lung )
- + pair of lungs SubClassOf anatomical collection
- + pair of lungs SubClassOf has member some left lung
- + pair of lungs SubClassOf has member some right lung
Changes for: embryonic head
- Added
Changes for: ovarian fossa
- Deleted
- - ovarian fossa definition A shallow depression on the lateral wall of the pelvis. This fossa has the following boundaries: superiorly: by the external iliac vessels anteriorly and inferiorly: by the broad ligament of the uterus posteriorly: by the ureter and internal iliac vessels { database cross reference=http://en.wikipedia.org/wiki/Ovarian_fossa }
- Added
- + ovarian fossa SubClassOf part of some greater sac
- + ovarian fossa definition A shallow depression on the lateral wall of the pelvis, wherein the ovary lies. This fossa has the following boundaries: superiorly: by the external iliac vessels anteriorly and inferiorly: by the broad ligament of the uterus posteriorly: by the ureter and internal iliac vessels { database cross reference=http://en.wikipedia.org/wiki/Ovarian_fossa , database cross reference=MGI:anna }
- + ovarian fossa has exact synonym Claudius fossa { database cross reference=MGI:anna }
Changes for: neural complex of Weberian apparatus
- Deleted
Changes for: pharyngeal slit
- Added
- + pharyngeal slit depicted by https://upload.wikimedia.org/wikipedia/commons/thumb/2/22/Gill_slits.png/280px-Gill_slits.png
- + pharyngeal slit taxon notes Some hemichordate species can have as many as 200 gill slits
- + pharyngeal slit taxon notes homologous to pharyngeal pouches
- + pharyngeal slit taxon notes may have been present in deuterostome ancestor[PMID:11961109]
Changes for: pharyngeal arch system
- Deleted
- - pharyngeal arch system SubClassOf embryonic structure
- - pharyngeal arch system SubClassOf endoderm-derived structure
Changes for: liver bud
- Deleted
- - liver bud SubClassOf developing anatomical structure
- Added
- + liver bud SubClassOf digestive tract diverticulum
- + liver bud SubClassOf endodermal part of digestive tract
- + liver bud SubClassOf epithelial sac
- + liver bud SubClassOf epithelium of foregut-midgut junction
Changes for: intervening zone
- Deleted
- - intervening zone SubClassOf ectoderm-derived structure
Changes for: epaxial musclulature
- Deleted
- - epaxial musclulature SubClassOf mesoderm-derived structure
Changes for: hypaxial musclulature
- Deleted
- - hypaxial musclulature SubClassOf mesoderm-derived structure
Changes for: breast
- Deleted
- - breast SubClassOf organism subdivision
- Added
- + breast SubClassOf external soft tissue zone
Changes for: musculature of larynx
- Deleted
- - musculature of larynx SubClassOf endoderm-derived structure
Changes for: tongue musculature
- Deleted
- - tongue musculature SubClassOf ectoderm-derived structure
- - tongue musculature SubClassOf endoderm-derived structure
Changes for: tendon sheath
- Added
- + tendon sheath SubClassOf has part some fibrous membrane of synovial tendon sheath
- + tendon sheath SubClassOf has part some synovial membrane of synovial tendon sheath
Changes for: set of muscles of vertebral column
- Deleted
Changes for: hippocampus stratum lacunosum moleculare
- Deleted
- - hippocampus stratum lacunosum moleculare definition A cytoarchitectural term denoting the outermost layer of the hippocampus (Stephan-75) (NeuroNames). { database cross reference=nif_annot:NeuroNames_defSource }
- Added
- + hippocampus stratum lacunosum moleculare definition Layer of the hippocampus lying just superficial to the stratum radiatum and bounded by the pial surface of the hippocampus. The fibers of the perforant pathway fibers from entorhinal cortex and several other brain areas terminate in this layer. Adapted from Paxinos, G. The rat central nervous system, 2nd ed, Academic Press, San Diego, 1995, pg. 460) { database cross reference=NIFSTD:birnlex_1359 }
Changes for: trigeminal nuclear complex
- Deleted
Changes for: hippocampus stratum lucidum
- Deleted
- - hippocampus stratum lucidum definition A cytoarchitectural term denoting the layer of the CA3 field of the hippocampus that is deep to the Stratum pyramidale hippocampi and superficial to the Stratum radiatum (Hof-2000). { database cross reference=http://en.wikipedia.org/wiki/Stratum_lucidum_of_hippocampus , database cross reference=nif_annot:NeuroNames_defSource }
- Added
- + hippocampus stratum lucidum definition Layer of hippocampus area CA3 lying superficial to the pyramidal cell layer that contains mossy fiber axons projecting from the dentate gyrus. A slight thickening in this layer marks the border in some species between areas CA2 and CA3. dapted from Paxinos, G. The rat central nervous system, 2nd ed, Academic Press, San Diego, 1995, pg. 460) { database cross reference=NIFSTD:birnlex_4108 }
Changes for: accessory olfactory bulb glomerular layer
- Deleted
Changes for: hippocampus alveus
- Deleted
Changes for: layer of synovial tissue
- Deleted
- - layer of synovial tissue SubClassOf connective tissue
- Added
- + layer of synovial tissue SubClassOf composed primarily of some connective tissue
Changes for: atlanto-occipital joint
- Deleted
- - atlanto-occipital joint SubClassOf lateral structure
Changes for: muscle tissue of prostate
- Added
- + muscle tissue of prostate database cross reference http://www.snomedbrowser.com/Codes/Details/251498008
- + muscle tissue of prostate has exact synonym prostatic muscle
- + muscle tissue of prostate has exact synonym prostatic musclular tissue
Changes for: obsolete left side of organism
- Added
- + obsolete left side of organism consider BSPO:0000000
Changes for: obsolete right side of organism
- Added
- + obsolete right side of organism consider BSPO:0000007
Changes for: subdivision of vertebral column
- Deleted
Changes for: internal arcuate fiber bundle
- Deleted
Changes for: dorsal external arcuate fiber bundle
- Deleted
Changes for: uncinate fasciculus
- Deleted
Changes for: periderm
- Deleted
- - periderm comment Taxon notes: In mice, the first non-basal layer formed at ~E9.5; it is a temporary structure composed of simple squamous epithelium that serves as the first barrier to the embryo’s physical environment, exists throughout the entire keratinocyte stratification process, and sheds off at ~E17, when it is replaced by corneocytes[MP]
- Added
- + periderm taxon notes In mice, the first non-basal layer formed at ~E9.5; it is a temporary structure composed of simple squamous epithelium that serves as the first barrier to the embryo’s physical environment, exists throughout the entire keratinocyte stratification process, and sheds off at ~E17, when it is replaced by corneocytes[MP]
Changes for: ventricular zone
- Deleted
- - ventricular zone SubClassOf ectoderm-derived structure
Changes for: pre-Botzinger complex
- Deleted
- - pre-Botzinger complex SubClassOf central nervous system cell part cluster
- - pre-Botzinger complex definition The group of interneurons within the medulla oblongata’s ventral respiratory group that are important for the generation of ventilatory (inspiratory) rhythmogenesis[MP]. The Pre-Bötzinger Complex (preBötC) is a cluster of interneurons in the ventrolateral medulla of the brainstem, which is essential to the generation of respiratory rhythm in mammals[WP]. { database cross reference=http://en.wikipedia.org/wiki/Pre-botzinger_complex , database cross reference=MP:0010745 }
- Added
- + pre-Botzinger complex SubClassOf cell cluster
- + pre-Botzinger complex SubClassOf ectoderm-derived structure
- + pre-Botzinger complex definition The group of interneurons within the medulla oblongata’s ventral respiratory group that are important for the generation of ventilatory (inspiratory) rhythmogenesis[MP].. { database cross reference=MP:0010745 }
Changes for: ciliary marginal zone
- Deleted
- - ciliary marginal zone SubClassOf ectoderm-derived structure
Changes for: neural plate
- Deleted
- - neural plate SubClassOf developing epithelial placode
Changes for: otic region
- Deleted
- - otic region SubClassOf anatomical cluster
- Added
- + otic region SubClassOf multi organ part structure
Changes for: sphenoid region
- Deleted
- - sphenoid region SubClassOf anatomical cluster
- Added
- + sphenoid region SubClassOf multi organ part structure
Changes for: olfactory region
- Deleted
- - olfactory region SubClassOf anatomical cluster
- Added
- + olfactory region SubClassOf multi organ part structure
Changes for: suspensorium
- Deleted
- - suspensorium SubClassOf endoderm-derived structure
- - suspensorium SubClassOf structure with developmental contribution from neural crest
Changes for: Weberian apparatus
- Deleted
- - Weberian apparatus SubClassOf mesoderm-derived structure
Changes for: vasculature of brain
- Deleted
- - vasculature of brain SubClassOf ectoderm-derived structure
Changes for: obsolete arthropod hypopharynx
- Deleted
- - arthropod hypopharynx SubClassOf anatomical cluster
- - arthropod hypopharynx SubClassOf part of some pharynx
- - arthropod hypopharynx database cross reference FBbt:00005751
- - arthropod hypopharynx database cross reference HAO:0000409
- - arthropod hypopharynx database cross reference TGMA:0000090
- - arthropod hypopharynx definition A median tonguelike structure arising from the mouth. { database cross reference=http://www.britannica.com/EBchecked/topic/279974/hypopharynx }
- - arthropod hypopharynx editor note this term should be ceded to the arthropod anatomy ontology
- - arthropod hypopharynx label arthropod hypopharynx
- Added
- + obsolete arthropod hypopharynx consider FBbt:00005751
- + obsolete arthropod hypopharynx consider HAO:0000409
- + obsolete arthropod hypopharynx consider TGMA:0000090
- + obsolete arthropod hypopharynx deprecated true
- + obsolete arthropod hypopharynx label obsolete arthropod hypopharynx
Changes for: skull
- Deleted
Changes for: body of fornix
- Deleted
Changes for: dentate gyrus molecular layer
- Added
- + dentate gyrus molecular layer SubClassOf composed primarily of some cell part
- + dentate gyrus molecular layer SubClassOf has part some nerve fiber
- + dentate gyrus molecular layer SubClassOf immediately deep to some pia mater
Changes for: spinal cord lateral horn
- Deleted
- - spinal cord lateral horn SubClassOf lateral structure
Changes for: facial nerve root
- Deleted
Changes for: hypoglossal nerve root
- Deleted
Changes for: trigeminal nerve root
- Deleted
Changes for: ganglion
- Deleted
- - ganglion SubClassOf neural tissue
- Added
- + ganglion SubClassOf cell cluster
- + ganglion SubClassOf composed primarily of some neural tissue
Changes for: parasympathetic nervous system
- Deleted
Changes for: zone of skin
- Deleted
- - zone of skin definition A sub-region of the skin. Note the distinct 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 { database cross reference=http://en.wikipedia.org/wiki/Skin , database cross reference=http://orcid.org/0000-0002-6601-2165 }
- Added
- + zone of skin SubClassOf has part some dermis
- + zone of skin SubClassOf has part some skin epidermis
- + zone of skin curator notes 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
- + zone of skin definition Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis. { database cross reference=http://en.wikipedia.org/wiki/Skin , database cross reference=http://orcid.org/0000-0002-6601-2165 }
Changes for: vermilion
- Deleted
- - vermilion SubClassOf ectoderm-derived structure
- - vermilion SubClassOf organism subdivision
- Added
- + vermilion SubClassOf skin of head
- + vermilion SubClassOf surrounds some lip
- + vermilion definition The zone of the skin that surrounds a lip and is colored red due to thin epithelium and presence of eleidin { database cross reference=UBERON:cjm }
- + vermilion has broad synonym vermilion border
- + vermilion has related synonym vermillion { has synonym type=dubious or contested synonym }
Changes for: upper vermilion
- Deleted
- - upper vermilion SubClassOf endoderm-derived structure
- - upper vermilion SubClassOf structure with developmental contribution from neural crest
- Added
- + upper vermilion SubClassOf skin of upper lip
Changes for: lower vermilion
- Deleted
- - lower vermilion SubClassOf endoderm-derived structure
- - lower vermilion SubClassOf structure with developmental contribution from neural crest
- Added
- + lower vermilion SubClassOf skin of lower lip
Changes for: tube
- Deleted
- - tube SubClassOf has part some anatomical space
- Added
- + tube SubClassOf has part some subdivision of tube
Changes for: pituitary gland
- Deleted
- - pituitary gland SubClassOf develops from some future pituitary gland
- Added
- + pituitary gland SubClassOf immediate transformation of some future pituitary gland
Changes for: islet of Langerhans
- Deleted
- - islet of Langerhans SubClassOf organ part
- Added
- + islet of Langerhans SubClassOf cell cluster
Changes for: blood vessel external elastic membrane
- Deleted
- - external elastic membrane label external elastic membrane
- Added
- + blood vessel external elastic membrane database cross reference FMA:68206
- + blood vessel external elastic membrane external ontology notes in FMA this is classified as an acellular membrane, which is inconsistent with our classification as a tissue layer. Requires further investigation { external ontology=FMA }
- + blood vessel external elastic membrane has exact synonym external elastic lamina { database cross reference=FMA:68206 }
- + blood vessel external elastic membrane has exact synonym external elastic membrane { database cross reference=MA:0002862 }
- + blood vessel external elastic membrane label blood vessel external elastic membrane
Changes for: hilar portion of hepatic duct
- Added
- + hilar portion of hepatic duct SubClassOf located in some liver
Changes for: pharyngeal arch 7 skeleton
- Deleted
Changes for: pharyngeal arch 3 skeleton
- Deleted
Changes for: pharyngeal arch 6 skeleton
- Deleted
Changes for: pharyngeal arch 4 skeleton
- Deleted
Changes for: pharyngeal arch 5 skeleton
- Deleted
Changes for: melon organ
- Added
- + melon organ SubClassOf has part some core of melon organ
Changes for: membrane organ
- Added
- + membrane organ has broad synonym membrane
Changes for: dorsal scute series
- Deleted
Changes for: abdominal scute series
- Deleted
Changes for: ampullary organ
- Added
- + ampullary organ has broad synonym ampullary receptor
- + ampullary organ has exact synonym ampullary electroreceptor
- + ampullary organ taxon notes The presence of these organs varies greatly among anamniotes, but an out-group analysis of their distribution in adult anamniotes suggests that they were present in primitive vertebrates and retained in living lampreys, cartilaginous fishes, lobe-finned fishes and basal ray-finned fishes (bichirs, sturgeons and paddlefishes). Ampullary organs do not occur in gars and bowfins, two of the three groups of neopterygian fishes, nor are they found in most teleost fishes, but they do appear to have re-evolved at least twice (and more likely three or more times) in five groups of teleosts (Northcutt, 1997).[http://icb.oxfordjournals.org/content/42/4/743]
Changes for: substratum of layer of retina
- Deleted
- - substratum of layer of retina SubClassOf ectoderm-derived structure
- - substratum of layer of retina SubClassOf organ component layer
- Added
Changes for: fornix of brain
- Deleted
Changes for: organ part
- Deleted
- - organ part SubClassOf multicellular anatomical structure
- Added
- + organ part SubClassOf anatomical structure
Changes for: lateral line nerve
- Deleted
- - lateral line nerve SubClassOf ectoderm-derived structure
Changes for: anatomical structure
- Deleted
- - anatomical structure definition Material anatomical entity that has inherent 3D shape and is generated by coordinated expression of the organism’s own genome. { database cross reference=CARO:0000003 }
- Added
- + anatomical structure definition Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism’s own genome. { database cross reference=CARO:0000003 }
- + anatomical structure has exact synonym connected biological structure { database cross reference=CARO:0000003 }
Changes for: organ
- Added
- + organ database cross reference CARO:0020004
Changes for: individual digit of digitopodial skeleton
- Deleted
Changes for: subendocardium layer
- Added
- + subendocardium layer SubClassOf adjacent to some endocardium
- + subendocardium layer SubClassOf adjacent to some myocardium
- + subendocardium layer SubClassOf composed primarily of some fibrous connective tissue
- + subendocardium layer SubClassOf has part some nerve
- + subendocardium layer SubClassOf structure with developmental contribution from neural crest
Changes for: heart layer
- Added
Changes for: eye trabecular meshwork
- Deleted
- - eye trabecular meshwork SubClassOf neural crest-derived structure
- Added
- + eye trabecular meshwork SubClassOf ectoderm-derived structure
Changes for: axial skeleton plus cranial skeleton
- Deleted
Changes for: inferior nasal concha
- Deleted
- - inferior nasal concha SubClassOf lateral structure
Changes for: occipital region
- Deleted
- - occipital region SubClassOf anatomical cluster
- Added
- + occipital region SubClassOf multi organ part structure
Changes for: post-hyoid pharyngeal arch skeleton
- Deleted
Changes for: hyoid arch skeleton
- Deleted
Changes for: mineralized skeletal tissue
- Deleted
- - mineralized tissue created by vertebrate_skeletal_anatomy_curators
- - mineralized tissue has obo namespace uberon/phenoscape-anatomy
- - mineralized tissue label mineralized tissue
- - mineralized tissue provenance notes This class was sourced from an external ontology (vertebrate_skeletal_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon
- Added
- + mineralized skeletal tissue database cross reference VSAO:0000013
- + mineralized skeletal tissue database cross reference XAO:0004039
- + mineralized skeletal tissue definition Skeletal tissue that is mineralized. { database cross reference=XAO:0004039 , database cross reference=XAO:EJS }
- + mineralized skeletal tissue has broad synonym mineralized tissue { database cross reference=VSAO:0000013 }
- + mineralized skeletal tissue has obo namespace uberon
- + mineralized skeletal tissue id UBERON:4000013
- + mineralized skeletal tissue label mineralized skeletal tissue
Changes for: musculature of body
- Added
- + musculature of body SubClassOf composed primarily of some musculature
Changes for: epiglottis
- Deleted
- - epiglottis SubClassOf anatomical cluster
- Added
- + epiglottis SubClassOf multi organ part structure
Changes for: red bone marrow
- Deleted
- - red bone marrow has related synonym red marrow { database cross reference=BTO:0001160 }
- Added
- + red bone marrow has exact synonym parenchymal red marrow { database cross reference=UBERON:cjm }
- + red bone marrow has exact synonym red marrow { database cross reference=BTO:0001160 }
- + red bone marrow has related synonym parenchyma of none marrow marrow { database cross reference=UBERON:cjm }
Changes for: reticuloendothelial system
- Deleted
- - reticuloendothelial system SubClassOf anatomical group
- Added
- + reticuloendothelial system SubClassOf anatomical structure
Changes for: preputial gland
- Deleted
- - preputial gland has related synonym set of preputial glands { database cross reference=FMA:71652 , has synonym type=plural term }
Changes for: throat
- Deleted
- - throat SubClassOf organism subdivision
- Added
- + throat SubClassOf external soft tissue zone
Changes for: limbic system
- Deleted
- - limbic system SubClassOf anatomical cluster
- - limbic system SubClassOf ectoderm-derived structure
- Added
- + limbic system SubClassOf organ system subdivision
Changes for: yellow bone marrow
- Deleted
- - yellow bone marrow has related synonym yellow marrow { database cross reference=BTO:0000635 }
- Added
- + yellow bone marrow SubClassOf part of some stroma of bone marrow
- + yellow bone marrow has exact synonym yellow marrow { database cross reference=BTO:0000635 }
Changes for: septum of telencephalon
- Deleted
- - septum of telencephalon SubClassOf anatomical cluster
- - septum of telencephalon SubClassOf ectoderm-derived structure
- - septum of telencephalon SubClassOf structure with developmental contribution from neural crest
- Added
- + septum of telencephalon SubClassOf cerebral hemisphere gray matter
Changes for: tunica intima of artery
- Added
- + tunica intima of artery SubClassOf endothelium of artery
Changes for: mucous gland
- Deleted
- Added
- + mucous gland has exact synonym glandula mucosa { database cross reference=http://en.wikipedia.org/wiki/Mucous_gland , has synonym type=latin term }
- + mucous gland has related synonym mucus-secreting gland
Changes for: scalp
- Deleted
- - scalp SubClassOf anatomical cluster
- Added
- + scalp SubClassOf multi organ part structure
Changes for: sympathetic trunk
- Deleted
- - sympathetic trunk SubClassOf lateral structure
Changes for: tunica adventitia of blood vessel
- Added
- + tunica adventitia of blood vessel SubClassOf composed primarily of some fibrous connective tissue
Changes for: mineralized bone tissue
- Deleted
- - mineralized bone tissue SubClassOf part of some mineralized extracellular matrix
- - mineralized bone tissue provenance notes This class was sourced from an external ontology (vertebrate_skeletal_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon
- Added
- + mineralized bone tissue SubClassOf has part some mineralized extracellular matrix
Changes for: cellular bone tissue
- Deleted
- - cellular bone tissue provenance notes This class was sourced from an external ontology (vertebrate_skeletal_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon
- Added
Changes for: acellular bone tissue
- Deleted
- - acellular bone tissue provenance notes This class was sourced from an external ontology (vertebrate_skeletal_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon
Changes for: connecting stalk vasculature
- Deleted
- - connecting stalk vasculature SubClassOf extraembryonic structure
- - connecting stalk vasculature SubClassOf mesoderm-derived structure
Changes for: fascia of Camper
- Deleted
- - fascia of Camper SubClassOf subcutaneous abdominal adipose tissue
- Added
- + fascia of Camper SubClassOf composed primarily of some adipose tissue
- + fascia of Camper SubClassOf integumentary system layer
- + fascia of Camper SubClassOf mesoderm-derived structure
Changes for: pelvic girdle skeleton
- Deleted
- - pelvic girdle skeleton SubClassOf mesoderm-derived structure
Changes for: major vestibular gland
- Added
- + major vestibular gland SubClassOf mucous gland
Changes for: anatomical system
- Deleted
- - anatomical system SubClassOf anatomical group
- - anatomical system definition Anatomical group that is has as its parts distinct anatomical structures interconnected by anatomical structures at a lower level of granularity[CARO]. A group of organs that work together to perform a certain task [Wikipedia]. { database cross reference=http://en.wikipedia.org/wiki/Organ_system , database cross reference=CARO:0000011 , database cross reference=CARO:MAH }
- Added
- + anatomical system SubClassOf anatomical structure
- + anatomical system SubClassOf has part some organ
- + anatomical system definition Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function. { database cross reference=CARO:0000011 }
- + anatomical system has exact synonym connected anatomical system { database cross reference=CARO:0000011 }
Changes for: anatomical group
- Deleted
- - anatomical group editor note Will be obsoleted in v2 of CARO [https://github.com/obophenotype/caro/issues/2]
- Added
- + anatomical group editor note Obsoleted in v2 of CARO [https://github.com/obophenotype/caro/issues/2]
Changes for: anatomical cluster
- Deleted
- - anatomical cluster SubClassOf anatomical group
- Added
- + anatomical cluster SubClassOf anatomical entity
Changes for: hyaloid vascular plexus
- Deleted
- - hyaloid vascular plexus SubClassOf mesoderm-derived structure
Changes for: intrahepatic part of hepatic duct
- Deleted
- - hepatic duct intrahepatic part SubClassOf arborizing epithelial duct system
- - hepatic duct intrahepatic part SubClassOf intrahepatic bile duct epithelium
- - hepatic duct intrahepatic part database cross reference EHDAA2:0000743
- - hepatic duct intrahepatic part database cross reference EHDAA:3053
- - hepatic duct intrahepatic part label hepatic duct intrahepatic part
- Added
- + intrahepatic part of hepatic duct SubClassOf intrahepatic bile duct
- + intrahepatic part of hepatic duct has exact synonym hepatic duct intrahepatic part { database cross reference=MA:0001637 }
- + intrahepatic part of hepatic duct label intrahepatic part of hepatic duct
Changes for: extrahepatic part of hepatic duct
- Deleted
- - hepatic duct extrahepatic part SubClassOf epithelial tube
- - hepatic duct extrahepatic part SubClassOf extrahepatic bile duct epithelium
- - hepatic duct extrahepatic part database cross reference EHDAA2:0000742
- - hepatic duct extrahepatic part database cross reference EHDAA:3051
- - hepatic duct extrahepatic part label hepatic duct extrahepatic part
- Added
- + extrahepatic part of hepatic duct SubClassOf bile duct
- + extrahepatic part of hepatic duct has exact synonym hepatic duct extrahepatic part { database cross reference=MA:0001636 }
- + extrahepatic part of hepatic duct label extrahepatic part of hepatic duct
Changes for: cerebellum vasculature
- Deleted
Changes for: mammillary axonal complex
- Deleted
- - mammillary axonal complex SubClassOf anatomical cluster
- - mammillary axonal complex SubClassOf ectoderm-derived structure
- Added
Changes for: meningeal cluster
- Deleted
- - meningeal cluster SubClassOf anatomical cluster
- - meningeal cluster SubClassOf composed primarily of some meninx
- - meningeal cluster SubClassOf ectoderm-derived structure
- - meningeal cluster SubClassOf structure with developmental contribution from neural crest
- Added
- + meningeal cluster EquivalentTo anatomical collection and bounding layer of some central nervous system and has member some meninx
- + meningeal cluster SubClassOf anatomical collection
- + meningeal cluster SubClassOf bounding layer of some central nervous system
- + meningeal cluster SubClassOf has member some meninx
Changes for: valvula cerebelli
- Added
- + valvula cerebelli database cross reference TAO:0000603
- + valvula cerebelli definition Brain structure which is caudally attached to the rostral medulla oblongata and extends into the tectal ventricle. The valvula cerebelli consists of a granular and a molecular layer along with aggregations of large Purkinje and eurydendroid cells and is uniquely present in ray-finned fishes. From Neuroanatomy of the Zebrafish Brain. { database cross reference=ISBN:3764351209 , database cross reference=ZFA:0000603 , database cross reference=ZFA:curator }
- + valvula cerebelli has exact synonym valvula cerebellum { database cross reference=ZFA:0000603 , has synonym type=plural term }
- + valvula cerebelli has obo namespace uberon
- + valvula cerebelli has related synonym valvula { database cross reference=ZFA:0000603 }
- + valvula cerebelli id UBERON:2000603
Changes for: visceromotor column
- Deleted
Changes for: lymphatic part of lymphoid system
- Deleted
- - lymphatic part of lymphoid system SubClassOf anatomical cluster
- Added
Changes for: non-lymphatic part of lymphoid system
- Deleted
- - non-lymphatic part of lymphoid system SubClassOf anatomical cluster
- Added
Changes for: statolith
- Deleted
- - statolith has narrow synonym calcareousstatoliths
- Added
- + statolith has narrow synonym calcareous statoliths
Changes for: quadrate bone
- Deleted
- - quadrate bone SubClassOf lateral structure
Changes for: right lung alveolar system
- Deleted
- - right lung alveolar system SubClassOf endoderm-derived structure
Changes for: left lung alveolar system
- Deleted
- - left lung alveolar system SubClassOf endoderm-derived structure
Changes for: alveolar system
- Deleted
- - alveolar system SubClassOf endoderm-derived structure
Changes for: ansa cervicalis
- Deleted
Changes for: cerebral hemisphere gray matter
- Deleted
- - cerebral hemisphere grey matter label cerebral hemisphere grey matter
- Added
- + cerebral hemisphere gray matter has exact synonym cerebral hemisphere grey matter
- + cerebral hemisphere gray matter label cerebral hemisphere gray matter
Changes for: hippocampus molecular layer
- Deleted
- - hippocampus molecular layer definition A cytoarchitectural region of the hippocampus consisting of a composite of the two outermost layers of the hippocampus, the Stratum lacunosum-moleculare and the Stratum radiatum (Carpenter-83). { database cross reference=nif_annot:NeuroNames_defSource }
- Added
- + hippocampus molecular layer definition A cytoarchitectural region of the hippocampus consisting of a composite of the two outermost layers of the hippocampus, the Stratum lacunosum-moleculare and the Stratum radiatum (Carpenter-83). In CA3, there is an additional layer lying above the pyramidal cell layer, the stratum lucidum, which is also included here. { database cross reference=NIFSTD:birnlex_1211 }
Changes for: gill raker row
- Deleted
- - gill raker row SubClassOf endoderm-derived structure
- - gill raker row SubClassOf structure with developmental contribution from neural crest
Changes for: hippocampus stratum oriens
- Deleted
- - hippocampus stratum oriens definition The term Stratum oriens is a cytoarchitectural term denoting the layer of the hippocampus that is deep to the Stratum pyramidale hippocampi and superficial to the alveus (Stephan-75). { database cross reference=nif_annot:NeuroNames_defSource }
- Added
- + hippocampus stratum oriens definition Layer that is part of the CA fields of the hippocampus consisting of a narrow relatively cell free layer located deep to the pyramidal cell layer extending through areas CA1, CA2 and CA3. (adapted from Paxinos The rat central nervous system, 2nd ed, Academic Press, San Diego, 1995) { database cross reference=NIFSTD:birnlex_4113 }
Changes for: epibranchial arborescent organ
- Deleted
- - epibranchial arborescent organ SubClassOf endoderm-derived structure
Changes for: spermatic cord
- Deleted
- - spermatic cord SubClassOf anatomical cluster
- Added
- + spermatic cord SubClassOf multi organ part structure
Changes for: photoreceptor array
- Deleted
- - photoreceptor array SubClassOf tissue
- Added
- + photoreceptor array SubClassOf organ component layer
Changes for: olfactory glomerulus
- Deleted
Changes for: caudate-putamen
- Deleted
Changes for: vasculature of liver
- Deleted
- - vasculature of liver SubClassOf endoderm-derived structure
Changes for: nasal skeleton
- Deleted
- - nasal skeleton SubClassOf neural crest-derived structure
Changes for: mammary bud
- Deleted
- - mammary bud SubClassOf develops from some mammary placode
- - mammary bud SubClassOf embryonic tissue
- - mammary bud SubClassOf part of some external ectoderm
- - mammary bud definition An outpocketing of the mammary placode that develops into the mammary gland.
- Added
- + mammary bud EquivalentTo epithelial bud and transformation of some mammary placode
- + mammary bud SubClassOf transformation of some mammary placode
- + mammary bud definition A bulb of epithelial cells that forms from the mammary placode that develops into the mammary gland.
Changes for: mesonephric juxtaglomerular apparatus
- Deleted
Changes for: mammary duct terminal end bud
- Deleted
- - mammary duct terminal end bud definition . { database cross reference=GO:0060763 }
- Added
- + mammary duct terminal end bud definition A unique club-shaped epithelial structure that develops at the tip of the mammary duct at the onset of puberty under the action of circulating hormones. { database cross reference=MGI:anna }
- + mammary duct terminal end bud development notes TEBs proliferate, ramify, and actively invade the fad pad to allow the formation of a complex branching structure; this process of branching morphogenesis concludes at ~10-12 weeks of age in mice, when TEBs have traversed the length of the fat pad and a fully developed ductal tree has formed
- + mammary duct terminal end bud structure notes terminal end buds (TEBs) consist of an outer layer of undifferentiated myoepithelial progenitor cells (‘cap cells’), and a multilayered inner core of luminal epithelial cells (‘body’) fated to form the walls of the ductal lumen; both layers have high rates of mitosis, consistent with a motile organ dedicated to ductal morphogenesis
Changes for: mammary placode
- Added
- + mammary placode SubClassOf part of some external ectoderm
Changes for: cerebellar glomerulus
- Deleted
Changes for: pilosebaceous unit
- Deleted
Changes for: mammary gland luminal epithelium
- Deleted
Changes for: prostate luminal epithelium
- Deleted
Changes for: endometrium luminal epithelium
- Deleted
- - endometrium luminal epithelium SubClassOf reproductive structure
Changes for: ureter subluminal urothelium
- Deleted
Changes for: ureter luminal urothelium
- Deleted
Changes for: piston cartilage
- Added
- + piston cartilage SubClassOf develops from some future piston
- + piston cartilage SubClassOf part of some head
- + piston cartilage has related synonym lamprey tongue cartilage
Changes for: inter limb-segment region
- Deleted
- - inter limb-segment region SubClassOf organism subdivision
- Added
- + inter limb-segment region SubClassOf external soft tissue zone
Changes for: deep layer of superior colliculus
- Deleted
- - deep layer of superior colliculus comment grouping teleost assuming homology of superior colliculus and optic tectum[cjm]
- Added
- + deep layer of superior colliculus editor note grouping teleost assuming homology of superior colliculus and optic tectum; however, this is dubious as tectal layers vary so widely. See: http://icb.oxfordjournals.org/content/42/4/743/T1.expansion.html
Changes for: superficial layer of superior colliculus
- Deleted
- - superficial layer of superior colliculus comment grouping teleost assuming homology of superior colliculus and optic tectum[cjm]
- Added
- + superficial layer of superior colliculus editor note grouping teleost assuming homology of superior colliculus and optic tectum; however, this is dubious as tectal layers vary so widely. See: http://icb.oxfordjournals.org/content/42/4/743/T1.expansion.html
Changes for: intermediate layer of superior colliculus
- Deleted
- - intermediate layer of superior colliculus comment grouping teleost assuming homology of superior colliculus and optic tectum[cjm]
- Added
- + intermediate layer of superior colliculus editor note grouping teleost assuming homology of superior colliculus and optic tectum; however, this is dubious as tectal layers vary so widely. See: http://icb.oxfordjournals.org/content/42/4/743/T1.expansion.html
Changes for: deep white layer of superior colliculus
- Added
- + deep white layer of superior colliculus SubClassOf deep layer of superior colliculus
- + deep white layer of superior colliculus editor note grouping teleost assuming homology of superior colliculus and optic tectum; however, this is dubious as tectal layers vary so widely. See: http://icb.oxfordjournals.org/content/42/4/743/T1.expansion.html
Changes for: arthropod optic lobe
- Deleted
- - arthropod optic lobe SubClassOf ectoderm-derived structure
Changes for: cephalopod optic lobe
- Deleted
- - cephalopod optic lobe SubClassOf ectoderm-derived structure
Changes for: cranial nerve II
- Deleted
Changes for: deep gray layer of superior colliculus
- Added
Changes for: cornea
- Deleted
- - cornea taxon notes Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman’s membrane in mammals
- Added
- + cornea SubClassOf has part some anterior limiting lamina of cornea
- + cornea SubClassOf has part some corneal epithelium
- + cornea SubClassOf multicellular anatomical structure
- + cornea taxon notes Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman’s membrane in mammals. In fish, and aquatic vertebrates in general, the cornea plays no role in focusing light, since it has virtually the same refractive index as water
Changes for: middle gray layer of superior colliculus
- Added
- + middle gray layer of superior colliculus SubClassOf intermediate layer of superior colliculus
- + middle gray layer of superior colliculus editor note grouping teleost assuming homology of superior colliculus and optic tectum; however, this is dubious as tectal layers vary so widely. See: http://icb.oxfordjournals.org/content/42/4/743/T1.expansion.html
Changes for: middle white layer of superior colliculus
- Added
- + middle white layer of superior colliculus SubClassOf intermediate layer of superior colliculus
- + middle white layer of superior colliculus editor note grouping teleost assuming homology of superior colliculus and optic tectum; however, this is dubious as tectal layers vary so widely. See: http://icb.oxfordjournals.org/content/42/4/743/T1.expansion.html
Changes for: white matter of superior colliculus
- Deleted
- Added
Changes for: gray matter layer of superior colliculus
- Deleted
- Added
Changes for: layer of superior colliculus
- Deleted
- - layer of superior colliculus EquivalentTo organ component layer and part of some superior colliculus
- - layer of superior colliculus SubClassOf ectoderm-derived structure
- - layer of superior colliculus SubClassOf organ component layer
- Added
- + layer of superior colliculus EquivalentTo nervous system cell part layer and part of some superior colliculus
- + layer of superior colliculus SubClassOf central nervous system cell part cluster
- + layer of superior colliculus SubClassOf nervous system cell part layer
- + layer of superior colliculus has exact synonym layer of optic tectum { has synonym type=taxonomic disambiguation }
- + layer of superior colliculus has related synonym tectal layer { has synonym type=taxonomic disambiguation }
- + layer of superior colliculus taxon notes The tectum in lampreys has more layers than the tectum in hagfishes, likely related to the fact that vision is less well developed in hagfishes. tectal lamination is almost identical in reptiles and birds and is more restricted in mammals[http://icb.oxfordjournals.org/content/42/4/743.full]
Changes for: zonal layer of superior colliculus
- Added
Changes for: superficial white layer of superior colliculus
- Added
Changes for: cerebral cortex
- Deleted
- Added
- + cerebral cortex present in taxon http://purl.obolibrary.org/obo/NCBITaxon_117569
- + cerebral cortex taxon notes hagfishes have independently evolved a highly laminated cerebral cortex, comparable in many ways to the cerebral cortex of mammals [http://icb.oxfordjournals.org/content/42/4/743]
Changes for: alisphenoid bone
- Deleted
- - alisphenoid bone SubClassOf lateral structure
Changes for: autopodial skeleton
- Deleted
- - autopodial skeleton SubClassOf mesoderm-derived structure
Changes for: anal fin distal radial element
- Deleted
- - anal fin distal radial element EquivalentTo anal fin radial element and part of some anal fin pterygiophore and connected to some lepidotrichium
- - anal fin distal radial element SubClassOf connected to some lepidotrichium
- - anal fin distal radial element SubClassOf distally connected to some anal fin lepidotrichium
Changes for: organismal segment
- Added
- + organismal segment has exact synonym serial element
Report for properties
ObjectProperty objects lost from source: 6
ObjectProperty objects new in target: 2
New ObjectProperty : aboral_to
- aboral to database cross reference BSPO:0015202
- aboral to id aboral_to
- aboral to definition nearer to the aboral opening of the organism, on the oral-aboral axis. { database cross reference=BSPO:cjm }
- aboral to label aboral_to
- aboral to has obo namespace uberon
- aboral to shorthand aboral_to
- TransitiveObjectProperty( aboral to )
New ObjectProperty : oral_to
- TransitiveObjectProperty( oral to )
- oral to label oral_to
- oral to database cross reference BSPO:0015201
- oral to id oral_to
- oral to definition nearer to the oral opening of the organism, on the oral-aboral axis. { database cross reference=BSPO:cjm }
- oral to has obo namespace uberon
- oral to shorthand oral_to
Changed ObjectProperty objects: 1
Changes for: contains process
- Deleted
- - InverseObjectProperties( contains process occurs in )
March 15, 2015
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