From 00a63e0a478d4f7527d587a458cf4ff62f578fba Mon Sep 17 00:00:00 2001 From: Aleix Puig <94959119+aleixpuigb@users.noreply.github.com> Date: Wed, 18 Oct 2023 15:28:06 +0100 Subject: [PATCH 01/11] =?UTF-8?q?Serialisation=20prot=C3=A9g=C3=A9=205.6.3?= =?UTF-8?q?=20(#3085)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Serialisation protégé 5.6.3 Serialisation protégé 5.6.3 * odd serialisation in annotation IAO:0000116 (editor notes) * change `IAO:0000116` to `rdfs:comment` * use `notes` in the case of multiple comment tags * add `notes` to accepted annotations list * change to `notes` another case multiple comment tag * use `curator_notes` instead of `notes` * fix comment OBO syntax * add EDITOR_NOTE to comments previously from `editor notes` annotation * replace `UBPROP:0000008` and `IAO:0000232` with `comment` when annotation in another axiom * normalize uberon-edit file --------- Co-authored-by: Anita Caron Co-authored-by: Anita Caron --- src/ontology/uberon-edit.obo | 94 ++++++++++++++++++------------------ 1 file changed, 47 insertions(+), 47 deletions(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 60339f803e..03c4879b1c 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -56,11 +56,11 @@ treat-xrefs-as-equivalent: VSAO treat-xrefs-as-is_a: VHOG remark: Aurelie Comte, Bill Bug, Catherine Leroy, Duncan Davidson and Trish Whetzel are also contributors. However their ORCIDs were not found. import: http://purl.obolibrary.org/obo/uberon/components/develops-from-chains.owl +import: http://purl.obolibrary.org/obo/uberon/components/hra_depiction_3d_images.owl import: http://purl.obolibrary.org/obo/uberon/components/hra_subset.owl import: http://purl.obolibrary.org/obo/uberon/components/in-subset.owl import: http://purl.obolibrary.org/obo/uberon/components/mappings.owl import: http://purl.obolibrary.org/obo/uberon/components/vasculature_class.owl -import: http://purl.obolibrary.org/obo/uberon/components/hra_depiction_3d_images.owl import: http://purl.obolibrary.org/obo/uberon/imports/merged_import.owl import: http://purl.obolibrary.org/obo/uberon/patterns/definitions.owl ontology: uberon/core @@ -928,7 +928,7 @@ intersection_of: UBERON:0000026 ! appendage intersection_of: has_quality PATO:0002236 ! aliform relationship: capable_of_part_of GO:0060361 ! flight relationship: never_in_taxon NCBITaxon:118072 {source="bgee"} ! Coelacanthimorpha -relationship: never_in_taxon NCBITaxon:186634 {seeAlso="Wikipedia:Flying_fish", source="bgee"} ! Otomorpha +relationship: never_in_taxon NCBITaxon:186634 {source="bgee", seeAlso="Wikipedia:Flying_fish"} ! Otomorpha relationship: never_in_taxon NCBITaxon:314147 {source="bgee"} ! Glires relationship: never_in_taxon NCBITaxon:6231 {source="bgee"} ! Nematoda relationship: never_in_taxon NCBITaxon:7878 {source="bgee"} ! Dipnomorpha @@ -7753,7 +7753,7 @@ xref: ENVO:02000026 xref: FMA:62961 xref: Wikipedia:Chyme is_a: UBERON:0006314 {source="WP"} ! bodily fluid -is_a: UBERON:0012112 {editor_note="consider changing to derivation relationship", source="FMA"} ! ingested food +is_a: UBERON:0012112 {source="FMA", comment="consider changing to derivation relationship"} ! ingested food disjoint_from: UBERON:0012113 ! bolus of food relationship: has_quality PATO:0001429 {gci_relation="part_of", gci_filler="UBERON:0000945"} ! acidic relationship: located_in UBERON:0004908 ! upper digestive tract @@ -10362,6 +10362,7 @@ property_value: taxon_notes "Most vertebrates have some form of duct to transfer id: UBERON:0001001 name: chitin-based cuticle def: "A cuticular covering that is composed primarily of chitin. The main structural component of arthropod cuticle is a polysaccharide, chitin, composed of N-acetylglucosamine units, together with proteins and lipids[WP]." [https://orcid.org/0000-0002-6601-2165, https://sourceforge.net/tracker/index.php?func=detail&aid=3348965&group_id=36855&atid=440764, Wikipedia:Arthropod_exoskeleton, Wikipedia:Cuticle#Invertebrate_zoology] +comment: EDITOR_NOTE TODO - split from exoskeleton? Also: See above sf item to see if this belongs in GO subset: efo_slim subset: uberon_slim synonym: "arthropod cuticle" RELATED [] @@ -10379,12 +10380,12 @@ intersection_of: composed_primarily_of CHEBI:17029 ! chitin relationship: develops_from UBERON:0007376 ! outer epithelium relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda relationship: part_of UBERON:0002416 ! integumental system -property_value: editor_note "TODO - split from exoskeleton? Also: See above sf item to see if this belongs in GO" xsd:string [Term] id: UBERON:0001002 name: cuticle def: "Tough but flexible, non-mineral outer coverings of an organism, or parts of an organism, that provide protection. Cuticles are non-homologous, differing in their origin, structure and chemical composition[WP]." [http://sourceforge.net/tracker/?func=detail&aid=3348965&group_id=36855&atid=440764, Wikipedia:Cuticle] +comment: EDITOR_NOTE TODO - check cuticle vs exoskeleton. Note that GO has a very generic definition of cuticle. See also arthropod-anatomy ontology. Note in ncit Cuticle is a plant part subset: grouping_class subset: non_informative subset: uberon_slim @@ -10395,7 +10396,6 @@ xref: Wikipedia:Cuticle is_a: UBERON:0000476 ! acellular anatomical structure disjoint_from: UBERON:0004882 ! eponychium relationship: only_in_taxon NCBITaxon:6072 {source="Rieger - Evolution of the Cuticle in the Lower Eumetazoa"} ! Eumetazoa -property_value: editor_note "TODO - check cuticle vs exoskeleton. Note that GO has a very generic definition of cuticle. See also arthropod-anatomy ontology. Note in ncit Cuticle is a plant part" xsd:string property_value: has_relational_adjective "cuticular" xsd:string [Term] @@ -10592,6 +10592,7 @@ property_value: has_relational_adjective "digestive" xsd:string id: UBERON:0001008 name: renal system def: "The renal system in an anatomical system that maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products." [DOI:10.1371/journal.pone.0099864, GO:0072001] +comment: EDITOR_NOTE In various sources such as Encyclopedia Britannica, the excretory and urinary systems are indeed the same system (see wikipedia talk page); we merge two BTO classes here subset: efo_slim subset: pheno_slim subset: uberon_slim @@ -10636,7 +10637,6 @@ relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: never_in_taxon NCBITaxon:110815 {source="Wikipedia"} ! Xenoturbella relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} ! Acoelomorpha relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -property_value: editor_note "In various sources such as Encyclopedia Britannica, the excretory and urinary systems are indeed the same system (see wikipedia talk page); we merge two BTO classes here" xsd:string property_value: external_definition "An anatomical system which consists of organs and tissues which produce, store, and excrete urine.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010257", ontology="AAO", source="AAO:BJB"} property_value: homology_notes "Evolution of vertebrate renal anatomy appears quite conservative when compared, for example, to evolution of respiratory and cardiovascular systems in vertebrates. Major anatomical changes in vertebrates kidneys separate those of birds and mammals from kidneys of lower vertebrates. General increase in animal size from fish to mammals is reflected by an increase in total number of nephrons per kidney, rather than by constant change in tubular dimensions.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000723", ontology="VHOG", source="ISBN:978-3540428541 Kapoor BG, Bhavna Khanna, Ichthyology Handbook (2004) p.406", source="http://bgee.unil.ch/"} property_value: taxon_notes "In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels" xsd:string {source="GO"} @@ -10962,6 +10962,7 @@ property_value: external_definition "White matter structure of CNS that contains id: UBERON:0001019 name: nerve fasciculus def: "A slender neuron projection bundle[FBbt]; A bundle of anatomical fibers, as of muscle or nerve (American Heritage Dictionary 4th ed)." [BIRNLEX:872, FBbt:00005101] +comment: EDITOR_NOTE note FBbt class not disjoint from tract. Consider merging with 'neuron projection bundle' subset: uberon_slim synonym: "fascicle" BROAD [FBbt:00005101] synonym: "fasciculus" EXACT LATIN [] @@ -10978,7 +10979,6 @@ xref: TGMA:0000088 xref: UMLS:C1185741 {source="ncithesaurus:Fascicle"} xref: Wikipedia:Nervous_system_fascicle is_a: UBERON:0000122 ! neuron projection bundle -property_value: editor_note "note FBbt class not disjoint from tract. Consider merging with 'neuron projection bundle'" xsd:string [Term] id: UBERON:0001020 @@ -11839,6 +11839,7 @@ property_value: external_ontology_notes "currently intended for invert structure id: UBERON:0001054 name: Malpighian tubule def: "A tubule that extends from the posterior part of the digestive tract which absorbs solutes, water, and wastes from the surrounding hemolymph. Each tubule consists of a single layer of cells that is closed off at the distal end with the proximal end joining the alimentary canal at the junction between the midgut and hindgut[WP,modified]." [Wikipedia:Malpighian_tubule_system] +comment: EDITOR_NOTE this will be ceded to the Arthropod Anatomy Ontology subset: efo_slim subset: uberon_slim synonym: "Malphigian tube" RELATED MISSPELLING [BTO:0000810] @@ -11856,7 +11857,6 @@ xref: TGMA:0001038 xref: Wikipedia:Malpighian_tubule is_a: UBERON:0009773 {source="GO"} ! renal tubule relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda -property_value: editor_note "this will be ceded to the Arthropod Anatomy Ontology" xsd:string property_value: taxon_notes "It is unclear as to whether the Malpighian tubules of arachnids and those of the Uniramia are homologous or the result of convergent evolution.[Wikipedia:Malpighian_tubule_system]" xsd:string [Term] @@ -12012,6 +12012,7 @@ id: UBERON:0001064 name: ventral pancreatic duct alt_id: UBERON:0005627 def: "A duct joining the pancreas to the common bile duct to supply pancreatic juices which aid in digestion provided by the exocrine pancreas. The pancreatic duct joins the common bile duct just prior to the ampulla of Vater, after which both ducts perforate the medial side of the second portion of the duodenum at the major duodenal papilla." [Wikipedia:Pancreatic_duct] +comment: EDITOR_NOTE in EHDAA2 this is an epithelium, in FMA the wall consists of epithelium and connective tissue subset: uberon_slim synonym: "canal of Wirsung" RELATED [BTO:0002362] synonym: "chief pancreatic duct" EXACT [FMA:16003] @@ -12042,13 +12043,13 @@ relationship: develops_from UBERON:0003924 {source="EHDAA2"} ! ventral pancreati relationship: part_of UBERON:0000017 ! exocrine pancreas property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1100.png" xsd:anyURI property_value: development_notes "Upon reaching its final destination, the ventral pancreatic bud fuses with the much larger dorsal pancreatic bud. At this point of fusion, the main ducts of the ventral and dorsal pancreatic buds fuse, forming the duct of Wirsung, the main pancreatic duct." xsd:string {source="WP"} -property_value: editor_note "in EHDAA2 this is an epithelium, in FMA the wall consists of epithelium and connective tissue" xsd:string property_value: homology_notes "These data show that ducts within the zebrafish pancreas originally arise in situ from isolated progenitor cells rather than arising from reiterative branching of the pancreatic epithelium. This process of pancreatic duct formation in zebrafish may be analogous to the mechanism of duct formation in the mammalian mammary and salivary glands. (...) A related mechanism of duct formation has also been proposed to occur within the mammalian pancreatic epithelium.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000256", ontology="VHOG", source="DOI:10.1016/j.ydbio.2005.04.035 Yee NS, Lorent K, Pack M, Exocrine pancreas development in zebrafish. Developmental Biology (2005)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0001065 name: parotid main excretory duct def: "The main excretory tubular canal that connects the parotid gland and the buccal mucosa and secretes a serous saliva into the vestibule of the oral cavity; it arises from the anterior surface of the gland, traversing the masseter muscle; the duct then pierces the buccinator muscle, moving medially, and opens out into the oral cavity near the second upper molar; saliva produced by acinar secretory cells in the glandular body flows sequentially through the intercalated ducts, striated ducts, and excretory ducts." [MP:0009530] +comment: EDITOR_NOTE we follow MP in identifying the 'parotid duct' with the main excretory duct, although in fact the parotid has many other ducts of different types subset: pheno_slim subset: uberon_slim synonym: "duct of parotid" BROAD [OBOL:automatic] @@ -12078,7 +12079,6 @@ relationship: channels_from UBERON:0001831 ! parotid gland relationship: contributes_to_morphology_of UBERON:0001831 ! parotid gland relationship: part_of UBERON:0001831 ! parotid gland property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/a1/Gray1023.png" xsd:anyURI -property_value: editor_note "we follow MP in identifying the 'parotid duct' with the main excretory duct, although in fact the parotid has many other ducts of different types" xsd:string [Term] id: UBERON:0001066 @@ -12140,6 +12140,7 @@ property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/d2/Gr id: UBERON:0001068 name: skin of back def: "A zone of skin that is part of a back [Automatically generated definition]." [OBOL:automatic] +comment: EDITOR_NOTE TODO - distinguish between entire skin of region and arbitrary zone of skin on region subset: pheno_slim synonym: "back skin" EXACT [] synonym: "back zone of skin" EXACT [OBOL:automatic] @@ -12154,7 +12155,6 @@ is_a: UBERON:0001085 {source="MA"} ! skin of trunk intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0001137 ! dorsum relationship: part_of UBERON:0011270 {source="MA"} ! dorsal trunk -property_value: editor_note "TODO - distinguish between entire skin of region and arbitrary zone of skin on region" xsd:string [Term] id: UBERON:0001069 @@ -12440,6 +12440,7 @@ property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/d0/Pe id: UBERON:0001079 name: prezygapophysis def: "Paired processes at the cephalic end of the neural arch. The articular facets of the prezygapophyses face dorsomedially and articulate with the lateroventrally facing facets of the postzygapophyses of the preceding vertebra." [AAO:Pugener_and_Maglia_2008] +comment: EDITOR_NOTE TODO - add distinct classes for hemal vs neural? subset: vertebrate_core synonym: "cranial articular process of vertebra" EXACT [] synonym: "neural prezygapophyses" RELATED PLURAL [TAO:0001325] @@ -12460,7 +12461,6 @@ xref: SCTID:42424006 xref: TAO:0001325 xref: ZFA:0001325 is_a: UBERON:0006062 ! zygapophysis -property_value: editor_note "TODO - add distinct classes for hemal vs neural?" xsd:string property_value: external_definition "Paired, anteromedially directed processes from the neural arches, ligamentously joined to the postzygapophyses of the preceding vertebra.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001325", ontology="TAO", source="ZFIN:curator"} [Term] @@ -12568,6 +12568,7 @@ property_value: homology_notes "As noted, the hearts of birds and mammals have f id: UBERON:0001084 name: skin of head def: "A zone of skin that is part of a head [Automatically generated definition]." [OBOL:automatic] +comment: EDITOR_NOTE TODO - distinguish between entire skin of region and arbitrary zone of skin on region synonym: "adult head zone of skin" EXACT [OBOL:automatic] synonym: "head skin" EXACT [] synonym: "head zone of skin" EXACT [OBOL:automatic] @@ -12582,12 +12583,12 @@ xref: UMLS:C0205029 {source="ncithesaurus:Head_Skin"} is_a: UBERON:0000014 ! zone of skin intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0000033 ! head -property_value: editor_note "TODO - distinguish between entire skin of region and arbitrary zone of skin on region" xsd:string [Term] id: UBERON:0001085 name: skin of trunk def: "A zone of skin that is part of a trunk [Automatically generated definition]." [OBOL:automatic] +comment: EDITOR_NOTE TODO - distinguish between entire skin of region and arbitrary zone of skin on region synonym: "torso zone of skin" EXACT [OBOL:automatic] synonym: "trunk skin" EXACT [] synonym: "trunk zone of skin" EXACT [OBOL:automatic] @@ -12603,7 +12604,6 @@ xref: UMLS:C0205031 {source="ncithesaurus:Skin_of_the_Trunk"} is_a: UBERON:0000014 ! zone of skin intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0002100 ! trunk -property_value: editor_note "TODO - distinguish between entire skin of region and arbitrary zone of skin on region" xsd:string [Term] id: UBERON:0001086 @@ -12708,6 +12708,7 @@ property_value: structure_notes "The fluid contains hyaluronan secreted by fibro id: UBERON:0001091 name: calcareous tooth def: "Skeletal element within the mouth (or in some species, upper part of the digestive tract) that is composed of dentine and is used in procuring or masticating food." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Tooth_(animal)] +comment: EDITOR_NOTE we place ZFA ctb 5 tooth here for now. Consider changing name from calcaeeous tooth. Note that sea cucumbers develop calcareous tooth-like structures subset: efo_slim subset: pheno_slim subset: uberon_slim @@ -12750,7 +12751,6 @@ relationship: never_in_taxon NCBITaxon:9257 {source="PMID:10210685"} ! Ornithorh relationship: never_in_taxon NCBITaxon:9761 ! Mysticeti relationship: part_of UBERON:0011595 {gci_relation="part_of", gci_filler="NCBITaxon:32523"} ! jaw region property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/14/Teeth_by_David_Shankbone.jpg" xsd:anyURI -property_value: editor_note "we place ZFA ctb 5 tooth here for now. Consider changing name from calcaeeous tooth. Note that sea cucumbers develop calcareous tooth-like structures" xsd:string property_value: has_relational_adjective "dental" xsd:string property_value: homology_notes "The ancestor of recent vertebrate teeth was a tooth-like structure on the outer body surface of jawless fishes.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001733", ontology="VHOG", source="PMID:19266065 Koussoulakou DS, Margaritis LH, Koussoulakos SL, A curriculum vitae of teeth: evolution, generation, regeneration. International Journal of Biological Sciences (2009)", source="http://bgee.unil.ch/"} property_value: taxon_notes "absent in living platypus, present in toothed Miocene platypus Obduron dicksoni" xsd:string {source="PMID:10210685"} @@ -12833,6 +12833,7 @@ property_value: vertebra_number "2" xsd:nonNegativeInteger id: UBERON:0001094 name: sacral vertebra def: "A vertebra bone that is part of the sacral region of the vertebral column." [http://orcid.org/0000-0002-6601-2165] +comment: EDITOR_NOTE todo - AAO placement to be confirmed by AAO curators (the AAO class may also include modified ribs) subset: pheno_slim subset: uberon_slim synonym: "sacral segment" EXACT [] @@ -12851,7 +12852,6 @@ xref: XAO:0003078 intersection_of: UBERON:0015010 ! sacral vertebra endochondral element intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue relationship: develops_from UBERON:0010745 ! sacral vertebra cartilage element -property_value: editor_note "todo - AAO placement to be confirmed by AAO curators (the AAO class may also include modified ribs)" xsd:string property_value: external_definition "Enlarged vertebra with transverse processes (diapophyses), and ocassionally ribs, that are modified and elaborated for support of the pelvic girdle.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000552", ontology="AAO", source="AAO:Duellman_and_Trueb_1994"} [Term] @@ -15950,7 +15950,7 @@ xref: Wikipedia:Peyer's_patch is_a: UBERON:0001962 {source="FMA", source="MA"} ! gut-associated lymphoid tissue relationship: never_in_taxon NCBITaxon:8459 {source="PMID:PMID:20181529"} ! Testudines relationship: only_in_taxon NCBITaxon:32524 {source="PMID:PMID:20181529"} ! Amniota -relationship: part_of UBERON:0000030 {editor_note="check this"} ! lamina propria +relationship: part_of UBERON:0000030 {comment="EDITOR_NOTE check this"} ! lamina propria relationship: part_of UBERON:0001242 ! intestinal mucosa property_value: external_ontology_notes "FMA has [set of?] [aggregated,small] lymphoid [follice,nodule] of [colon, SI, I, etc]" xsd:string {external_ontology="FMA"} property_value: external_ontology_notes "Pp is a syn for Aggregated lymphoid follicle of small intestine; but MA uses Pp as covering both SI and LI. MA also includes follicle as a part. WP says duodenum and jejunum lack PPs" xsd:string {external_ontology="MA"} @@ -22424,7 +22424,7 @@ relationship: preaxialmost_part_of UBERON:0002398 ! manus property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Thumb-up.jpg" xsd:anyURI property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/2/2c/Thumbs_up.jpg" xsd:anyURI property_value: taxon_notes "Not present in Anurans (Phenotype RCN Oct 2012)" xsd:string -property_value: taxon_notes "This class represents the standard tetrapod configuration. Wagner proposes that avian digits I,II,III develop from C2,C3,C4. To support this scheme we have separate classes representing the avian digits (here called alula, manual digit, major digit)." xsd:string {scope="NCBITaxon:8782", seeAlso="UBERON:0012260", source="PMID:10220427", source="PhenoscapeRCN"} +property_value: taxon_notes "This class represents the standard tetrapod configuration. Wagner proposes that avian digits I,II,III develop from C2,C3,C4. To support this scheme we have separate classes representing the avian digits (here called alula, manual digit, major digit)." xsd:string {scope="NCBITaxon:8782", source="PMID:10220427", source="PhenoscapeRCN", seeAlso="UBERON:0012260"} [Term] id: UBERON:0001464 @@ -28122,7 +28122,7 @@ relationship: part_of UBERON:0010272 ! hyoid apparatus property_value: axiom_lost_from_external_ontology "relationship loss: part_of hyoid plate (AAO:0000664)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000684", ontology="AAO"} property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1f/Gray186.png" xsd:anyURI property_value: external_definition "Paired processes that extend posterolaterally from the posterior margin of the hyoid plate. These processes are the ossified posteromedial processes and invest the laryngeal apparatus.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000684", ontology="AAO", source="AAO:LAP"} -property_value: taxon_notes "The hyoid bone is derived from the lower half of the second gill arch in fish, which separates the first gill slit from the spiracle. In many animals, it also incorporates elements of other gill arches, and has a correspondingly greater number of cornua. Amphibians and reptiles may have many cornua, while mammals (including humans) have two pairs, and birds only one. In birds, and some reptiles, the body of the hyoid is greatly extended forward, creating a solid bony support for the tongue. The howler monkey Alouatta has a pneumatized hyoid bone, one of the few cases of postcranial pneumatization of bones outside Saurischia." xsd:string {seeAlso="https://github.com/obophenotype/uberon/issues/548", source="WP"} +property_value: taxon_notes "The hyoid bone is derived from the lower half of the second gill arch in fish, which separates the first gill slit from the spiracle. In many animals, it also incorporates elements of other gill arches, and has a correspondingly greater number of cornua. Amphibians and reptiles may have many cornua, while mammals (including humans) have two pairs, and birds only one. In birds, and some reptiles, the body of the hyoid is greatly extended forward, creating a solid bony support for the tongue. The howler monkey Alouatta has a pneumatized hyoid bone, one of the few cases of postcranial pneumatization of bones outside Saurischia." xsd:string {source="WP", seeAlso="https://github.com/obophenotype/uberon/issues/548"} [Term] id: UBERON:0001686 @@ -34096,7 +34096,7 @@ xref: VHOG:0001625 xref: Wikipedia:Olfactory_tubercle is_a: UBERON:0000125 {source="EHDAA2"} ! neural nucleus relationship: contributes_to_morphology_of UBERON:0002894 ! olfactory cortex -relationship: dubious_for_taxon NCBITaxon:9443 {editor_note="check EHDAA2", source="MP"} ! Primates +relationship: dubious_for_taxon NCBITaxon:9443 {source="MP", comment="EDITOR_NOTE check EHDAA2"} ! Primates relationship: mutually_spatially_disjoint_with UBERON:0001882 {source="ABA"} ! nucleus accumbens relationship: part_of UBERON:0002894 {source="EHDAA2-inferred", source="MA", source="VHOG", source="Wikipedia"} ! olfactory cortex relationship: part_of UBERON:0005401 {source="BTO"} ! cerebral hemisphere gray matter @@ -35075,7 +35075,7 @@ xref: Wikipedia:Pineal_gland xref: XAO:0000160 xref: ZFA:0000019 is_a: UBERON:0010134 {source="MA"} ! secretory circumventricular organ -relationship: capable_of GO:0030187 {editor_note="add secretion"} ! melatonin biosynthetic process +relationship: capable_of GO:0030187 {comment="EDITOR_NOTE add secretion"} ! melatonin biosynthetic process relationship: contributes_to_morphology_of UBERON:0001899 ! epithalamus relationship: has_part CL:0000652 ! pinealocyte relationship: has_part CL:0002220 ! interstitial cell of pineal gland @@ -38620,7 +38620,7 @@ xref: Wikipedia:Spinal_accessory_nerve xref: XAO:0004214 intersection_of: UBERON:0001021 ! nerve intersection_of: extends_fibers_into UBERON:0020358 ! accessory XI nerve nucleus -relationship: dubious_for_taxon NCBITaxon:8292 {seeAlso="http://code.google.com/p/xenopus-anatomy-ontology/issues/detail?id=7", source="VHOG", source="Wikipedia"} ! Amphibia +relationship: dubious_for_taxon NCBITaxon:8292 {source="VHOG", source="Wikipedia", seeAlso="http://code.google.com/p/xenopus-anatomy-ontology/issues/detail?id=7"} ! Amphibia relationship: innervates UBERON:0001737 ! larynx relationship: innervates UBERON:3010692 {gci_relation="part_of", gci_filler="NCBITaxon:8292", source="ISBN:080184780X"} ! m. cucullaris relationship: only_in_taxon NCBITaxon:32523 ! Tetrapoda @@ -44581,7 +44581,7 @@ xref: Wikipedia:Nerve_root is_a: UBERON:0000122 ! neuron projection bundle relationship: extends_fibers_into UBERON:0001017 ! central nervous system relationship: extends_fibers_into UBERON:0001021 ! nerve -relationship: part_of UBERON:0001016 {editor_note="we do not commit to CNS or PNS to allow for flexibility with this class"} ! nervous system +relationship: part_of UBERON:0001016 {comment="EDITOR_NOTE we do not commit to CNS or PNS to allow for flexibility with this class"} ! nervous system property_value: editor_note "We consider cranial nerve roots to be primarily CNS structures, but model spinal nerve roots as PNS structures, due to the existence of ganglia on the roots." xsd:string property_value: external_definition "The continuation of the neurite bundle and associated glia of a nerve, inside the central nervous system[FBbt:00007602, FBC:DOS]." xsd:string {source="FBbt:00007602, FBC:DOS"} property_value: external_ontology_notes "FMA has 'central zone of nerve' which is the superclass of cranial nerve tracts, which the FMA sometimes calls roots" xsd:string {external_ontology="FMA"} @@ -45475,7 +45475,7 @@ property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/4/43/Ce id: UBERON:0002246 name: dorsal thoracic nucleus def: "Two column-shaped nuclear masses formed by large cells. Clarke's nuclei are located in the regions dorsolateral to the central canal in the thoratic and upper lumbar segments." [NLXANAT:20090102] -comment: "Created by Sarah M. Maynard" xsd:string +comment: Created by Sarah M. Maynard subset: uberon_slim synonym: "Clarke's column" EXACT [] synonym: "Clarke's nuclei" RELATED PLURAL [NLXANAT:20090102] @@ -47106,6 +47106,7 @@ property_value: taxon_notes "the basic trilaminar structure of the dentate gyrus id: UBERON:0002305 name: layer of hippocampus def: "The layers of the laminar structure of the hippocampus." [MP:0000813, Wikipedia:Hippocampus_anatomy#Hippocampal_Cells_and_Layers] +comment: EDITOR_NOTE TODO - check NIF xref subset: pheno_slim synonym: "cytoarchitectural fields of hippocampal formation" EXACT [BIRNLEX:1192] synonym: "hippocampus layer" EXACT [] @@ -47120,12 +47121,12 @@ xref: Wikipedia:Hippocampus_anatomy#Hippocampal_Cells_and_Layers intersection_of: UBERON:0016548 ! central nervous system gray matter layer intersection_of: part_of UBERON:0002421 ! hippocampal formation relationship: contributes_to_morphology_of UBERON:0002421 ! hippocampal formation -property_value: editor_note "TODO - check NIF xref" xsd:string [Term] id: UBERON:0002306 name: nasal mucus def: "Mucus produced in the nasal cavity, by the respiratory segment of the nasal mucosa." [http://orcid.org/0000-0002-6601-2165] +comment: EDITOR_NOTE TODO - split nasal vs respiratory tract? subset: uberon_slim synonym: "respiratory mucus" RELATED [BTO:0003603] xref: BTO:0003603 @@ -47138,7 +47139,6 @@ xref: UMLS:C0225392 {source="ncithesaurus:Nasal_Mucus"} xref: Wikipedia:Nasal_mucus#Respiratory_system intersection_of: UBERON:0000912 ! mucus intersection_of: produced_by UBERON:0015786 ! respiratory segment of nasal mucosa -property_value: editor_note "TODO - split nasal vs respiratory tract?" xsd:string property_value: function_notes "protects the olfactory epithelium and allows odors to dissolve so that they can be detected by olfactory receptor neurons" xsd:string [Term] @@ -47263,6 +47263,7 @@ id: UBERON:0002313 name: hippocampus pyramidal layer alt_id: UBERON:0005369 def: "A cytoarchitectural term denoting the layer of the hippocampus in which pyramidal cells are predominant. Its location is superficial to the Stratum oriens; it is deep to the Stratum radiatum in area CA1 and area CA2 and deep to the Stratum lucidum in area CA3 (Stephan-75) (NeuroNames)." [BIRNLEX:1444] +comment: EDITOR_NOTE this layer changes in its depthwise spatial relation across its extent subset: pheno_slim synonym: "gyrus occipitalis inferior" RELATED LATIN [NeuroNames:156] synonym: "gyrus occipitalis tertius" RELATED LATIN [NeuroNames:156] @@ -47285,7 +47286,6 @@ intersection_of: UBERON:0002305 ! layer of hippocampus intersection_of: deep_to UBERON:0007637 ! hippocampus stratum lucidum intersection_of: immediately_superficial_to UBERON:0005371 ! hippocampus stratum oriens relationship: composed_primarily_of CL:0000598 ! pyramidal neuron -property_value: editor_note "this layer changes in its depthwise spatial relation across its extent" xsd:string [Term] id: UBERON:0002314 @@ -47498,6 +47498,7 @@ relationship: part_of UBERON:0004190 {source="GO"} ! renal glomerulus vasculatur id: UBERON:0002321 name: extraglomerular mesangium def: "The tissue comprised of mesangial cells that fill the triangular space between the macula densa and the afferent and efferent arterioles of the juxtaglomerular apparatus." [ISBN:0-683-40008-8, MP:0011340] +comment: EDITOR_NOTE check MA part_ofs - should be spatially disjoint from renal glomerulus? subset: pheno_slim xref: EMAPA:28278 xref: FMA:84141 @@ -47507,7 +47508,6 @@ relationship: overlaps UBERON:0000074 ! renal glomerulus relationship: part_of UBERON:0001229 {source="MA"} ! renal corpuscle relationship: part_of UBERON:0002303 {source="MA"} ! juxtaglomerular apparatus relationship: part_of UBERON:0002319 {source="MA"} ! mesangium -property_value: editor_note "check MA part_ofs - should be spatially disjoint from renal glomerulus?" xsd:string [Term] id: UBERON:0002322 @@ -47529,6 +47529,7 @@ id: UBERON:0002323 name: coelemic cavity lumen alt_id: UBERON:0000169 def: "The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities." [BTO:0001707] +comment: EDITOR_NOTE check the FMA placement here; ncit placement of body cavity here probably not correct subset: uberon_slim subset: vertebrate_core synonym: "body cavity" BROAD [BTO:0001707] @@ -47555,7 +47556,6 @@ xref: ZFA:0001438 is_a: UBERON:0002553 ! anatomical cavity relationship: luminal_space_of UBERON:0011997 ! coelom relationship: transformation_of UBERON:0003886 {evidence="definitional"} ! future coelemic cavity lumen -property_value: editor_note "check the FMA placement here; ncit placement of body cavity here probably not correct" xsd:string property_value: external_definition "Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA]." xsd:string {date_retrieved="2012-09-12", external_class="ZFA:0001438", ontology="ZFA", source="ZFIN:curator"} property_value: external_definition "The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO]." xsd:string {date_retrieved="2012-09-12", external_class="BTO:0001707", ontology="BTO", source="BTO"} property_value: taxon_notes "In mammals it forms the peritoneal, pleural, and pericardial cavities" xsd:string @@ -47721,8 +47721,8 @@ relationship: only_in_taxon NCBITaxon:7711 {source="GOTAX:0000352"} ! Chordata property_value: axiom_lost_from_external_ontology "relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000155", ontology="TAO"} property_value: axiom_lost_from_external_ontology "relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000155", ontology="TAO"} property_value: axiom_lost_from_external_ontology "relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010569", ontology="AAO"} +property_value: curator_notes "EDITOR_NOTE currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk" xsd:string property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: editor_note "currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk" xsd:string property_value: external_definition "Post-cranial axial segments which form sclerotome and dermomyotome.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010569", ontology="AAO", source="AAO:EJS"} property_value: external_definition "Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000155", ontology="TAO", source="ZFIN:curator"} property_value: has_relational_adjective "somitic" xsd:string @@ -48075,9 +48075,9 @@ relationship: dubious_for_taxon NCBITaxon:117565 {source="ISBN:0073040584", sour relationship: existence_starts_during UBERON:0000110 {source="PMID:11523831"} ! neurula stage relationship: only_in_taxon NCBITaxon:89593 {notes="Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells", source="ISBN:0073040584"} ! Craniata relationship: part_of UBERON:0002346 {source="XAO", source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! neurectoderm +property_value: curator_notes "EDITOR_NOTE consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams)." xsd:string property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png" xsd:anyURI property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI -property_value: editor_note "consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams)." xsd:string property_value: external_definition "A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000045", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010578", ontology="AAO", source="AAO:EJS"} property_value: homology_notes "A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831]" xsd:string {source="PMID:11523831"} @@ -48188,6 +48188,7 @@ property_value: taxon_notes "Thoracic vertebrae in all species are defined as th id: UBERON:0002348 name: epicardium def: "A region of the serous membrane that forms the innermost layer of the pericardium and the outer surface of the heart." [http://orcid.org/0000-0002-6601-2165] +comment: EDITOR_NOTE TODO - check links with UBERON:0002425 visceral serous pericardium. develops from proepicardium. WP:Epicardium -- When considered as a part of the pericardium, it is the inner layer, or visceral pericardium, continuous with the serous layer. subset: pheno_slim subset: uberon_slim subset: vertebrate_core @@ -48211,7 +48212,6 @@ relationship: attaches_to UBERON:0002349 {source="FMA"} ! myocardium relationship: develops_from UBERON:0004160 ! proepicardium relationship: part_of UBERON:0000948 {source="multiple"} ! heart relationship: part_of UBERON:0002425 {source="FMA-inferred"} ! visceral serous pericardium -property_value: editor_note "TODO - check links with UBERON:0002425 visceral serous pericardium. develops from proepicardium. WP:Epicardium -- When considered as a part of the pericardium, it is the inner layer, or visceral pericardium, continuous with the serous layer." xsd:string property_value: external_definition "External layer of the heart.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005057", ontology="TAO", source="ZFIN:curator"} property_value: external_definition "The inner layer of the pericardium that is in contact with the surface of the heart.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010409", ontology="AAO", source="AAO:BJB"} property_value: function_notes "The visceral pericardium apparently produces the pericardial fluid, which lubricates motion between the inner and outer layers of the pericardium. During ventricular contraction, the wave of depolarization moves from endocardial to epicardial surface. [Wikipedia:Epicardium]" xsd:string @@ -48220,6 +48220,7 @@ property_value: function_notes "The visceral pericardium apparently produces the id: UBERON:0002349 name: myocardium def: "The middle layer of the heart, comprised mainly of striated cardiac muscle fibers." [ISBN:0-683-40008-8, MP:0005329] +comment: EDITOR_NOTE TODO - check 'Myocardum proper' in FMA. We superclass the more generic class for now. FMA has is_a muscle layer - should we add this? ZFA and BTO both have is_a 'cardiac muscle' (tissue?). But in U we also follow FMA and have cardiac muscle tissue of myocardium (there is also Fibrocollagenous connective tissue of myocardium), which would be identical (see issue-10). Note that GO also treats left/right ventricular cardiac muscle tissue synonymous with ventricular myocardium subset: efo_slim subset: pheno_slim subset: uberon_slim @@ -48257,7 +48258,6 @@ relationship: has_part UBERON:0002350 ! conducting system of heart relationship: part_of UBERON:0000383 ! musculature of body relationship: part_of UBERON:0000948 ! heart property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/6e/Glanzstreifen.jpg" xsd:anyURI -property_value: editor_note "TODO - check 'Myocardum proper' in FMA. We superclass the more generic class for now. FMA has is_a muscle layer - should we add this? ZFA and BTO both have is_a 'cardiac muscle' (tissue?). But in U we also follow FMA and have cardiac muscle tissue of myocardium (there is also Fibrocollagenous connective tissue of myocardium), which would be identical (see issue-10). Note that GO also treats left/right ventricular cardiac muscle tissue synonymous with ventricular myocardium" xsd:string property_value: external_definition "Robust muscular tunic of the heart which forms the basic part of its walls. Its external surface is covered by the pericardium and its internal one by the endocardium. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000083", ontology="VHOG", source="http://bgee.unil.ch/"} property_value: external_definition "The middle layer of the heart, consisting of cardiac muscle.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010410", ontology="AAO", source="AAO:BJB"} property_value: has_relational_adjective "myocardial" xsd:string @@ -49719,6 +49719,7 @@ property_value: structure_notes "the nasolacrimal duct, the sac is lined by stra id: UBERON:0002393 name: pharyngotympanic tube def: "Organ with organ cavity which connects the cavity of the middle ear to the cavity of the pharynx. Examples: There are only two pharyngotympanic tubes, the right and the left pharyngotympanic tubes.[FMA]." [FMA:FMA, Wikipedia:Eustachian_tube] +comment: EDITOR_NOTE we follow FMA in making this an organ, but include a separate class for the part that is epithelium, which is equivalent to the EHDAA2 structure. From this we infer the developmental relationship subset: organ_slim subset: pheno_slim subset: uberon_slim @@ -49748,7 +49749,6 @@ relationship: has_part UBERON:0010062 ! pharyngotympanic tube epithelium relationship: part_of UBERON:0001756 ! middle ear property_value: axiom_lost_from_external_ontology "relationship loss: part_of braincase and otic capsule skeleton (AAO:0000052)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000146", ontology="AAO"} property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/4/40/Ear-anatomy-text-small-en.svg" xsd:anyURI -property_value: editor_note "we follow FMA in making this an organ, but include a separate class for the part that is epithelium, which is equivalent to the EHDAA2 structure. From this we infer the developmental relationship" xsd:string property_value: external_definition "Furrow on the ventral surface of the otic capsule, and occasionally also the parasphenoid, that houses the Eustachian tube.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000146", ontology="AAO", source="AAO:LAP"} property_value: external_definition "The narrow channel connecting the nasopharynx and the middle ear. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001145", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/auditory+tube"} property_value: homology_notes "The tympanic cavity and auditory tube of an amniote develop from the first embryonic pharyngeal pouch, so they are homologous to the first gill pouch, or spiracle, of a fish. We are uncertain whether this homology strictly applies to the middle ear cavity and auditory tube of lissamphibians, which show certain peculiarities in their development.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001145", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.417", source="http://bgee.unil.ch/"} @@ -49952,6 +49952,7 @@ property_value: has_relational_adjective "manual" xsd:string id: UBERON:0002399 name: lesser omentum def: "The double layer of peritoneum that extends from the liver to the lesser curvature of the stomach and the start of the duodenum. [WP,unvetted]." [Wikipedia:Lesser_omentum] +comment: EDITOR_NOTE exact part of and develops from relationships need to be established subset: uberon_slim synonym: "gastrohepatic omentum" RELATED [Wikipedia:Lesser_omentum] synonym: "omentum minus" RELATED LATIN [Wikipedia:Lesser_omentum] @@ -49972,7 +49973,6 @@ relationship: develops_from UBERON:0005626 {source="EHDAA2", source="Wikipedia"} relationship: part_of UBERON:0001178 {source="FMA"} ! visceral peritoneum relationship: part_of UBERON:0005626 {source="MA"} ! ventral mesogastrium property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray984.png" xsd:anyURI -property_value: editor_note "exact part of and develops from relationships need to be established" xsd:string property_value: external_definition "A membranous extension of the peritoneum from the peritoneal layers covering the ventral and the dorsal surfaces of the stomach and the first part of the duodenum. The lesser omentum extends from the portal fissure of the liver to the diaphragm, where the layers separate to enclose the end of the esophagus. It also forms two ligaments, one associated with the liver, the hepatogastric ligament, and the other, the heptatoduodenal ligament, with the duodenum. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000357", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/lesser+omentum"} [Term] @@ -74714,7 +74714,7 @@ relationship: part_of UBERON:5003622 ! manual digit 2 plus metapodial segment property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/d/d5/Index_finger.JPG" xsd:anyURI property_value: has_relational_adjective "indicis" xsd:string property_value: taxon_notes "Anurans lack manual digit 1, so manual digit 2 is the digit after the prepollex (Phenotype RCN Oct 2012)" xsd:string -property_value: taxon_notes "This class represents the standard tetrapod configuration. Wagner proposes that avian digits I,II,III develop from C2,C3,C4. To support this scheme we have separate classes representing the avian digits (here called alula, manual digit, major digit)." xsd:string {scope="NCBITaxon:8782", seeAlso="UBERON:0012261", source="PMID:10220427", source="PhenoscapeRCN"} +property_value: taxon_notes "This class represents the standard tetrapod configuration. Wagner proposes that avian digits I,II,III develop from C2,C3,C4. To support this scheme we have separate classes representing the avian digits (here called alula, manual digit, major digit)." xsd:string {scope="NCBITaxon:8782", source="PMID:10220427", source="PhenoscapeRCN", seeAlso="UBERON:0012261"} [Term] id: UBERON:0003623 @@ -74751,7 +74751,7 @@ relationship: ambiguous_for_taxon NCBITaxon:8782 ! Aves relationship: part_of UBERON:0012141 {source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! manual digitopodium region relationship: part_of UBERON:5003623 ! manual digit 3 plus metapodial segment property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/f/fd/Middle_finger.jpg" xsd:anyURI -property_value: taxon_notes "This class represents the standard tetrapod configuration. Wagner proposes that avian digits I,II,III develop from C2,C3,C4. To support this scheme we have separate classes representing the avian digits (here called alula, manual digit, major digit)." xsd:string {scope="NCBITaxon:8782", seeAlso="UBERON:0012262", source="PMID:10220427", source="PhenoscapeRCN"} +property_value: taxon_notes "This class represents the standard tetrapod configuration. Wagner proposes that avian digits I,II,III develop from C2,C3,C4. To support this scheme we have separate classes representing the avian digits (here called alula, manual digit, major digit)." xsd:string {scope="NCBITaxon:8782", source="PMID:10220427", source="PhenoscapeRCN", seeAlso="UBERON:0012262"} [Term] id: UBERON:0003624 @@ -76084,7 +76084,7 @@ xref: Wikipedia:Canine_tooth intersection_of: UBERON:0001091 ! calcareous tooth intersection_of: has_quality PATO:0005021 ! unicuspidate disjoint_from: UBERON:0007120 ! premolar tooth -relationship: has_part UBERON:0006844 {count="1", editor_note="cardinality not allowed with transitivity in OWL"} ! cusp of tooth +relationship: has_part UBERON:0006844 {count="1", comment="EDITOR_NOTE cardinality not allowed with transitivity in OWL"} ! cusp of tooth relationship: never_in_taxon NCBITaxon:337687 {notes="Although there are a few exceptions, the dental formula for the great majority of cricetids is 1.0.0.3", source="Wikipedia:Cricetidae"} ! Muroidea relationship: only_in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/5/57/Azawakh_K9.jpg" xsd:anyURI @@ -76163,6 +76163,7 @@ relationship: part_of UBERON:0001091 ! calcareous tooth id: UBERON:0003679 name: mouth floor def: "The ventral area of the mouth. In organisms with a tongue, this is the area under the ventral surface of the tongue[ncit, modified]." [http://orcid.org/0000-0002-6601-2165, ncithesaurus:Floor_of_the_Mouth] +comment: EDITOR_NOTE reclassify after CARO2 overhaul subset: efo_slim subset: pheno_slim synonym: "floor of mouth" EXACT [FMA:86592] @@ -76180,7 +76181,6 @@ xref: SCTID:245786002 xref: UMLS:C0026638 {source="ncithesaurus:Floor_of_the_Mouth"} is_a: UBERON:0001444 ! subdivision of head relationship: part_of UBERON:0000165 ! mouth -property_value: editor_note "reclassify after CARO2 overhaul" xsd:string [Term] id: UBERON:0003680 @@ -113228,7 +113228,7 @@ name: seminal fluid def: "A substance formed from the secretion of one or more glands of the male genital tract in which sperm cells are suspended." [http://orcid.org/0000-0002-6601-2165] synonym: "male genital fluid" RELATED [] synonym: "male genital secretion" RELATED [] -synonym: "milt" NARROW [PMID:31287811, PMID:35203131] {http://purl.obolibrary.org/obo/IAO_0000232="A secretion from the glands of the male reproductive system in some aquatic animals that contains sperm and is sprayed onto the eggs."} +synonym: "milt" NARROW [PMID:31287811, PMID:35203131] {comment="CURATOR NOTE A secretion from the glands of the male reproductive system in some aquatic animals that contains sperm and is sprayed onto the eggs."} synonym: "seminal fluid" RELATED [BTO:0001232] synonym: "seminal plasma" EXACT [BTO:0001232] xref: BTO:0001232 @@ -118700,7 +118700,7 @@ xref: SCTID:304572005 xref: UMLS:C1704302 {source="ncithesaurus:Bicuspid_Tooth"} xref: Wikipedia:Premolar is_a: UBERON:0013164 ! molariform tooth -relationship: has_part UBERON:0006844 {editor_note="cardinality not allowed with transitivity in OWL", min_count="2", taxon_notes="some premolars may have 3 cusps"} ! cusp of tooth +relationship: has_part UBERON:0006844 {min_count="2", comment="TAXON NOTE some premolars may have 3 cusps", comment="cardinality not allowed with transitivity in OWL"} ! cusp of tooth relationship: never_in_taxon NCBITaxon:337687 {notes="Although there are a few exceptions, the dental formula for the great majority of cricetids is 1.0.0.3", source="Wikipedia:Cricetidae"} ! Muroidea property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/6c/Gray1003.png" xsd:anyURI property_value: taxon_notes "In humans, there are two premolars per quadrant, making eight premolars total in the mouth. They have at least two cusps. Premolars can be considered as a 'transitional tooth' during chewing, or mastication. It has properties of both the anterior canines and posterior molars, and so food can be transferred from the canines to the premolars and finally to the molars for grinding, instead of directly from the canines to the molars. The premolars in humans are the maxillary first premolar, maxillary second premolar, mandibular first premolar, and the mandibular second premolar. There is always one large buccal cusp, especially so in the mandibular first premolar. The lower second premolar almost always presents with two lingual cusps. Premolar teeth by definition are permanent teeth distal to the canines preceded by deciduous molars. In primitive mammals there are four premolars per quadrant. The most mesial two have been lost in Catarrhines. Paleontologists refer to human premolars as Pm3 and Pm4" xsd:string @@ -139086,7 +139086,7 @@ name: spleen marginal sinus def: "The border region surrounding the spleen B cell follicles and the periarteriolar lymphoid sheath that separates it from the marginal zone that mediates lymphocyte entry into the white pulp from the blood." [MP:MP] subset: pheno_slim synonym: "splenic marginal sinus" EXACT [MP:0002363] -xref: EMAPA:37964 {source="MA:th", seeAlso="https://github.com/obophenotype/mouse-anatomy-ontology/issues/117"} +xref: EMAPA:37964 {seeAlso="https://github.com/obophenotype/mouse-anatomy-ontology/issues/117", source="MA:th"} xref: MA:0000754 xref: NCIT:C49776 xref: UMLS:C1710157 {source="ncithesaurus:Splenic_Marginal_Sinus"} @@ -142049,7 +142049,7 @@ synonym: "ventral nasal capsule" EXACT [PMID:21270050] xref: AAO:0000303 is_a: UBERON:0010363 {source="TAO"} ! endochondral element relationship: develops_from UBERON:0005945 {source="TAO"} ! neurocranial trabecula -relationship: dubious_for_taxon NCBITaxon:8292 {editor_note="check AAO"} ! Amphibia +relationship: dubious_for_taxon NCBITaxon:8292 {comment="EDITOR_NOTE check AAO"} ! Amphibia relationship: never_in_taxon NCBITaxon:8782 ! Aves relationship: overlaps UBERON:0001703 {source="TAO"} ! neurocranium relationship: part_of UBERON:0002241 {source="TAO"} ! chondrocranium @@ -151884,7 +151884,7 @@ xref: SCTID:361795009 xref: Wikipedia:Malleolus is_a: UBERON:0005913 ! zone of bone organ relationship: part_of UBERON:0004410 ! distal epiphysis of fibula -property_value: taxon_notes "In bovids, the distal end of the fibula is present only as the lateral malleolus, a separate bone that articulates with the lateral side of the distal tibia." xsd:string {scope="NCBITaxon:9895", seeAlso="UBERON:0004410", source="UBERON:skansa"} +property_value: taxon_notes "In bovids, the distal end of the fibula is present only as the lateral malleolus, a separate bone that articulates with the lateral side of the distal tibia." xsd:string {scope="NCBITaxon:9895", source="UBERON:skansa", seeAlso="UBERON:0004410"} [Term] id: UBERON:0012292 @@ -159006,6 +159006,7 @@ relationship: part_of UBERON:0001737 ! larynx id: UBERON:0014374 name: embryoid body def: "Embryoid bodies (EBs) are three-dimensional aggregates of pluripotent stem cells." [EFO:0004988, https://github.com/obophenotype/uberon/issues/245] +comment: EDITOR_NOTE in future this class may be ceded to another ontology if it falls outside the scope of in-vivo, non-pathological biology subset: efo_slim synonym: "embryonic body" RELATED [Wikipedia:Embryoid_body] xref: BTO:0001718 @@ -159014,7 +159015,6 @@ xref: MESH:D058732 xref: Wikipedia:Embryoid_body is_a: UBERON:0002050 {source="EFO"} ! embryonic structure relationship: composed_primarily_of CL:0002248 {source="Wikipedia"} ! pluripotent stem cell -property_value: editor_note "in future this class may be ceded to another ontology if it falls outside the scope of in-vivo, non-pathological biology" xsd:string property_value: external_definition "Embryoid bodies are structures resembling embryos, occurring in several types of germ cell tumors[BTO]." xsd:string {reference="Dorlands_Medical_Dictionary:MerckSource", source="BTO:0001718"} [Term] @@ -181506,7 +181506,7 @@ id: UBERON:0034930 name: auricular feather intersection_of: UBERON:0000022 ! feather intersection_of: surrounds UBERON:0001691 ! external ear -relationship: has_quality PATO:0001297 {editor_note="request more specific terms from PATO"} ! reflectivity +relationship: has_quality PATO:0001297 {comment="EDITOR_NOTE request more specific terms from PATO"} ! reflectivity property_value: function_notes "the auricular feathers play a role in hearing by reflecting and funneling sound into the external acoustic meatus" xsd:string [Term] @@ -223935,7 +223935,7 @@ property_value: dcterms-date "2022-10-31T07:56:47Z" xsd:dateTime id: UBERON:8480041 name: testicular sheath def: "Bilayer sheath that covers both the insect male mature gonad and a portion of genital disc-derived structures. It is composed of an outer pigment cell layer, an inner muscle cell layer, and their respective basal laminae." [PMID:9553045] -synonym: "testis sheath" EXACT [] {http://purl.obolibrary.org/obo/IAO_0000232="https://www.fortunejournals.com/ijpaes/admin/php/uploads/798_pdf.pdf"} +synonym: "testis sheath" EXACT [] {comment="CURATOR NOTE https://www.fortunejournals.com/ijpaes/admin/php/uploads/798_pdf.pdf"} is_a: UBERON:0004923 ! organ component layer relationship: dc-contributor https://orcid.org/0000-0002-0819-0473 ! Paula Duek Roggli relationship: in_taxon NCBITaxon:50557 ! Insecta From 0e9292a61d619c84b1e0f07374ce9c1048442f94 Mon Sep 17 00:00:00 2001 From: aleixpuig <94959119+aleixpuigb@users.noreply.github.com> Date: Thu, 19 Oct 2023 10:18:09 +0100 Subject: [PATCH 02/11] Fixes #3081 Unsats caused by an issue involving tail Fixes #3081 Unsats caused by an issue involving tail --- src/ontology/uberon-edit.obo | 1 - 1 file changed, 1 deletion(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 03c4879b1c..37502fab83 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -53528,7 +53528,6 @@ xref: VHOG:0000201 xref: XAO:0000107 xref: ZFA:0000077 is_a: UBERON:0005423 ! developing anatomical structure -relationship: has_potential_to_develop_into UBERON:0007812 ! post-anal tail relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0000922 ! embryo property_value: editor_note "See notes from https://github.com/obophenotype/uberon/wiki/The-neural-crest" xsd:string From f71e60f4a3f6c9ab378c48f16b4184ffe1bce19c Mon Sep 17 00:00:00 2001 From: aleixpuig <94959119+aleixpuigb@users.noreply.github.com> Date: Mon, 23 Oct 2023 10:07:24 +0100 Subject: [PATCH 03/11] Addresses #3086 NTR pulmonary interlobular septum Addresses #3086 NTR pulmonary interlobular septum --- src/ontology/uberon-edit.obo | 16 +++++++++++++++- 1 file changed, 15 insertions(+), 1 deletion(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 37502fab83..821046a909 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -73137,8 +73137,8 @@ id: UBERON:0003532 name: hindlimb skin def: "A zone of skin that is part of a hindlimb [Automatically generated definition]." [OBOL:automatic] synonym: "hind limb skin" EXACT [OBOL:automatic] -synonym: "lower limb skin" EXACT [https://orcid.org/0000-0002-0819-0473] synonym: "lower limb skin" EXACT [FMA:23102] +synonym: "lower limb skin" EXACT [https://orcid.org/0000-0002-0819-0473] synonym: "skin of hind limb" EXACT [OBOL:automatic] synonym: "skin of hindlimb" EXACT [OBOL:automatic] synonym: "skin of lower extremity" EXACT [OBOL:automatic] @@ -224538,6 +224538,20 @@ intersection_of: part_of UBERON:0004027 ! chorionic plate relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 property_value: dcterms-date "2023-09-14T09:09:36Z" xsd:dateTime +[Term] +id: UBERON:8600022 +name: pulmonary interlobular septum +def: "A septum that surrounds and gives shape to the secondary pulmonary lobules. A pulmonary interlobular septum is composed of connective tissue within which run the pulmonary venules and lymphatic vessels." [doi:10.53347/rID-8764, PMID:3259815] +synonym: "fibrous septum" RELATED [PMID:3259815] +synonym: "interlobular interstitium" RELATED [doi:10.53347/rID-8764] +synonym: "interlobular septa" BROAD PLURAL [PMID:3259815] +synonym: "interlobular septum" BROAD [doi:10.53347/rID-8764] +is_a: UBERON:0000114 ! lung connective tissue +is_a: UBERON:0003037 ! septum +relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 +relationship: surrounds UBERON:0010369 ! secondary pulmonary lobule +property_value: dcterms-date "2023-10-23T08:52:12Z" xsd:dateTime + [Typedef] id: aboral_to name: aboral to From f86fd4a0132ecf361c272091395a0f716ddbeef8 Mon Sep 17 00:00:00 2001 From: aleixpuig <94959119+aleixpuigb@users.noreply.github.com> Date: Mon, 23 Oct 2023 14:20:58 +0100 Subject: [PATCH 04/11] Add vessel relations --- src/ontology/uberon-edit.obo | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 821046a909..d0c82f8665 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -224549,6 +224549,8 @@ synonym: "interlobular septum" BROAD [doi:10.53347/rID-8764] is_a: UBERON:0000114 ! lung connective tissue is_a: UBERON:0003037 ! septum relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 +relationship: overlaps UBERON:0002016 ! pulmonary vein +relationship: overlaps UBERON:0018227 ! pulmonary lymphatic vessel relationship: surrounds UBERON:0010369 ! secondary pulmonary lobule property_value: dcterms-date "2023-10-23T08:52:12Z" xsd:dateTime From 3f84ba0a48537c4c86f31a04e5e2163e2623f78f Mon Sep 17 00:00:00 2001 From: aleixpuig <94959119+aleixpuigb@users.noreply.github.com> Date: Mon, 23 Oct 2023 14:32:23 +0100 Subject: [PATCH 05/11] Unite all axioms in one sentence. --- src/ontology/uberon-edit.obo | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index d0c82f8665..79f9b5f603 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -224541,7 +224541,7 @@ property_value: dcterms-date "2023-09-14T09:09:36Z" xsd:dateTime [Term] id: UBERON:8600022 name: pulmonary interlobular septum -def: "A septum that surrounds and gives shape to the secondary pulmonary lobules. A pulmonary interlobular septum is composed of connective tissue within which run the pulmonary venules and lymphatic vessels." [doi:10.53347/rID-8764, PMID:3259815] +def: "A septum that surrounds and gives shape to the secondary pulmonary lobules, it is composed of connective tissue within which run the pulmonary venules and lymphatic vessels." [doi:10.53347/rID-8764, PMID:3259815] synonym: "fibrous septum" RELATED [PMID:3259815] synonym: "interlobular interstitium" RELATED [doi:10.53347/rID-8764] synonym: "interlobular septa" BROAD PLURAL [PMID:3259815] From 271a282d120d1e6cfc39b2466d8b46fc5a197f1f Mon Sep 17 00:00:00 2001 From: aleixpuig <94959119+aleixpuigb@users.noreply.github.com> Date: Tue, 24 Oct 2023 10:08:29 +0100 Subject: [PATCH 06/11] Add dbxref and remove synonym --- src/ontology/uberon-edit.obo | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 79f9b5f603..83a4b5931f 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -73137,8 +73137,8 @@ id: UBERON:0003532 name: hindlimb skin def: "A zone of skin that is part of a hindlimb [Automatically generated definition]." [OBOL:automatic] synonym: "hind limb skin" EXACT [OBOL:automatic] -synonym: "lower limb skin" EXACT [FMA:23102] synonym: "lower limb skin" EXACT [https://orcid.org/0000-0002-0819-0473] +synonym: "lower limb skin" EXACT [FMA:23102] synonym: "skin of hind limb" EXACT [OBOL:automatic] synonym: "skin of hindlimb" EXACT [OBOL:automatic] synonym: "skin of lower extremity" EXACT [OBOL:automatic] @@ -224541,8 +224541,7 @@ property_value: dcterms-date "2023-09-14T09:09:36Z" xsd:dateTime [Term] id: UBERON:8600022 name: pulmonary interlobular septum -def: "A septum that surrounds and gives shape to the secondary pulmonary lobules, it is composed of connective tissue within which run the pulmonary venules and lymphatic vessels." [doi:10.53347/rID-8764, PMID:3259815] -synonym: "fibrous septum" RELATED [PMID:3259815] +def: "A septum that surrounds and gives shape to the secondary pulmonary lobules, it is composed of connective tissue within which run the pulmonary venules and lymphatic vessels." [doi:10.53347/rID-8764, PMID:22283705, PMID:3259815] synonym: "interlobular interstitium" RELATED [doi:10.53347/rID-8764] synonym: "interlobular septa" BROAD PLURAL [PMID:3259815] synonym: "interlobular septum" BROAD [doi:10.53347/rID-8764] From 2494303464a3bfe08fa1a798e686ea1e6bbe602b Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Tue, 24 Oct 2023 11:09:04 +0200 Subject: [PATCH 07/11] Add xrefs curated in Biomappings (#2950) * Update uberon-edit.obo * Update uberon-edit.obo * Remove names --- src/ontology/uberon-edit.obo | 61 ++++++++++++++++++++++++++++++++++++ 1 file changed, 61 insertions(+) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 37502fab83..728a925225 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -784,6 +784,7 @@ synonym: "Komplexauge" RELATED [BTO:0001921] synonym: "zusammengesetztes Auge" RELATED [BTO:0001921] xref: BTO:0001921 xref: HAO:0000217 +xref: IDOMAL:0002421 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: TGMA:0000024 xref: Wikipedia:Compound_eye intersection_of: UBERON:0000970 ! eye @@ -2175,6 +2176,7 @@ def: "The surface (external) layer of ectoderm which begins to proliferate short subset: pheno_slim synonym: "surface (external) ectoderm" EXACT [] synonym: "surface ectoderm" EXACT [MP:0012532] +xref: BTO:0006242 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: EHDAA2:0001968 xref: EHDAA:1494 xref: EHDAA:350 @@ -2815,6 +2817,7 @@ xref: BILS:0000106 xref: EFO:0001322 xref: EHDAA:27 xref: FBdv:00005288 +xref: IDOMAL:0000302 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: NCIT:C12601 xref: PdumDv:0000100 xref: VHOG:0000745 @@ -4992,6 +4995,7 @@ property_value: taxon_notes "In humans it is a tendon-like structure that has de id: UBERON:0000353 name: parenchyma def: "Functional part of an organ in the body. This is in contrast to the stroma, which refers to the structural tissue of organs, being exactly, connective tissues." [Wikipedia:Parenchyma] +xref: BTO:0001539 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: EHDAA:3015 xref: EHDAA:3905 xref: EHDAA:3999 @@ -6931,6 +6935,7 @@ xref: EV:0100000 xref: FMA:7149 xref: galen:AnatomicalSystem xref: HAO:0000011 +xref: IDOMAL:0002460 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: MA:0000003 xref: NCIT:C12919 xref: SCTID:278195005 @@ -7246,6 +7251,7 @@ name: anatomical cluster def: "Anatomical group whose component anatomical structures lie in close proximity to each other." [FBbt:00007277] subset: common_anatomy subset: upper_level +xref: IDOMAL:0002461 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: VHOG:0001737 is_a: UBERON:0034923 ! disconnected anatomical group relationship: present_in_taxon NCBITaxon:33090 ! Viridiplantae @@ -7336,6 +7342,7 @@ xref: BILA:0000054 xref: CARO:0000054 xref: EHDAA2:0003054 xref: HAO:0000054 +xref: IDOMAL:0002459 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: TAO:0001512 xref: TGMA:0001846 xref: VHOG:0001724 @@ -7974,6 +7981,7 @@ xref: EMAPA:16039 xref: FMA:69068 xref: GAID:963 xref: http://neurolex.org/wiki/Category\:Embryonic_organism +xref: IDOMAL:0000646 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: MAT:0000226 xref: MESH:D004622 xref: MIAA:0000019 @@ -35972,6 +35980,7 @@ synonym: "nucleus preopticus lateralis" RELATED LATIN [NeuroNames:381] xref: BAMS:LPO xref: BIRNLEX:1722 xref: BM:Die-Hy-LPO +xref: BTO:0006166 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: DHBA:10471 xref: EMAPA:35483 xref: FMA:62326 @@ -36597,6 +36606,7 @@ xref: BAMS:R xref: BAMS:RN xref: BIRNLEX:1478 xref: BM:MB-RN +xref: BTO:0006329 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: DHBA:12247 xref: EHDAA2:0004706 xref: EMAPA:35724 @@ -39175,6 +39185,7 @@ synonym: "nucleus praeopticus medialis" RELATED LATIN [NeuroNames:380] synonym: "nucleus preopticus medialis" RELATED LATIN [NeuroNames:380] xref: BAMS:MPO xref: BIRNLEX:706 +xref: BTO:0006167 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: DHBA:10470 xref: DMBA:15604 xref: EMAPA:35549 @@ -42489,6 +42500,7 @@ xref: FMA:72429 xref: HBA:9021 xref: MA:0001020 xref: MBA:1052 +xref: mesh:D045042 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: neuronames:504 {source="BIRNLEX:1437"} xref: UMLS:C0262306 {source="BIRNLEX:1437"} xref: Wikipedia:Pedunculopontine_tegmental_nucleus @@ -44772,6 +44784,7 @@ def: "Group of neurons situated on the ventral surface of the fornix at the leve subset: uberon_slim synonym: "organum subfornicale" RELATED LATIN [Wikipedia:Subfornical_organ] xref: BAMS:SFO +xref: BTO:0006266 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: DHBA:12104 xref: EMAPA:35830 xref: FMA:75260 @@ -45923,6 +45936,7 @@ def: "The celiac ganglia are two large irregularly shaped masses of nerve tissue subset: uberon_slim synonym: "coeliac ganglion" EXACT [FMA:77570] xref: BAMS:GCE +xref: BTO:0006296 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: EHDAA2:0000266 xref: EHDAA:8946 xref: EMAPA:19321 @@ -50319,6 +50333,7 @@ subset: vertebrate_core synonym: "vertebra bone" EXACT [] synonym: "vertebrae" EXACT PLURAL [PHENOSCAPE:ad] xref: AAO:0000691 +xref: BTO:0006196 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: CALOHA:TS-2352 xref: EFO:0001371 xref: EMAPA:32740 @@ -50863,6 +50878,7 @@ xref: BAMS:LH xref: BAMS:LHA xref: BIRNLEX:4037 xref: BM:Die-Hy-HLA +xref: BTO:0006481 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: EMAPA:35480 xref: FMA:62030 xref: GAID:640 @@ -55666,6 +55682,7 @@ xref: BAMS:MEPO xref: BAMS:MnPO xref: BIRNLEX:1208 xref: BM:MPO +xref: BTO:0006168 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: DHBA:13063 xref: FMA:62323 xref: HBA:4548 @@ -57226,6 +57243,7 @@ xref: BAMS:OV xref: BAMS:SoC xref: BAMS:VOLT xref: BIRNLEX:1400 +xref: BTO:0006268 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: DHBA:12106 xref: DMBA:15582 xref: EMAPA:37742 {source="MA:th"} @@ -57740,6 +57758,7 @@ xref: BAMS:P xref: BIRNLEX:1464 xref: BM:CST xref: BM:Me-PyT +xref: BTO:0006132 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: DHBA:12776 xref: DMBA:17756 xref: EMAPA:36600 @@ -57993,6 +58012,7 @@ synonym: "tractus rubrospinalis" RELATED LATIN [Wikipedia:Rubrospinal_tract] xref: BAMS:rs xref: BAMS:rust xref: BIRNLEX:1476 +xref: BTO:0006159 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: DHBA:12782 xref: DMBA:17792 xref: FMA:72640 @@ -58904,6 +58924,7 @@ synonym: "lateral occipitotemporal gyrus (heimer-83)" EXACT [] xref: BAMS:ITG xref: BIRNLEX:1577 xref: BM:Tel-ITG +xref: BTO:0006175 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: DHBA:12142 xref: FMA:61907 xref: HBA:4147 @@ -58929,6 +58950,7 @@ synonym: "tractus olivocerebellaris" RELATED LATIN [NeuroNames:804] xref: BAMS:oc xref: BAMS:oct xref: BIRNLEX:1579 +xref: BTO:0006157 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: DHBA:12747 xref: FMA:72638 xref: MBA:404 @@ -59380,6 +59402,7 @@ synonym: "gyrus temporalis superior" RELATED LATIN [Wikipedia:Superior_temporal_ xref: BAMS:STG xref: BIRNLEX:1648 xref: BM:Tel-STG +xref: BTO:0006177 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: DHBA:12140 xref: EFO:0001944 xref: FMA:61905 @@ -59431,6 +59454,7 @@ synonym: "medial temporal gyrus" RELATED [Wikipedia:Middle_temporal_gyrus] synonym: "middle (medial) temporal gyrus" RELATED [BAMS:MTG] xref: BAMS:MTG xref: BIRNLEX:1653 +xref: BTO:0006176 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: DHBA:12141 xref: EFO:0002466 xref: FMA:61906 @@ -65453,6 +65477,7 @@ synonym: "olfactory placodes" EXACT PLURAL [] synonym: "placoda nasalis" EXACT LATIN [] synonym: "placoda olfactoria" EXACT LATIN [] xref: AAO:0011076 +xref: BTO:0006222 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: EFO:0003420 xref: EHDAA2:0001232 xref: EHDAA:1504 @@ -65613,6 +65638,7 @@ synonym: "epitrichium" RELATED [MP:0013530] synonym: "EVL" RELATED [ZFA:0001185] synonym: "periderm" RELATED [] synonym: "skin periderm" EXACT [EHDAA2:0001846] +xref: BTO:0003377 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: EHDAA2:0001846 xref: EHDAA:6538 xref: FMA:295662 @@ -65722,6 +65748,7 @@ synonym: "archinephric duct" RELATED [VHOG:0000082] synonym: "ductus pronephricus" RELATED LATIN [Wikipedia:Pronephric_duct] synonym: "pronephric ducts" RELATED PLURAL [ZFA:0000150] xref: AAO:0011088 +xref: BTO:0005991 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: NCIT:C34279 xref: SCTID:361406002 xref: TAO:0000150 @@ -66146,6 +66173,7 @@ synonym: "Leydig's duct" RELATED [Wikipedia:Wolffian_duct] synonym: "renal duct" RELATED [] synonym: "Wolffian duct" EXACT [GOC:yaf, Wikipedia:Wolffian_duct, ZFA:0000546] xref: AAO:0000637 +xref: BTO:0005990 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: EHDAA2:0001243 xref: EHDAA:1590 xref: EMAPA:16577 @@ -66551,6 +66579,7 @@ synonym: "sclerotomes" EXACT PLURAL [TAO:0001080] synonym: "sclerotomus" RELATED LATIN [Wikipedia:Sclerotome] xref: AAO:0010571 xref: AEO:0000212 +xref: BTO:0006255 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: EHDAA2:0003439 xref: EMAPA:31159 xref: FMA:295652 @@ -76169,6 +76198,7 @@ synonym: "floor of mouth" EXACT [FMA:86592] synonym: "floor of oval cavity" EXACT [] synonym: "floor of the oval cavity" EXACT [] synonym: "sublingual region" NARROW [GAID:1283] +xref: BTO:0006184 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: CALOHA:TS-2207 xref: EFO:0001923 xref: EMAPA:37911 {source="MA:th"} @@ -76339,6 +76369,7 @@ comment: Design pattern notes: check whether this fits the foramen design patter subset: pheno_slim subset: vertebrate_core xref: AAO:0010826 +xref: BTO:0006035 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: EMAPA:37868 {source="MA:th"} xref: FMA:75306 xref: GAID:228 @@ -78986,6 +79017,7 @@ synonym: "choroid plexus epithelial tissue" EXACT [OBOL:automatic] synonym: "epithelial tissue of chorioid plexus of cerebral hemisphere" EXACT [OBOL:automatic] synonym: "epithelial tissue of choroid plexus" EXACT [OBOL:automatic] synonym: "epithelium of choroid plexus" EXACT [FMA:242811] +xref: BTO:0006008 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: EMAPA:36608 xref: FMA:242811 xref: MA:0000824 @@ -79406,6 +79438,7 @@ synonym: "gland of reproductive system" EXACT [OBOL:automatic] synonym: "reproductive gland" EXACT [MA:0001751] synonym: "reproductive system gland" EXACT [OBOL:automatic] synonym: "sex gland" EXACT [MP:0000653] +xref: BTO:0006162 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: MA:0001751 intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0000990 ! reproductive system @@ -80647,6 +80680,7 @@ synonym: "epimere mesoderm" RELATED [] synonym: "mesenchyma dermatomiale" RELATED LATIN [Wikipedia:Dermatomal_mesenchyme] xref: AAO:0011028 xref: AEO:0001017 +xref: BTO:0006248 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: EHDAA2_RETIRED:0003428 xref: EHDAA:1719 xref: EHDAA:1725 @@ -89506,6 +89540,7 @@ synonym: "otic region" RELATED [] synonym: "periotic" RELATED [] synonym: "periotic capsule" RELATED [VHOG:0000854] xref: AAO:0010143 +xref: BTO:0005981 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: SCTID:361515007 xref: VHOG:0000854 is_a: UBERON:0010363 ! endochondral element @@ -101085,6 +101120,7 @@ subset: pheno_slim synonym: "circumventricular organ" EXACT [NLXANAT:20090312] synonym: "circumventricular organ of neuraxis" EXACT [FMA:84081] synonym: "CVO" EXACT ABBREVIATION [NLXANAT:20090312] +xref: BTO:0006267 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: EMAPA:35243 xref: FMA:84081 xref: MA:0002942 @@ -102852,6 +102888,7 @@ def: "Multi-tissue structure that arises from the heart rudiment and will become subset: vertebrate_core synonym: "early primitive heart tube" NARROW [EMAPA:16208] synonym: "primitive heart tube" EXACT [EMAPA:16215] +xref: BTO:0006179 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: EHDAA2:0001512 xref: EHDAA:424 xref: EHDAA:436 @@ -122821,6 +122858,7 @@ name: spinothalamic tract def: "A tract that originates from neurons in the spinal central gray and projects to various somatosensory nuclei of the thalamus. It is formed in the medulla by merger of the anterior spinothalamic tract and lateral spinothalamic tract (adapted from Braininfo.org)." [NLXANAT:1010017] xref: BAMS:spth xref: BAMS:stt +xref: BTO:0006128 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: DHBA:12789 xref: MBA:871 xref: MESH:D013133 @@ -128648,6 +128686,7 @@ synonym: "lateral line organ" BROAD [ZFA:0000243] synonym: "neuromast organ" EXACT [PHENOSCAPE:wd] synonym: "neuromasts" EXACT PLURAL [ZFA:0000243] xref: AAO:0001004 +xref: BTO:0006219 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: EFO:0003513 xref: TAO:0000243 xref: ZFA:0000243 @@ -130618,6 +130657,7 @@ name: epibranchial ganglion def: "Cranial ganglion which develops from an epibranchial placode." [PMID:20133851, ZFIN:curator] comment: Epibranchial ganglia orchestrate the development of the cranial neurogenic crest synonym: "epibranchial ganglia" EXACT PLURAL [ZFA:0001555] +xref: BTO:0006250 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: TAO:0001555 xref: ZFA:0001555 is_a: UBERON:0001714 {source="ZFA"} ! cranial ganglion @@ -143007,6 +143047,7 @@ def: "A cartilage element that is part of a splanchnocranium." [OBOL:automatic] subset: efo_slim synonym: "pharyngeal arch cartilages" EXACT PLURAL [ZFA:0001460] synonym: "splanchnocranium cartilage" EXACT [ZFA:0001460] +xref: BTO:0006051 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: EFO:0003689 xref: TAO:0001460 xref: ZFA:0001460 @@ -149099,6 +149140,7 @@ id: UBERON:0011895 name: endomysium def: "A layer of connective tissue that ensheaths a muscle fiber and is composed mostly from reticular fibers. It also contains capillaries, nerves and lymphatics. The term cardiac skeleton is sometimes considered synonymous with endomysium, but sometimes it refers to the combination of the endomysium and perimysium." [Wikipedia:Endomysium] synonym: "fascia of muscle fiber" EXACT [FMA:9729] +xref: BTO:0006241 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: FMA:9729 xref: NCIT:C32517 xref: SCTID:91739007 @@ -149199,6 +149241,7 @@ def: "Plantaris is a vestigial structure and one of the superficial muscles of t subset: efo_slim synonym: "musculus plantaris" EXACT LATIN [] synonym: "plantaris" EXACT [FMA:22543] +xref: BTO:0006312 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: EFO:0001979 xref: EMAPA:36254 xref: FMA:22543 @@ -155101,6 +155144,7 @@ synonym: "rete mirabilia" RELATED [Wikipedia:Rete_mirabile] synonym: "rete mirabilis" RELATED [Wikipedia:Rete_mirabile] synonym: "retie mirabilia" RELATED PLURAL [Wikipedia:Rete_mirabile] synonym: "wonderful net" RELATED [Wikipedia:Rete_mirabile] +xref: BTO:0006363 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: FMA:76728 xref: Wikipedia:Rete_mirabile is_a: UBERON:0002049 ! vasculature @@ -158577,6 +158621,7 @@ subset: pheno_slim synonym: "arterial blood" EXACT [FMA:83066] synonym: "blood in artery" EXACT [FMA:83066] synonym: "portion of arterial blood" EXACT [FMA:83066] +xref: BTO:0006188 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: FMA:83066 intersection_of: UBERON:0000178 ! blood intersection_of: located_in UBERON:0001637 ! artery @@ -158588,6 +158633,7 @@ def: "A blood that is part of a vein." [OBOL:automatic] synonym: "blood in vein" EXACT [FMA:83067] synonym: "portion of venous blood" EXACT [FMA:83067] synonym: "venous blood" EXACT [FMA:83067] +xref: BTO:0006187 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: FMA:83067 intersection_of: UBERON:0000178 ! blood intersection_of: located_in UBERON:0001638 ! vein @@ -165498,6 +165544,7 @@ def: "Light reflecting layer found in a variety of different types of eye." [htt subset: functional_classification synonym: "tapetal layer" EXACT [] synonym: "tapetum layer" EXACT [] +xref: BTO:0001350 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: SPD:0000343 is_a: UBERON:0000479 ! tissue relationship: has_quality PATO:0001297 ! reflectivity @@ -181852,6 +181899,7 @@ def: "One of several small clusters of chemoreceptors, baroreceptors, and suppor synonym: "aortic bodies" RELATED PLURAL [Wikipedia:Aortic_body] synonym: "aortic glands" RELATED PLURAL [Wikipedia:Aortic_body] synonym: "Zuckerkandl's body" RELATED [Wikipedia:Aortic_body] +xref: BTO:0006193 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: MESH:D001016 xref: NCIT:C97112 xref: SCTID:75061007 @@ -182459,6 +182507,7 @@ is_a: UBERON:0000058 ! duct [Term] id: UBERON:0035053 name: interlobular duct of salivary gland +xref: BTO:0006341 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: FMA:60053 intersection_of: UBERON:0014716 ! interlobular duct intersection_of: part_of UBERON:0001044 ! saliva-secreting gland @@ -187833,6 +187882,7 @@ relationship: present_in_taxon NCBITaxon:8292 ! Amphibia [Term] id: UBERON:0036243 name: vaginal fluid +xref: BTO:0003084 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} def: "Fluid that lines the vaginal walls that consists of multiple secretions that collect in the vagina from different glands." [http://www.bumc.bu.edu/sexualmedicine/physicianinformation/female-genital-anatomy/] synonym: "vaginal discharge" RELATED [] synonym: "vaginal secretion" RELATED [] @@ -191637,6 +191687,7 @@ property_value: provenance_notes "This class was sourced from an external ontolo [Term] id: UBERON:2000293 name: synencephalon +xref: BTO:0006476 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: ZFA:0000293 is_a: UBERON:0000481 ! multi-tissue structure relationship: part_of UBERON:0001894 ! diencephalon @@ -191669,6 +191720,7 @@ property_value: provenance_notes "This class was sourced from an external ontolo [Term] id: UBERON:2000298 name: vent +xref: BTO:0006431 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: ZFA:0000298 is_a: UBERON:0003102 ! surface structure property_value: provenance_notes "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string {source="http://purl.obolibrary.org/obo/tao.owl"} @@ -191919,6 +191971,7 @@ synonym: "branchiospine" EXACT [PSPUB:0000164] synonym: "gill rakers" EXACT PLURAL [TAO:0000356] synonym: "gill-raker" EXACT [TAO:0000356] synonym: "gillraker" EXACT [TAO:0000356] +xref: BTO:0002149 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: ZFA:0000356 is_a: UBERON:0008907 ! dermal bone relationship: never_in_taxon NCBITaxon:40674 {source="https://github.com/obophenotype/uberon/issues/2050"} ! Mammalia @@ -212011,6 +212064,7 @@ property_value: provenance_notes "This class was sourced from an external ontolo [Term] id: UBERON:3010489 name: muscular artery +xref: BTO:0004724 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} def: "Part of the external carotid which delivers blood to the mm rectus cervicis and interhyoideus posterior." [AAO:BJB] is_a: UBERON:0001637 ! artery relationship: part_of UBERON:0001070 ! external carotid artery @@ -212336,6 +212390,7 @@ property_value: provenance_notes "This class was sourced from an external ontolo [Term] id: UBERON:3010586 name: vasa efferentia +xref: BTO:0002254 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} def: "Sperm travel through these 4 or 5 fine ducts which pass through the mesorchium from the testis to the sexual kidney." [AAO:BMZ] is_a: UBERON:0006946 ! efferent duct property_value: provenance_notes "This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string {source="http://purl.obolibrary.org/obo/aao.owl"} @@ -214079,6 +214134,7 @@ def: "Median fin that is located posterior to the anus." [TAO:curator] synonym: "nageoire anale" EXACT [PSPUB:0000164] synonym: "proctoptère" EXACT [PSPUB:0000136] synonym: "proctoptérygie" EXACT [PAPUB:0000142, PSPUB:0000140] +xref: BTO:0004652 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: ZFA:0001162 intersection_of: UBERON:0008897 ! fin intersection_of: has_skeleton UBERON:4000166 ! anal fin skeleton @@ -214094,6 +214150,7 @@ synonym: "tail" RELATED [VSAO:0000164] synonym: "tail fin" RELATED [VSAO:0000164] synonym: "uroptère" EXACT [PSPUB:0000135] synonym: "uroptérygie" EXACT [PSPUB:0000140] +xref: BTO:0001827 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: ZFA:0001058 intersection_of: UBERON:0008897 ! fin intersection_of: has_skeleton UBERON:4000167 ! caudal fin skeleton @@ -217092,6 +217149,7 @@ relationship: dc-contributor https://orcid.org/0000-0003-3162-7490 ! Wasila M Da [Term] id: UBERON:4300194 name: photophore +xref: BTO:0001477 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} def: "A light-emitting organ which appears as luminous spots on various marine animals, including fish and cephalopods." [PHENOSCAPE] {comment="https://en.wikipedia.org/wiki/Photophore"} is_a: UBERON:0000062 ! organ relationship: dc-contributor https://orcid.org/0000-0003-3162-7490 ! Wasila M Dahdul @@ -222871,6 +222929,7 @@ name: cerebral nuclei def: "One of three components of the cerebrum that is a composite structure of the endbrain defined on the basis of origin from the ventricular ridge of the embryonic Encephalon. It consists of the extended striatum and the extended pallidum." [neuronames:2677] comment: This was added as a more precise mapping to the Allen brain atlas (as opposed to collection of basal ganglia) synonym: "CNU" EXACT [MBA:623] +xref: BTO:0006534 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: DHBA:10331 xref: HBA:4275 xref: MBA:623 @@ -223523,6 +223582,7 @@ property_value: seeAlso "https://github.com/obophenotype/uberon/issues/476" xsd: [Term] id: UBERON:8450002 name: excretory system +xref: BTO:0006338 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} def: "An anatomical system that eliminates waste products that arise as a result of metabolic activity." [GO:0007588] intersection_of: UBERON:0000467 ! anatomical system intersection_of: capable_of GO:0046903 ! secretion @@ -223924,6 +223984,7 @@ property_value: dcterms-date "2022-11-22T09:15:50Z" xsd:dateTime [Term] id: UBERON:8480040 name: ovarian fluid +xref: BTO:0004569 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} def: "Fish ovary secretion released with eggs." [PMID:8526977] is_a: UBERON:0006537 ! female reproductive gland secretion relationship: dc-contributor https://orcid.org/0000-0002-0819-0473 ! Paula Duek Roggli From ae623e836148fefe904b0aba99320c13e209f58a Mon Sep 17 00:00:00 2001 From: aleixpuig <94959119+aleixpuigb@users.noreply.github.com> Date: Tue, 24 Oct 2023 11:01:42 +0100 Subject: [PATCH 08/11] Remove axiom that will be replaced in a new PR --- src/ontology/uberon-edit.obo | 1 - 1 file changed, 1 deletion(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 83a4b5931f..6660988931 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -224548,7 +224548,6 @@ synonym: "interlobular septum" BROAD [doi:10.53347/rID-8764] is_a: UBERON:0000114 ! lung connective tissue is_a: UBERON:0003037 ! septum relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -relationship: overlaps UBERON:0002016 ! pulmonary vein relationship: overlaps UBERON:0018227 ! pulmonary lymphatic vessel relationship: surrounds UBERON:0010369 ! secondary pulmonary lobule property_value: dcterms-date "2023-10-23T08:52:12Z" xsd:dateTime From 21e7141a3034e7ca684d9a4a880fdcc0cececc4d Mon Sep 17 00:00:00 2001 From: Anita Caron Date: Wed, 25 Oct 2023 16:21:13 +0100 Subject: [PATCH 09/11] Make base for GO import (#3097) * `make_base` for GO import * refresh imports * add mirror_from `go-base.owl` Co-authored-by: Nico Matentzoglu * update imports --------- Co-authored-by: Anita Caron Co-authored-by: Nico Matentzoglu --- src/ontology/Makefile | 5 +- src/ontology/imports/merged_import.owl | 1255 +++++++++--------------- src/ontology/uberon-odk.yaml | 3 +- 3 files changed, 443 insertions(+), 820 deletions(-) diff --git a/src/ontology/Makefile b/src/ontology/Makefile index 3951dcad80..f81e195d50 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -427,8 +427,9 @@ mirror-cl: | $(TMPDIR) .PHONY: mirror-go .PRECIOUS: $(MIRRORDIR)/go.owl mirror-go: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/go/go-base.owl --create-dirs -o $(MIRRORDIR)/go.owl --retry 4 --max-time 200 &&\ - $(ROBOT) convert -i $(MIRRORDIR)/go.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I http://purl.obolibrary.org/obo/go/go-base.owl -o $@.tmp.owl && \ + $(ROBOT) remove -i $@.tmp.owl --base-iri http://purl.obolibrary.org/obo/GO_ --base-iri http://purl.obolibrary.org/obo/GOREL_ --base-iri http://purl.obolibrary.org/obo/GOCHE_ --axioms external --preserve-structure false --trim false -o $@.tmp.owl &&\ + mv $@.tmp.owl $(TMPDIR)/$@.owl; fi ## ONTOLOGY: envo diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl index 44bebed8e7..fa2f60b947 100644 --- a/src/ontology/imports/merged_import.owl +++ b/src/ontology/imports/merged_import.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2023-09-18") + +Annotation(owl:versionInfo "2023-10-24") Declaration(Class()) Declaration(Class()) @@ -833,7 +833,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1093,7 +1092,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1439,6 +1437,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1463,7 +1462,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1706,6 +1704,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2170,6 +2169,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2196,8 +2196,11 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -2229,7 +2232,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3964,6 +3966,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -5119,13 +5122,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -5425,7 +5424,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -5884,10 +5882,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -6109,6 +6105,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8102,6 +8099,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -9076,7 +9076,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -10042,6 +10041,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -10566,6 +10566,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -10648,6 +10649,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -11166,7 +11168,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -11218,6 +11219,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -11477,6 +11479,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -11572,6 +11576,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -11695,6 +11700,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -11723,6 +11729,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -11753,6 +11760,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -12082,6 +12090,8 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -12104,7 +12114,6 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -12119,8 +12128,6 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -12164,9 +12171,7 @@ Declaration(AnnotationProperty() Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -12190,7 +12195,6 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -12207,7 +12211,6 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -12219,7 +12222,7 @@ Declaration(AnnotationProperty(rdfs:label)) Declaration(AnnotationProperty(rdfs:seeAlso)) Declaration(AnnotationProperty(owl:deprecated)) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) ############################ @@ -12250,35 +12253,26 @@ AnnotationAssertion(rdfs:isDefinedBy "curator note"@en) AnnotationAssertion(rdfs:label "curator note") -# Annotation Property: (term tracker item) - -AnnotationAssertion( "IAO:0000233") -AnnotationAssertion( "external") -AnnotationAssertion( "term_tracker_item") -AnnotationAssertion( "true"^^xsd:boolean) -AnnotationAssertion( "true"^^xsd:boolean) -AnnotationAssertion( "term_tracker_item") -AnnotationAssertion(rdfs:label "term tracker item") - # Annotation Property: (expand assertion to) AnnotationAssertion(rdfs:label "expand assertion to") # Annotation Property: (preferred_root) -AnnotationAssertion( "IAO:0000700") -AnnotationAssertion( "external") -AnnotationAssertion( "has_ontology_root_term") -AnnotationAssertion( "true"^^xsd:boolean) -AnnotationAssertion( "true"^^xsd:boolean) -AnnotationAssertion( "has_ontology_root_term") -AnnotationAssertion(rdfs:label "has ontology root term") AnnotationAssertion(rdfs:label "preferred_root") # Annotation Property: (term replaced by) AnnotationAssertion(rdfs:label "term replaced by") +# Annotation Property: () + +SubAnnotationPropertyOf( ) + +# Annotation Property: () + +SubAnnotationPropertyOf( ) + # Annotation Property: (never in taxon) AnnotationAssertion( "tooth SubClassOf 'never in taxon' value 'Aves'") @@ -12433,10 +12427,6 @@ SubAnnotationPropertyOf( ) -# Annotation Property: () - -SubAnnotationPropertyOf( ) - # Annotation Property: () SubAnnotationPropertyOf( ) @@ -12465,14 +12455,6 @@ SubAnnotationPropertyOf( ) -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - # Annotation Property: () SubAnnotationPropertyOf( ) @@ -12641,18 +12623,10 @@ SubAnnotationPropertyOf( ) -# Annotation Property: () - -SubAnnotationPropertyOf( ) - # Annotation Property: () SubAnnotationPropertyOf( ) -# Annotation Property: () - -SubAnnotationPropertyOf( ) - # Annotation Property: () SubAnnotationPropertyOf( ) @@ -12757,7 +12731,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "BFO:0000050") -AnnotationAssertion( "external") AnnotationAssertion( "quality") AnnotationAssertion( "spatial") AnnotationAssertion( "part_of") @@ -12792,7 +12765,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. An occurre AnnotationAssertion( "has_part"@en) AnnotationAssertion( ) AnnotationAssertion( "BFO:0000051") -AnnotationAssertion( "external") AnnotationAssertion( "quality") AnnotationAssertion( "spatial") AnnotationAssertion( "has_part") @@ -12815,12 +12787,9 @@ AnnotationAssertion( "preceded_by"@en) AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:preceded_by") AnnotationAssertion( "BFO:0000062") -AnnotationAssertion( "external") -AnnotationAssertion( "preceded_by") AnnotationAssertion( ) AnnotationAssertion( "preceded_by") AnnotationAssertion(rdfs:label "preceded by"@en) -AnnotationAssertion(rdfs:label "preceded by") SubObjectPropertyOf( ) InverseObjectProperties( ) TransitiveObjectProperty() @@ -12832,12 +12801,9 @@ ObjectPropertyRange( "precedes"@en) AnnotationAssertion( "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point."@en) AnnotationAssertion( "BFO:0000063") -AnnotationAssertion( "external") -AnnotationAssertion( "precedes") AnnotationAssertion( ) AnnotationAssertion( "precedes") AnnotationAssertion(rdfs:label "precedes"@en) -AnnotationAssertion(rdfs:label "precedes") SubObjectPropertyOf( ) TransitiveObjectProperty() ObjectPropertyDomain( ) @@ -12851,8 +12817,6 @@ AnnotationAssertion( "unfolds in"@en) AnnotationAssertion( "unfolds_in"@en) AnnotationAssertion( "BFO:0000066") -AnnotationAssertion( "external") -AnnotationAssertion( "occurs_in") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -12860,7 +12824,6 @@ AnnotationAssertion( "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant") AnnotationAssertion(rdfs:isDefinedBy ) AnnotationAssertion(rdfs:label "occurs in"@en) -AnnotationAssertion(rdfs:label "occurs in") AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Occurs_in"^^xsd:anyURI) InverseObjectProperties( ) ObjectPropertyDomain( ) @@ -13270,7 +13233,7 @@ SubObjectPropertyOf( ) FunctionalObjectProperty() -# Object Property: (bearer of) +# Object Property: (has characteristic) AnnotationAssertion( "bearer of"@en) AnnotationAssertion( "this apple is bearer of this red color"@en) @@ -13281,12 +13244,8 @@ AnnotationAssertion( "is bearer of"@en) AnnotationAssertion( ) AnnotationAssertion( "RO:0000053") -AnnotationAssertion( "external") -AnnotationAssertion( "bearer_of") -AnnotationAssertion( "bearer_of") AnnotationAssertion( "has_characteristic") AnnotationAssertion(rdfs:label "has characteristic"@en) -AnnotationAssertion(rdfs:label "bearer of") InverseFunctionalObjectProperty() ObjectPropertyRange( ) @@ -13299,11 +13258,8 @@ AnnotationAssertion( "a relation between a continuant and a process, in which the continuant is somehow involved in the process"@en) AnnotationAssertion( "participates_in"@en) AnnotationAssertion( "RO:0000056") -AnnotationAssertion( "external") -AnnotationAssertion( "participates_in") AnnotationAssertion( "participates_in") AnnotationAssertion(rdfs:label "participates in"@en) -AnnotationAssertion(rdfs:label "participates in") InverseObjectProperties( ) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -13319,11 +13275,8 @@ AnnotationAssertion( "has_participant"@en) AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:has_participant") AnnotationAssertion( "RO:0000057") -AnnotationAssertion( "external") -AnnotationAssertion( "has_participant") AnnotationAssertion( "has_participant") AnnotationAssertion(rdfs:label "has participant"@en) -AnnotationAssertion(rdfs:label "has participant") ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -13544,13 +13497,10 @@ has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000") AnnotationAssertion( ) AnnotationAssertion( "RO:0002007") -AnnotationAssertion( "external") -AnnotationAssertion( "bounding_layer_of") AnnotationAssertion( ) AnnotationAssertion( "bounding_layer_of") AnnotationAssertion(rdfs:comment "A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane.") AnnotationAssertion(rdfs:label "bounding layer of"@en) -AnnotationAssertion(rdfs:label "bounding layer of") SubObjectPropertyOf( ) ObjectPropertyDomain( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) ObjectPropertyRange( ) @@ -13561,8 +13511,6 @@ AnnotationAssertion( ) AnnotationAssertion( "2017-05-24T09:30:46Z"^^xsd:dateTime) AnnotationAssertion( "RO:0002013") -AnnotationAssertion( "external") -AnnotationAssertion( "has_regulatory_component_activity") AnnotationAssertion( "has_regulatory_component_activity") AnnotationAssertion(rdfs:label "has regulatory component activity") SubObjectPropertyOf( ) @@ -13574,8 +13522,6 @@ AnnotationAssertion( ) AnnotationAssertion( "2017-05-24T09:31:01Z"^^xsd:dateTime) AnnotationAssertion( "RO:0002014") -AnnotationAssertion( "external") -AnnotationAssertion( "has_negative_regulatory_component_activity") AnnotationAssertion( "has_negative_regulatory_component_activity") AnnotationAssertion(rdfs:comment "By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.") AnnotationAssertion(rdfs:label "has negative regulatory component activity") @@ -13712,12 +13658,9 @@ TransitiveObjectProperty() AnnotationAssertion( "David Osumi-Sutherland") AnnotationAssertion( "starts_at_end_of") AnnotationAssertion( "RO:0002087") -AnnotationAssertion( "external") -AnnotationAssertion( "immediately_preceded_by") AnnotationAssertion( "immediately_preceded_by") AnnotationAssertion(rdfs:comment "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)"@en) AnnotationAssertion(rdfs:label "immediately preceded by"@en) -AnnotationAssertion(rdfs:label "immediately preceded by") SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -13729,13 +13672,10 @@ AnnotationAssertion( "meets") AnnotationAssertion( ) AnnotationAssertion( "RO:0002090") -AnnotationAssertion( "external") -AnnotationAssertion( "immediately_precedes") AnnotationAssertion( ) AnnotationAssertion( "immediately_precedes") AnnotationAssertion(rdfs:comment "X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)"@en) AnnotationAssertion(rdfs:label "immediately precedes"@en) -AnnotationAssertion(rdfs:label "immediately precedes") SubObjectPropertyOf( ) # Object Property: (has soma location) @@ -13833,7 +13773,6 @@ AnnotationAssertion(Annotation( "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)") AnnotationAssertion( ) AnnotationAssertion( "RO:0002131") -AnnotationAssertion( "external") AnnotationAssertion( "spatial") AnnotationAssertion( "overlaps") AnnotationAssertion( ) @@ -14045,12 +13984,9 @@ AnnotationAssertion( "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit."@en) AnnotationAssertion( ) AnnotationAssertion( "RO:0002180") -AnnotationAssertion( "external") -AnnotationAssertion( "has_component") AnnotationAssertion( ) AnnotationAssertion( "has_component") AnnotationAssertion(rdfs:label "has component"@en) -AnnotationAssertion(rdfs:label "has component") AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) @@ -14144,14 +14080,11 @@ AnnotationAssertion( "regulates (processual)") AnnotationAssertion( "false"^^xsd:boolean) AnnotationAssertion( "RO:0002211") -AnnotationAssertion( "external") -AnnotationAssertion( "regulates") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "regulates") AnnotationAssertion(rdfs:label "regulates"@en) -AnnotationAssertion(rdfs:label "regulates") AnnotationAssertion(rdfs:label "regulates (processual)") SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -14167,14 +14100,11 @@ AnnotationAssertion( "negatively regulates (process to process)") AnnotationAssertion( ) AnnotationAssertion( "RO:0002212") -AnnotationAssertion( "external") -AnnotationAssertion( "negatively_regulates") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "negatively_regulates") AnnotationAssertion(rdfs:label "negatively regulates"@en) -AnnotationAssertion(rdfs:label "negatively regulates") SubObjectPropertyOf( ) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -14187,14 +14117,11 @@ AnnotationAssertion( "positively regulates (process to process)") AnnotationAssertion( ) AnnotationAssertion( "RO:0002213") -AnnotationAssertion( "external") -AnnotationAssertion( "positively_regulates") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "positively_regulates") AnnotationAssertion(rdfs:label "positively regulates"@en) -AnnotationAssertion(rdfs:label "positively regulates") SubObjectPropertyOf( ) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -14211,12 +14138,9 @@ AnnotationAssertion( ) AnnotationAssertion( "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\".") AnnotationAssertion( "RO:0002215") -AnnotationAssertion( "external") -AnnotationAssertion( "capable_of") AnnotationAssertion( ) AnnotationAssertion( "capable_of") AnnotationAssertion(rdfs:label "capable of"@en) -AnnotationAssertion(rdfs:label "capable of") SubObjectPropertyOf( ) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -14227,11 +14151,8 @@ AnnotationAssertion( ) AnnotationAssertion( "has function in") AnnotationAssertion( "RO:0002216") -AnnotationAssertion( "external") -AnnotationAssertion( "capable_of_part_of") AnnotationAssertion( "capable_of_part_of") AnnotationAssertion(rdfs:label "capable of part of"@en) -AnnotationAssertion(rdfs:label "capable of part of") AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -14261,7 +14182,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "RO:0002220") -AnnotationAssertion( "external") AnnotationAssertion( "spatial") AnnotationAssertion( "adjacent_to") AnnotationAssertion( ) @@ -14326,12 +14246,9 @@ AnnotationAssertion( "Chris Mungall") AnnotationAssertion( "started by") AnnotationAssertion( "RO:0002224") -AnnotationAssertion( "external") -AnnotationAssertion( "starts_with") AnnotationAssertion( ) AnnotationAssertion( "starts_with") AnnotationAssertion(rdfs:label "starts with"@en) -AnnotationAssertion(rdfs:label "starts with") SubObjectPropertyOf( ) SubObjectPropertyOf( ) TransitiveObjectProperty() @@ -14381,12 +14298,9 @@ AnnotationAssertion( "Chris Mungall") AnnotationAssertion( "finished by") AnnotationAssertion( "RO:0002230") -AnnotationAssertion( "external") -AnnotationAssertion( "ends_with") AnnotationAssertion( ) AnnotationAssertion( "ends_with") AnnotationAssertion(rdfs:label "ends with"@en) -AnnotationAssertion(rdfs:label "ends with") SubObjectPropertyOf( ) SubObjectPropertyOf( ) TransitiveObjectProperty() @@ -14398,12 +14312,9 @@ AnnotationAssertion( ) AnnotationAssertion( "starts with process that occurs in") AnnotationAssertion( "RO:0002231") -AnnotationAssertion( "external") -AnnotationAssertion( "has_start_location") AnnotationAssertion( ) AnnotationAssertion( "has_start_location") AnnotationAssertion(rdfs:label "has start location"@en) -AnnotationAssertion(rdfs:label "has start location") SubObjectPropertyOf( ) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -14415,12 +14326,9 @@ AnnotationAssertion( ) AnnotationAssertion( "ends with process that occurs in") AnnotationAssertion( "RO:0002232") -AnnotationAssertion( "external") -AnnotationAssertion( "has_end_location") AnnotationAssertion( ) AnnotationAssertion( "has_end_location") AnnotationAssertion(rdfs:label "has end location"@en) -AnnotationAssertion(rdfs:label "has end location") SubObjectPropertyOf( ) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -14432,15 +14340,12 @@ AnnotationAssertion( ) AnnotationAssertion( "consumes") AnnotationAssertion( "RO:0002233") -AnnotationAssertion( "external") -AnnotationAssertion( "has_input") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "has_input") AnnotationAssertion(rdfs:label "has input"@en) -AnnotationAssertion(rdfs:label "has input") AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Has_input"^^xsd:anyURI) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -14453,15 +14358,12 @@ AnnotationAssertion( ) AnnotationAssertion( "produces") AnnotationAssertion( "RO:0002234") -AnnotationAssertion( "external") -AnnotationAssertion( "has_output") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "has_output") AnnotationAssertion(rdfs:label "has output"@en) -AnnotationAssertion(rdfs:label "has output") AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Has_output"^^xsd:anyURI) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -14634,11 +14536,8 @@ AnnotationAssertion( "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint.") AnnotationAssertion( ) AnnotationAssertion( "RO:0002295") -AnnotationAssertion( "external") -AnnotationAssertion( "results_in_developmental_progression_of") AnnotationAssertion( "results_in_developmental_progression_of") AnnotationAssertion(rdfs:label "results in developmental progression of"@en) -AnnotationAssertion(rdfs:label "results in developmental progression of") AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -14652,14 +14551,11 @@ AnnotationAssertion( ) AnnotationAssertion( "http://www.geneontology.org/GO.doc.development.shtml"^^xsd:anyURI) AnnotationAssertion( "RO:0002296") -AnnotationAssertion( "external") -AnnotationAssertion( "results_in_development_of") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "results_in_development_of") AnnotationAssertion(rdfs:label "results in development of"@en) -AnnotationAssertion(rdfs:label "results in development of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -14671,14 +14567,11 @@ AnnotationAssertion( ) AnnotationAssertion( "GOC:mtg_berkeley_2013") AnnotationAssertion( "RO:0002297") -AnnotationAssertion( "external") -AnnotationAssertion( "results_in_formation_of") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "results_in_formation_of") AnnotationAssertion(rdfs:label "results in formation of"@en) -AnnotationAssertion(rdfs:label "results in formation of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -14692,14 +14585,11 @@ AnnotationAssertion( ) AnnotationAssertion( "GOC:mtg_berkeley_2013") AnnotationAssertion( "RO:0002298") -AnnotationAssertion( "external") -AnnotationAssertion( "results_in_morphogenesis_of") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "results_in_morphogenesis_of") AnnotationAssertion(rdfs:label "results in morphogenesis of"@en) -AnnotationAssertion(rdfs:label "results in morphogenesis of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -14712,14 +14602,11 @@ AnnotationAssertion( ) AnnotationAssertion( "GOC:mtg_berkeley_2013") AnnotationAssertion( "RO:0002299") -AnnotationAssertion( "external") -AnnotationAssertion( "results_in_maturation_of") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "results_in_maturation_of") AnnotationAssertion(rdfs:label "results in maturation of"@en) -AnnotationAssertion(rdfs:label "results in maturation of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -14729,8 +14616,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "RO:0002304") -AnnotationAssertion( "external") -AnnotationAssertion( "causally_upstream_of,_positive_effect") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "causally_upstream_of,_positive_effect") @@ -14746,8 +14631,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "RO:0002305") -AnnotationAssertion( "external") -AnnotationAssertion( "causally_upstream_of,_negative_effect") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "causally_upstream_of,_negative_effect") @@ -14777,14 +14660,11 @@ AnnotationAssertion( ) AnnotationAssertion( "GOC:mtg_berkeley_2013") AnnotationAssertion( "RO:0002315") -AnnotationAssertion( "external") -AnnotationAssertion( "results_in_acquisition_of_features_of") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "results_in_acquisition_of_features_of") AnnotationAssertion(rdfs:label "results in acquisition of features of"@en) -AnnotationAssertion(rdfs:label "results in acquisition of features of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) ObjectPropertyRange( ) @@ -14909,11 +14789,8 @@ AnnotationAssertion( ) AnnotationAssertion( "regulates levels of (process to entity)") AnnotationAssertion( "RO:0002332") -AnnotationAssertion( "external") -AnnotationAssertion( "regulates_levels_of") AnnotationAssertion( "regulates_levels_of") AnnotationAssertion(rdfs:label "regulates levels of"@en) -AnnotationAssertion(rdfs:label "regulates levels of") SubObjectPropertyOf( ) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -14936,12 +14813,9 @@ AnnotationAssertion( ) AnnotationAssertion( "regulated by (processual)") AnnotationAssertion( "RO:0002334") -AnnotationAssertion( "external") -AnnotationAssertion( "regulated_by") AnnotationAssertion( ) AnnotationAssertion( "regulated_by") AnnotationAssertion(rdfs:label "regulated by"@en) -AnnotationAssertion(rdfs:label "regulated by") SubObjectPropertyOf( ) TransitiveObjectProperty() ObjectPropertyDomain( ) @@ -14952,12 +14826,9 @@ ObjectPropertyRange( "inverse of negatively regulates") AnnotationAssertion( ) AnnotationAssertion( "RO:0002335") -AnnotationAssertion( "external") -AnnotationAssertion( "negatively_regulated_by") AnnotationAssertion( ) AnnotationAssertion( "negatively_regulated_by") AnnotationAssertion(rdfs:label "negatively regulated by"@en) -AnnotationAssertion(rdfs:label "negatively regulated by") SubObjectPropertyOf( ) # Object Property: (positively regulated by) @@ -14965,12 +14836,9 @@ SubObjectPropertyOf( "inverse of positively regulates") AnnotationAssertion( ) AnnotationAssertion( "RO:0002336") -AnnotationAssertion( "external") -AnnotationAssertion( "positively_regulated_by") AnnotationAssertion( ) AnnotationAssertion( "positively_regulated_by") AnnotationAssertion(rdfs:label "positively regulated by"@en) -AnnotationAssertion(rdfs:label "positively regulated by") SubObjectPropertyOf( ) # Object Property: (related via localization to) @@ -14989,14 +14857,11 @@ ObjectPropertyRange( "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination.") AnnotationAssertion( ) AnnotationAssertion( "RO:0002338") -AnnotationAssertion( "external") -AnnotationAssertion( "has_target_start_location") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "has_target_start_location") AnnotationAssertion(rdfs:label "has target start location"@en) -AnnotationAssertion(rdfs:label "has target start location") SubObjectPropertyOf( ) # Object Property: (has target end location) @@ -15004,14 +14869,11 @@ SubObjectPropertyOf( "This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l.") AnnotationAssertion( ) AnnotationAssertion( "RO:0002339") -AnnotationAssertion( "external") -AnnotationAssertion( "has_target_end_location") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "has_target_end_location") AnnotationAssertion(rdfs:label "has target end location"@en) -AnnotationAssertion(rdfs:label "has target end location") SubObjectPropertyOf( ) # Object Property: (results in transport along) @@ -15019,11 +14881,8 @@ SubObjectPropertyOf( "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l ") AnnotationAssertion( ) AnnotationAssertion( "RO:0002341") -AnnotationAssertion( "external") -AnnotationAssertion( "results_in_transport_along") AnnotationAssertion( "results_in_transport_along") AnnotationAssertion(rdfs:label "results in transport along"@en) -AnnotationAssertion(rdfs:label "results in transport along") SubObjectPropertyOf( ) # Object Property: (results in transport across) @@ -15031,12 +14890,9 @@ SubObjectPropertyOf( "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m.") AnnotationAssertion( ) AnnotationAssertion( "RO:0002342") -AnnotationAssertion( "external") -AnnotationAssertion( "results_in_transport_across") AnnotationAssertion( ) AnnotationAssertion( "results_in_transport_across") AnnotationAssertion(rdfs:label "results in transport across"@en) -AnnotationAssertion(rdfs:label "results in transport across") SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -15045,11 +14901,8 @@ SubObjectPropertyOf( "'pollen tube growth' results_in growth_of some 'pollen tube'") AnnotationAssertion( ) AnnotationAssertion( "RO:0002343") -AnnotationAssertion( "external") -AnnotationAssertion( "results_in_growth_of") AnnotationAssertion( "results_in_growth_of") AnnotationAssertion(rdfs:label "results in growth of"@en) -AnnotationAssertion(rdfs:label "results in growth of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -15058,11 +14911,8 @@ SubObjectPropertyOf( "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)") AnnotationAssertion( ) AnnotationAssertion( "RO:0002344") -AnnotationAssertion( "external") -AnnotationAssertion( "results_in_transport_to_from_or_in") AnnotationAssertion( "results_in_transport_to_from_or_in") AnnotationAssertion(rdfs:label "results in transport to from or in"@en) -AnnotationAssertion(rdfs:label "results in transport to from or in") SubObjectPropertyOf( ) # Object Property: (member of) @@ -15107,13 +14957,10 @@ SubObjectPropertyOf( "inverse of has output") AnnotationAssertion( ) AnnotationAssertion( "RO:0002353") -AnnotationAssertion( "external") -AnnotationAssertion( "output_of") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "output_of") AnnotationAssertion(rdfs:label "output of"@en) -AnnotationAssertion(rdfs:label "output of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -15302,11 +15149,8 @@ AnnotationAssertion( "inverse of upstream of") AnnotationAssertion( ) AnnotationAssertion( "RO:0002404") -AnnotationAssertion( "external") -AnnotationAssertion( "causally_downstream_of") AnnotationAssertion( "causally_downstream_of") AnnotationAssertion(rdfs:label "causally downstream of"@en) -AnnotationAssertion(rdfs:label "causally downstream of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -15316,11 +15160,8 @@ InverseObjectProperties( ) AnnotationAssertion( ) AnnotationAssertion( "RO:0002405") -AnnotationAssertion( "external") -AnnotationAssertion( "immediately_causally_downstream_of") AnnotationAssertion( "immediately_causally_downstream_of") AnnotationAssertion(rdfs:label "immediately causally downstream of"@en) -AnnotationAssertion(rdfs:label "immediately causally downstream of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -15382,13 +15223,10 @@ AnnotationAssertion(rdfs:label "caus AnnotationAssertion( "p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q.") AnnotationAssertion( ) AnnotationAssertion( "RO:0002411") -AnnotationAssertion( "external") -AnnotationAssertion( "causally_upstream_of") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "causally_upstream_of") AnnotationAssertion(rdfs:label "causally upstream of"@en) -AnnotationAssertion(rdfs:label "causally upstream of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) TransitiveObjectProperty() @@ -15399,11 +15237,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "RO:0002412") -AnnotationAssertion( "external") -AnnotationAssertion( "immediately_causally_upstream_of") AnnotationAssertion( "immediately_causally_upstream_of") AnnotationAssertion(rdfs:label "immediately causally upstream of"@en) -AnnotationAssertion(rdfs:label "immediately causally upstream of") SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -15414,9 +15249,7 @@ AnnotationAssertion( ) AnnotationAssertion( "influences (processual)") AnnotationAssertion( "RO:0002418") -AnnotationAssertion( "external") AnnotationAssertion( "affects") -AnnotationAssertion( "causally_upstream_of_or_within") AnnotationAssertion( "causally_upstream_of_or_within") AnnotationAssertion(rdfs:label "causally upstream of or within") SubObjectPropertyOf( ) @@ -15429,8 +15262,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "RO:0002427") -AnnotationAssertion( "external") -AnnotationAssertion( "causally_downstream_of_or_within") AnnotationAssertion( ) AnnotationAssertion( "causally_downstream_of_or_within") AnnotationAssertion(rdfs:label "causally downstream of or within") @@ -15893,8 +15724,6 @@ AnnotationAssertion( ) AnnotationAssertion( "") AnnotationAssertion( "RO:0002565") -AnnotationAssertion( "external") -AnnotationAssertion( "results_in_movement_of") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -16008,8 +15837,6 @@ AnnotationAssertion( "directly regulates (processual)") AnnotationAssertion( ) AnnotationAssertion( "RO:0002578") -AnnotationAssertion( "external") -AnnotationAssertion( "directly_regulates") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -16040,8 +15867,6 @@ SubObjectPropertyOf( (results in assembly of) AnnotationAssertion( "RO:0002588") -AnnotationAssertion( "external") -AnnotationAssertion( "results_in_assembly_of") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -16053,8 +15878,6 @@ SubObjectPropertyOf( (results in disassembly of) AnnotationAssertion( "RO:0002590") -AnnotationAssertion( "external") -AnnotationAssertion( "results_in_disassembly_of") AnnotationAssertion( "results_in_disassembly_of") AnnotationAssertion(rdfs:label "results in disassembly of") SubObjectPropertyOf( ) @@ -16064,11 +15887,8 @@ SubObjectPropertyOf( "p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c") AnnotationAssertion( "RO:0002592") -AnnotationAssertion( "external") -AnnotationAssertion( "results_in_organization_of") AnnotationAssertion( "results_in_organization_of") AnnotationAssertion(rdfs:label "results in organization of") -SubObjectPropertyOf( ) SubObjectPropertyOf( ) # Object Property: (causal relation between material entity and a process) @@ -16118,8 +15938,6 @@ SubObjectPropertyOf( "Inverse of 'causal agent in process'") AnnotationAssertion( ) AnnotationAssertion( "RO:0002608") -AnnotationAssertion( "external") -AnnotationAssertion( "process_has_causal_agent") AnnotationAssertion( "process_has_causal_agent") AnnotationAssertion(rdfs:label "process has causal agent") SubObjectPropertyOf( ) @@ -16131,8 +15949,6 @@ AnnotationAssertion( "directly positively regulates (process to process)") AnnotationAssertion( ) AnnotationAssertion( "RO:0002629") -AnnotationAssertion( "external") -AnnotationAssertion( "directly_positively_regulates") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -16149,8 +15965,6 @@ AnnotationAssertion( "directly negatively regulates (process to process)") AnnotationAssertion( ) AnnotationAssertion( "RO:0002630") -AnnotationAssertion( "external") -AnnotationAssertion( "directly_negatively_regulates") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -16166,13 +15980,10 @@ AnnotationAssertion( "a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix.") AnnotationAssertion( ) AnnotationAssertion( "RO:0003000") -AnnotationAssertion( "external") -AnnotationAssertion( "produces") AnnotationAssertion( ) AnnotationAssertion( "produces") AnnotationAssertion(rdfs:comment "Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue.") AnnotationAssertion(rdfs:label "produces"@en) -AnnotationAssertion(rdfs:label "produces") InverseObjectProperties( ) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -16183,12 +15994,9 @@ AnnotationAssertion( "a produced_by b iff some process that occurs_in b has_output a.") AnnotationAssertion( ) AnnotationAssertion( "RO:0003001") -AnnotationAssertion( "external") -AnnotationAssertion( "produced_by") AnnotationAssertion( ) AnnotationAssertion( "produced_by") AnnotationAssertion(rdfs:label "produced by"@en) -AnnotationAssertion(rdfs:label "produced by") ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -16198,8 +16006,6 @@ AnnotationAssertion( ) AnnotationAssertion( "2018-12-13T11:26:17Z"^^xsd:dateTime) AnnotationAssertion( "RO:0004007") -AnnotationAssertion( "external") -AnnotationAssertion( "has_primary_input_or_output") AnnotationAssertion( ) AnnotationAssertion( "has_primary_input_or_output") AnnotationAssertion(rdfs:label "has primary input or output") @@ -16211,8 +16017,6 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( "2018-12-13T11:26:32Z"^^xsd:dateTime) AnnotationAssertion( "RO:0004008") -AnnotationAssertion( "external") -AnnotationAssertion( "has_primary_output") AnnotationAssertion( ) AnnotationAssertion( "has_primary_output") AnnotationAssertion(rdfs:label "has primary output") @@ -16225,8 +16029,6 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( "2018-12-13T11:26:56Z"^^xsd:dateTime) AnnotationAssertion( "RO:0004009") -AnnotationAssertion( "external") -AnnotationAssertion( "has_primary_input") AnnotationAssertion( ) AnnotationAssertion( "has_primary_input") AnnotationAssertion(rdfs:label "has primary input") @@ -16334,14 +16136,11 @@ AnnotationAssertion( ) AnnotationAssertion( "2020-06-08T17:21:33Z"^^xsd:dateTime) AnnotationAssertion( "RO:0012003") -AnnotationAssertion( "external") -AnnotationAssertion( "acts_on_population_of") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "acts_on_population_of") AnnotationAssertion(rdfs:label "acts on population of"@en) -AnnotationAssertion(rdfs:label "acts on population of") SubObjectPropertyOf( ) # Object Property: (results in fusion of) @@ -16349,14 +16148,11 @@ SubObjectPropertyOf( ) AnnotationAssertion( "2021-02-26T07:28:29Z"^^xsd:dateTime) AnnotationAssertion( "RO:0012008") -AnnotationAssertion( "external") -AnnotationAssertion( "results_in_fusion_of") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "results_in_fusion_of") AnnotationAssertion(rdfs:label "results in fusion of"@en) -AnnotationAssertion(rdfs:label "results in fusion of") SubObjectPropertyOf( ) # Object Property: (indirectly causally upstream of) @@ -16462,8 +16258,6 @@ AnnotationAssertion(rdfs:label "devi AnnotationAssertion( "A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C.") AnnotationAssertion( ) AnnotationAssertion( "RO:0019000") -AnnotationAssertion( "gene_ontology") -AnnotationAssertion( "regulates_characteristic") AnnotationAssertion( "regulates_characteristic") AnnotationAssertion(rdfs:label "regulates characteristic") SubObjectPropertyOf( ) @@ -16475,8 +16269,6 @@ ObjectPropertyRange( "A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C.") AnnotationAssertion( ) AnnotationAssertion( "RO:0019001") -AnnotationAssertion( "gene_ontology") -AnnotationAssertion( "positively_regulates_characteristic") AnnotationAssertion( "positively_regulates_characteristic") AnnotationAssertion(rdfs:label "positively regulates characteristic") SubObjectPropertyOf( ) @@ -16486,8 +16278,6 @@ SubObjectPropertyOf( "A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C.") AnnotationAssertion( ) AnnotationAssertion( "RO:0019002") -AnnotationAssertion( "gene_ontology") -AnnotationAssertion( "negatively_regulates_characteristic") AnnotationAssertion( "negatively_regulates_characteristic") AnnotationAssertion(rdfs:label "negatively regulates characteristic") SubObjectPropertyOf( ) @@ -16498,8 +16288,6 @@ AnnotationAssertion( ) AnnotationAssertion( "2018-09-26T01:08:58Z"^^xsd:dateTime) AnnotationAssertion( "RO:0040036") -AnnotationAssertion( "external") -AnnotationAssertion( "results_in_changes_to_anatomical_or_cellular_structure") AnnotationAssertion( "results_in_changes_to_anatomical_or_cellular_structure") AnnotationAssertion(rdfs:label "results in changes to anatomical or cellular structure") SubObjectPropertyOf( ) @@ -16734,7 +16522,6 @@ AnnotationAssertion(Annotation( ) "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] ") AnnotationAssertion(rdfs:isDefinedBy ) AnnotationAssertion(rdfs:label "role"@en) -EquivalentClasses( ) SubClassOf( ) # Class: (generically dependent continuant) @@ -20636,7 +20423,6 @@ AnnotationAssertion( "CHEBI:24431") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "chemical entity") -SubClassOf( ) # Class: (biological role) @@ -26041,7 +25827,6 @@ AnnotationAssertion( "CHEBI:36080") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "protein") -EquivalentClasses( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -30686,16 +30471,6 @@ DisjointClasses( ) DisjointClasses( ) -# Class: (native cell) - -AnnotationAssertion(Annotation( "CARO:mah") "A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment).") -AnnotationAssertion( "CARO:0000013") -AnnotationAssertion( "cell in vivo") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12).") -AnnotationAssertion(rdfs:label "native cell") -SubClassOf( ) - # Class: (fibroblast neural crest derived) AnnotationAssertion(Annotation( "https://orcid.org/0000-0001-5208-3432") "Any fibroblast that is deriived from the neural crest.") @@ -30737,7 +30512,6 @@ AnnotationAssertion( "germ line stem cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf(Annotation( "true") ) # Class: (male germ cell) @@ -30762,8 +30536,6 @@ AnnotationAssertion( "WBbt:0006799") AnnotationAssertion(rdfs:label "spermatocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (spermatid) @@ -30778,8 +30550,6 @@ AnnotationAssertion( "nematoblast") AnnotationAssertion(rdfs:label "spermatid") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (sperm) @@ -30796,7 +30566,6 @@ AnnotationAssertion( "spermatozoon") AnnotationAssertion(rdfs:label "sperm") SubClassOf(Annotation( "true") ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (spermatogonium) @@ -30811,7 +30580,6 @@ AnnotationAssertion( "spermatogonial cell") AnnotationAssertion(rdfs:label "spermatogonium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) # Class: (female germ cell) @@ -30854,7 +30622,6 @@ AnnotationAssertion( "oogonial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (egg cell) @@ -30870,8 +30637,7 @@ AnnotationAssertion( "mature oocyte") AnnotationAssertion( "ovum") AnnotationAssertion(rdfs:label "egg cell") -AnnotationAssertion( "https://www.swissbiopics.org/api/image/Egg_cell.svg"^^xsd:anyURI) -SubClassOf( ) +AnnotationAssertion( "https://www.swissbiopics.org/api/image/Egg_cell.svg"^^xsd:anyURI) SubClassOf(Annotation( "true") ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -30896,7 +30662,6 @@ SubClassOf( ObjectSomeValuesFrom( "glioblast") SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (neuroblast (sensu Vertebrata)) @@ -30920,8 +30685,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "This term applies to metazoan. For plant stem cells, consider using PO:0004011 ‘initial cell’ or its parent PO:0004010 ‘meristematic cell’.") AnnotationAssertion(rdfs:label "stem cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -30932,7 +30696,7 @@ AnnotationAssertion( "unipotent stem cell") AnnotationAssertion( "unipotential stem cell") AnnotationAssertion(rdfs:label "single fate stem cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) # Class: (epithelial fate stem cell) @@ -30955,7 +30719,7 @@ AnnotationAssertion( "VHOG:0001485") AnnotationAssertion( "blood forming stem cell") AnnotationAssertion( "hemopoietic stem cell") -AnnotationAssertion(Annotation( ) "HSC") +AnnotationAssertion(Annotation( ) "HSC") AnnotationAssertion( "colony forming unit hematopoietic") AnnotationAssertion( ) AnnotationAssertion( ) @@ -30970,8 +30734,8 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:add") Annotation( "ISBN:0721601464") "A progenitor cell committed to the erythroid lineage.") AnnotationAssertion( "BTO:0004911") -AnnotationAssertion(Annotation( ) "BFU-E") -AnnotationAssertion(Annotation( ) "CFU-E") +AnnotationAssertion(Annotation( ) "BFU-E") +AnnotationAssertion(Annotation( ) "CFU-E") AnnotationAssertion( "blast forming unit erythroid") AnnotationAssertion( "burst forming unit erythroid") AnnotationAssertion( "colony forming unit erythroid") @@ -30989,16 +30753,15 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Originally this term had some plant germ line cell children.") AnnotationAssertion(rdfs:label "germ line cell") -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -DisjointClasses( ) # Class: (monoblast) AnnotationAssertion(Annotation( "GOC:add") Annotation( "PMID:1104740") Annotation( "http://en.wikipedia.org/wiki/Monoblast") Annotation( "http://www.copewithcytokines.de") "A myeloid progenitor cell committed to the monocyte lineage. This cell is CD11b-positive, has basophilic cytoplasm, euchromatin, and the presence of a nucleolus.") AnnotationAssertion( "CALOHA:TS-1195") AnnotationAssertion( "FMA:83553") -AnnotationAssertion(Annotation( ) "CFU-M") +AnnotationAssertion(Annotation( ) "CFU-M") AnnotationAssertion( "colony forming unit macrophage") AnnotationAssertion( "colony forming unit monocyte") AnnotationAssertion( "monocyte stem cell") @@ -31017,7 +30780,7 @@ AnnotationAssertion( "multipotent cell") AnnotationAssertion( "multipotent stem cell") AnnotationAssertion(rdfs:label "multi fate stem cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) # Class: (common myeloid progenitor) @@ -31025,9 +30788,9 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( "BTO:0004730") AnnotationAssertion( "common myeloid precursor") -AnnotationAssertion(Annotation( "ISBN:0878932437") Annotation( ) "CFU-GEMM") -AnnotationAssertion(Annotation( "ISBN:0878932437") Annotation( ) "CFU-S") -AnnotationAssertion(Annotation( "ISBN:0878932437") Annotation( ) "CMP") +AnnotationAssertion(Annotation( "ISBN:0878932437") Annotation( ) "CFU-GEMM") +AnnotationAssertion(Annotation( "ISBN:0878932437") Annotation( ) "CFU-S") +AnnotationAssertion(Annotation( "ISBN:0878932437") Annotation( ) "CMP") AnnotationAssertion(Annotation( "ISBN:0878932437") "colony forming unit granulocyte, erythrocyte, macrophage, and megakaryocyte") AnnotationAssertion(Annotation( "ISBN:0878932437") "multipotential myeloid stem cell") AnnotationAssertion(Annotation( "ISBN:0878932437") "myeloid stem cell") @@ -31067,8 +30830,8 @@ AnnotationAssertion( "common lymphocyte precursor") AnnotationAssertion( "common lymphocyte progenitor") AnnotationAssertion( "common lymphoid precursor") -AnnotationAssertion(Annotation( ) "CLP") -AnnotationAssertion(Annotation( ) "ELP") +AnnotationAssertion(Annotation( ) "CLP") +AnnotationAssertion(Annotation( ) "ELP") AnnotationAssertion( "committed lymphopoietic stem cell") AnnotationAssertion( "early lymphocyte progenitor") AnnotationAssertion( "lymphoid stem cell") @@ -31096,7 +30859,7 @@ AnnotationAssertion( "blast cell") AnnotationAssertion(rdfs:comment "define using PATO mulit-potent or oligopotent?") AnnotationAssertion(rdfs:label "non-terminally differentiated cell") -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (myoblast) @@ -31108,7 +30871,6 @@ AnnotationAssertion( "FMA:70335") AnnotationAssertion( "VHOG:0001529") AnnotationAssertion(rdfs:label "myoblast") -SubClassOf( ) SubClassOf( ) # Class: (fibroblast) @@ -31191,7 +30953,7 @@ AnnotationAssertion(Annotation( "VHOG:0001532") AnnotationAssertion( "XAO:0000031") AnnotationAssertion(rdfs:label "ciliated cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (ependymal cell) @@ -31219,8 +30981,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "epithelial cell") -AnnotationAssertion( "https://www.swissbiopics.org/api/image/Epithelial_cells.svg"^^xsd:anyURI) -SubClassOf( ) +AnnotationAssertion( "https://www.swissbiopics.org/api/image/Epithelial_cells.svg"^^xsd:anyURI) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses( ) @@ -31237,7 +30999,6 @@ AnnotationAssertion(Annotation( "duct epithelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) # Class: (branched duct epithelial cell) @@ -31254,7 +31015,6 @@ AnnotationAssertion(rdfs:label "bloo EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (non-branched duct epithelial cell) @@ -31270,7 +31030,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "columnar/cuboidal epithelial cell") SubClassOf( ) -SubClassOf( ) # Class: (squamous epithelial cell) @@ -31294,14 +31053,13 @@ SubClassOf( ObjectSomeValuesFrom( "stratified epithelial cell") SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (circulating cell) AnnotationAssertion(Annotation( "GOC:add") "A cell which moves among different tissues of the body, via blood, lymph, or other medium.") AnnotationAssertion(rdfs:label "circulating cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (blood cell) @@ -31316,10 +31074,8 @@ SubClassOf(Annotation( # Class: (epithelial cell of lung) AnnotationAssertion(Annotation( "https://orcid.org/0000-0001-5208-3432") "An epithelial cell of the lung.") -AnnotationAssertion( ) AnnotationAssertion( "BTO:0004299") AnnotationAssertion( "lung epithelial cell") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "epithelial cell of lung") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) @@ -31332,8 +31088,6 @@ AnnotationAssertion( "pancreatic epithelial cell") AnnotationAssertion(rdfs:label "epithelial cell of pancreas") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (T cell) @@ -31403,9 +31157,7 @@ AnnotationAssertion( "The term \"neuroepithelial cell\" is used to describe both this cell type and neurecto-epithelial cell (CL:0000710).") AnnotationAssertion(rdfs:label "sensory epithelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) -SubClassOf( ) # Class: (interneuron) @@ -31568,6 +31320,7 @@ SubClassOf( ObjectSomeValuesFrom( (glial cell) AnnotationAssertion(Annotation( "MESH:D009457") "A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons.") +AnnotationAssertion( ) AnnotationAssertion( "BTO:0002606") AnnotationAssertion( "CALOHA:TS-0415") AnnotationAssertion( "FBbt:00005144") @@ -31575,6 +31328,7 @@ AnnotationAssertion( "neuroglial cell") AnnotationAssertion( "neuroglia") AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Not all glial cells develop from glioblasts, with microglia developing from the mesoderm instead. See https://github.com/obophenotype/cell-ontology/issues/1571") AnnotationAssertion(rdfs:label "glial cell") SubClassOf( ) @@ -31586,7 +31340,7 @@ AnnotationAssertion( "CALOHA:TS-2027") AnnotationAssertion( "FMA:54538") AnnotationAssertion( "macrogliocyte") -AnnotationAssertion(Annotation( "doi:10.1152/physrev.2001.81.2.871") Annotation( ) "macroglia") +AnnotationAssertion(Annotation( "doi:10.1152/physrev.2001.81.2.871") Annotation( ) "macroglia") AnnotationAssertion(rdfs:label "macroglial cell") SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -31637,15 +31391,15 @@ AnnotationAssertion( "bone marrow stromal cells") AnnotationAssertion( "colony-forming unit-fibroblast") AnnotationAssertion(Annotation( "PMID:11378515") "marrow stromal cells") -AnnotationAssertion(Annotation( ) "BMSC") -AnnotationAssertion(Annotation( ) "CFU-F") -AnnotationAssertion(Annotation( "PMID:11378515") Annotation( ) "MSC") +AnnotationAssertion(Annotation( ) "BMSC") +AnnotationAssertion(Annotation( ) "CFU-F") +AnnotationAssertion(Annotation( "PMID:11378515") Annotation( ) "MSC") AnnotationAssertion( "mesenchymal precursor cell") -AnnotationAssertion(Annotation( "MESH:D044982") Annotation( ) "mesenchymal progenitor cells") +AnnotationAssertion(Annotation( "MESH:D044982") Annotation( ) "mesenchymal progenitor cells") AnnotationAssertion( "mesenchymal stem cell") AnnotationAssertion( "mesenchymal stromal cell") -AnnotationAssertion(Annotation( ) "mesenchymal stromal cells") -AnnotationAssertion(Annotation( "MESH:D044982") Annotation( ) "stem cells, mesenchymal") +AnnotationAssertion(Annotation( ) "mesenchymal stromal cells") +AnnotationAssertion(Annotation( "MESH:D044982") Annotation( ) "stem cells, mesenchymal") AnnotationAssertion(rdfs:comment "Many but not all mesenchymal cells derive from the mesoderm. MSCs are reportedly CD3-negative, CD4-negative, CD5-negative, CD8-negative, CD11a-negative, CD11b-negative, CD14-negative, CD19-negative, CD29-positive, CD31-negative, CD34-negative, CD38-negative, CD40-negative, CD44-positive, CD45-negative, CD49-positive, CD54-positive, CD66b-negative, CD79a-negative, CD80-negative, CD102-positive, CD106-positive, CD117-positive, CD121a-positive, CD121b-positive, CD123-positive, CD124-positive, CD133-negative, CD146-positive, CD166-positive, CD271-positive, B220-negative, Gr1-negative, MHCI-positive, MHCII-negative, SSEA4-negative, sca1-positive, Ter119-negative, and glycophorin A-negative. Cultured MSCs are capable of producing stem cell factor, IL7, IL8, IL11, TGF-beta, cofilin, galectin-1, laminin-receptor 1, cyclophilin A, and MMP-2.") AnnotationAssertion(rdfs:label "mesenchymal stem cell") AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/cell-ontology/issues/474") @@ -31709,7 +31463,7 @@ SubClassOf( ObjectSomeValuesFrom( (professional antigen presenting cell) AnnotationAssertion(Annotation( "GOC:add") Annotation( "ISBN:0781735149") "A cell capable of processing and presenting lipid and protein antigens to T cells in order to initiate an immune response.") -AnnotationAssertion(Annotation( ) "APC") +AnnotationAssertion(Annotation( ) "APC") AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Note change of name; nearly all somatic cells can present antigens to T cells via MHC Class I complexes leading to effector responses, but professional antigen presenting cells constitutively express MHC Class II as well as costimulatory molecules, and thus can initiate immune responses via T cells.") AnnotationAssertion(rdfs:label "professional antigen presenting cell") @@ -31746,16 +31500,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "melanocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) -SubClassOf( ) -SubClassOf( ) # Class: (visual pigment cell) AnnotationAssertion( "pigment cell") AnnotationAssertion(rdfs:label "visual pigment cell") SubClassOf( ) -SubClassOf( ) # Class: (glandular epithelial cell) @@ -31765,18 +31515,15 @@ AnnotationAssertion( "glandular epithelial cell") SubClassOf( ) SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (secretory cell) AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "ISBN:0721662544") "A cell that specializes in controlled release of one or more substances.") -AnnotationAssertion( ) AnnotationAssertion( "BTO:0003659") AnnotationAssertion( "FMA:86916") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "secretory cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (exocrine cell) @@ -31786,7 +31533,6 @@ AnnotationAssertion( "exocrine cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) # Class: (glycosaminoglycan secreting cell) @@ -31874,8 +31620,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "endocrine cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) -SubClassOf( ) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) SubClassOf( ObjectSomeValuesFrom( )) # Class: (enteroendocrine cell) @@ -32016,6 +31761,7 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( "BTO:0003939") AnnotationAssertion( "FMA:18688") +AnnotationAssertion(Annotation( "PMID:16790079") "corpus luteum cell") AnnotationAssertion( "lutein cell") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "luteal cell") @@ -32042,7 +31788,6 @@ AnnotationAssertion( "Note that the Amphibian Anatomy Ontology (AA) has a class 'leydig cells' but this is unrelated") AnnotationAssertion(rdfs:label "Leydig cell") SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -32063,7 +31808,6 @@ AnnotationAssertion(rdfs:comment "He AnnotationAssertion(rdfs:label "hepatocyte") SubClassOf( ) SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -32074,7 +31818,7 @@ SubClassOf( ObjectSomeValuesFrom( "FB:ma") "A cell whose primary function is to shorten.") AnnotationAssertion(rdfs:label "contractile cell") -SubClassOf( ) +SubClassOf( ) # Class: (myoepithelial cell) @@ -32087,7 +31831,6 @@ AnnotationAssertion( "myoepithelial cell") SubClassOf( ) SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (muscle cell) @@ -32102,11 +31845,9 @@ AnnotationAssertion( "muscle fiber") AnnotationAssertion( "myocyte") AnnotationAssertion(rdfs:label "muscle cell") -AnnotationAssertion( "https://www.swissbiopics.org/api/image/Muscle_cells.svg"^^xsd:anyURI) +AnnotationAssertion( "https://www.swissbiopics.org/api/image/Muscle_cells.svg"^^xsd:anyURI) SubClassOf( ) SubClassOf( ) -SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (cell of skeletal muscle) @@ -32120,8 +31861,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cell of skeletal muscle") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (slow muscle cell) @@ -32165,7 +31905,6 @@ AnnotationAssertion( "receptor cell") AnnotationAssertion(rdfs:label "sensory receptor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) # Class: (pain receptor cell) @@ -32235,7 +31974,7 @@ AnnotationAssertion( "CALOHA:TS-0868") AnnotationAssertion( "FMA:86740") AnnotationAssertion(rdfs:label "photoreceptor cell") -AnnotationAssertion( "https://www.swissbiopics.org/api/image/Photoreceptor_cell.svg"^^xsd:anyURI) +AnnotationAssertion( "https://www.swissbiopics.org/api/image/Photoreceptor_cell.svg"^^xsd:anyURI) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) @@ -32243,7 +31982,7 @@ SubClassOf(Annotation( AnnotationAssertion(Annotation( "FB:ma") "A cell whose function is determined by the generation or the reception of an electric signal.") AnnotationAssertion(rdfs:label "electrically active cell") -SubClassOf( ) +SubClassOf( ) # Class: (lining cell) @@ -32266,7 +32005,7 @@ SubClassOf( ObjectSomeValuesFrom( "JB:jb") "A cell whose primary function is to prevent the transport of stuff across compartments.") AnnotationAssertion(rdfs:label "barrier cell") -SubClassOf( ) +SubClassOf( ) # Class: (Sertoli cell) @@ -32305,7 +32044,7 @@ SubClassOf( ObjectSomeValuesFrom( "FB:ma") "A cell that moves by its own activities.") AnnotationAssertion(rdfs:label "motile cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (ectodermal cell) @@ -32341,19 +32080,19 @@ AnnotationAssertion(Annotation( "FMA:68647") AnnotationAssertion( "non-nucleated cell") AnnotationAssertion(rdfs:label "anucleate cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) DisjointClasses( ) # Class: (single nucleate cell) AnnotationAssertion(Annotation( "FB:ma") Annotation( "GOC:tfm") "A cell with a single nucleus.") AnnotationAssertion(rdfs:label "single nucleate cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (binucleate cell) AnnotationAssertion(rdfs:label "binucleate cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (multinucleate cell) @@ -32364,7 +32103,7 @@ AnnotationAssertion( "syncytial cell") AnnotationAssertion( "syncytium") AnnotationAssertion(rdfs:label "multinucleate cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (erythrocyte) @@ -32411,11 +32150,10 @@ AnnotationAssertion( "FMA:83806") AnnotationAssertion( "MESH:D010586") AnnotationAssertion(rdfs:label "phagocyte") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf( ) SubClassOf( ) -SubClassOf( ) # Class: (macrophage) @@ -32497,18 +32235,17 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "transitional epithelial cell") SubClassOf( ) -SubClassOf( ) # Class: (eukaryotic cell) AnnotationAssertion( "MESH:D005057") AnnotationAssertion(rdfs:label "eukaryotic cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (Eumycetozoan cell) AnnotationAssertion(rdfs:label "Eumycetozoan cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) # Class: (eye photoreceptor cell) @@ -32524,7 +32261,7 @@ SubClassOf( "TAIR:sr") "A cell whose primary function is to provide structural support, to provide strength and physical integrity to the organism.") AnnotationAssertion(rdfs:label "structural cell") -SubClassOf( ) +SubClassOf( ) # Class: (somatotropin secreting cell) @@ -32556,10 +32293,8 @@ SubClassOf( (tracheal epithelial cell) AnnotationAssertion(Annotation( "GOC:tfm") "An epithelial cell found in the trachea.") -AnnotationAssertion( ) AnnotationAssertion( "FMA:74793") AnnotationAssertion( "tracheocyte") -AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "This class is for the vertebrate tracheal structure. For the analagous insect cell type, see 'respiratory tube epithelial cell'") AnnotationAssertion(rdfs:label "tracheal epithelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -32640,7 +32375,7 @@ SubClassOf( ObjectSomeValuesFrom( "FB:ma") "A cell that is specialised to accumulate a particular substance(s).") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "stuff accumulating cell") -SubClassOf( ) +SubClassOf( ) # Class: (extracellular matrix secreting cell) @@ -32650,14 +32385,14 @@ SubClassOf( (oxygen accumulating cell) AnnotationAssertion(rdfs:label "oxygen accumulating cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (migratory neural crest cell) AnnotationAssertion(Annotation( "doi:10.1016/j.stem.2015.02.017") "A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body.") AnnotationAssertion( "FMA:86667") AnnotationAssertion(rdfs:label "migratory neural crest cell") -SubClassOf( ) +SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -32666,7 +32401,6 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:tfm") Annotation( "PMID:5025404") "A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors.") AnnotationAssertion(rdfs:label "mesenchyme condensation cell") -SubClassOf( ) SubClassOf( ) # Class: (adrenal medulla chromaffin cell) @@ -32706,7 +32440,6 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion(rdfs:label "scleral cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (choroidal cell of the eye) @@ -32715,15 +32448,13 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion(rdfs:label "choroidal cell of the eye") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (extraembryonic cell) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "extraembryonic cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (amnioserosal cell) @@ -32806,7 +32537,6 @@ AnnotationAssertion(Annotation( "epidermal cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) # Class: (animal zygote) @@ -32898,19 +32628,20 @@ AnnotationAssertion(rdfs:label "male EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) SubClassOf(Annotation( "true") ) -SubClassOf( ) # Class: (polyploid cell) -AnnotationAssertion(Annotation( "FB:ma") "A cell whose nucleus, or nuclei, each contain more than two haploid genomes.") +AnnotationAssertion(Annotation( "https://bio.libretexts.org/Bookshelves/Introductory_and_General_Biology/Biology_(Kimball)/07%3A_Cell_Division/7.04%3A_Polyploidy"^^xsd:anyURI) Annotation( "FB:ma") Annotation( "PMID:32646579") "A cell that contains more than two haploid sets of chromosomes.") AnnotationAssertion(rdfs:label "polyploid cell") -SubClassOf( ) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (haploid cell) AnnotationAssertion(Annotation( "FB:ma") Annotation( "GOC:tfm") "A cell whose nucleus contains a single haploid genome.") +AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "haploid cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (endopolyploid cell) @@ -33002,7 +32733,6 @@ AnnotationAssertion(Annotation( "CALOHA:TS-1119") AnnotationAssertion( "FMA:83434") AnnotationAssertion( "white adipose cell") -AnnotationAssertion( "white fat cell") AnnotationAssertion( "white adipocyte") AnnotationAssertion(rdfs:label "white fat cell") SubClassOf( ) @@ -33112,7 +32842,7 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "JB:jb") "A cell whose primary function is to protect the organism.") AnnotationAssertion(rdfs:label "defensive cell") -SubClassOf( ) +SubClassOf( ) # Class: (follicle cell of egg chamber) @@ -33164,7 +32894,6 @@ SubClassOf( ObjectSomeValuesFrom( "An epithelial somatic cell associated with a maturing oocyte.") AnnotationAssertion(rdfs:label "follicular epithelial cell") SubClassOf( ) -SubClassOf( ) # Class: (granulosa cell) @@ -33241,7 +32970,6 @@ SubClassOf( "GOC:tfm") Annotation( "ISBN:0198529171") "A paracrine cell is a secretory cell that secretes an agonist into intercellular spaces in which it diffuses to a target cell other than that which produced it.") AnnotationAssertion(rdfs:label "paracrine cell") SubClassOf( ) -SubClassOf( ) # Class: (cardiac muscle myoblast) @@ -33261,8 +32989,6 @@ AnnotationAssertion(Annotation( "satellite cell") AnnotationAssertion(rdfs:label "smooth muscle myoblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) -SubClassOf( ) # Class: (skeletal muscle myoblast) @@ -33271,16 +32997,13 @@ AnnotationAssertion( "skeletal myoblast") AnnotationAssertion(rdfs:label "skeletal muscle myoblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (fungal cell) AnnotationAssertion(rdfs:label "fungal cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -DisjointClasses( ) # Class: (syncytiotrophoblast cell) @@ -33295,7 +33018,7 @@ AnnotationAssertion( "syncytiotrophoblast cell") AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/cell-ontology/issues/2100") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (afferent neuron) @@ -33329,7 +33052,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma.") AnnotationAssertion(rdfs:label "neuron") -AnnotationAssertion( "https://www.swissbiopics.org/api/image/Neuron_cells.svg"^^xsd:anyURI) +AnnotationAssertion( "https://www.swissbiopics.org/api/image/Neuron_cells.svg"^^xsd:anyURI) SubClassOf( ) SubClassOf( ) SubClassOf( ) @@ -33343,8 +33066,6 @@ AnnotationAssertion( "Derived from UBERON:0002342 neural crest.") AnnotationAssertion(rdfs:label "melanoblast") SubClassOf( ) -SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (lymphocyte) @@ -33376,17 +33097,6 @@ EquivalentClasses( ObjectIntersection SubClassOf(Annotation( "true") ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (animal cell) - -AnnotationAssertion( "A native cell that is part of some Metazoa.") -AnnotationAssertion( "metazoan cell") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "animal cell") -AnnotationAssertion( "https://www.swissbiopics.org/api/image/Animal_cells.svg"^^xsd:anyURI) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (basophilic erythroblast) AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "ISBN:0721601464") "A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. This cell is CD71-positive and lacks hematopoeitic lineage markers.") @@ -33487,8 +33197,8 @@ AnnotationAssertion(Annotation( "ISBN:0721601464") Annotation( "PMCID:PMC2213186") Annotation( "PMCID:PMC548021") "granulocyte-macrophage progenitor") AnnotationAssertion( "granulocyte/monocyte precursor") AnnotationAssertion( "granulocyte/monocyte progenitor") -AnnotationAssertion(Annotation( "ISBN:0721601464") Annotation( "PMCID:PMC2213186") Annotation( "PMCID:PMC548021") Annotation( ) "CFU-GM") -AnnotationAssertion(Annotation( "ISBN:0721601464") Annotation( "PMCID:PMC2213186") Annotation( "PMCID:PMC548021") Annotation( ) "GMP") +AnnotationAssertion(Annotation( "ISBN:0721601464") Annotation( "PMCID:PMC2213186") Annotation( "PMCID:PMC548021") Annotation( ) "CFU-GM") +AnnotationAssertion(Annotation( "ISBN:0721601464") Annotation( "PMCID:PMC2213186") Annotation( "PMCID:PMC548021") Annotation( ) "GMP") AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Originally described in the dendritic cell ontology (DC_CL:0000042)(PMID:19243617). GMPs are reportedly CD16-positive, CD32-positive, CD34-positive, CD38-positive, CD45RA-positive, CD110-negative, CD117-positive, CD123-positive, and SCA1-negative.") AnnotationAssertion(rdfs:label "granulocyte monocyte progenitor cell") @@ -33528,8 +33238,8 @@ AnnotationAssertion( "BTO:0004044") AnnotationAssertion( "FMA:67766") AnnotationAssertion( "amacrine neuron") -AnnotationAssertion(Annotation( "doi:10.1038/s41598-020-66092-9") Annotation( ) "AC") -AnnotationAssertion(Annotation( "doi:10.1038/s41598-020-66092-9") Annotation( ) Annotation( ) "ACs") +AnnotationAssertion(Annotation( "doi:10.1038/s41598-020-66092-9") Annotation( ) "AC") +AnnotationAssertion(Annotation( "doi:10.1038/s41598-020-66092-9") Annotation( ) Annotation( ) "ACs") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "amacrine cell") @@ -33551,10 +33261,8 @@ SubClassOf( ObjectSomeValuesFrom( (angioblastic mesenchymal cell) AnnotationAssertion(Annotation( "GOC:dsd") Annotation( "GOC:tfm") Annotation( "PMID:12768659") "A mesenchymal stem cell capable of developing into blood vessel endothelium.") -AnnotationAssertion( ) AnnotationAssertion( "angioblast") AnnotationAssertion( "chondroplast") -AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "These cells are reportedly CD31-positive, CD34-positive, CD144-positive, CD309-positive, and TAL1-positive.") AnnotationAssertion(rdfs:label "angioblastic mesenchymal cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) @@ -33621,7 +33329,6 @@ AnnotationAssertion( "corneal epithelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) # Class: (monocyte) @@ -33669,7 +33376,7 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:add") Annotation( "GOC:tfm") "An erythrocyte lacking a nucleus.") AnnotationAssertion( "red blood cell") -AnnotationAssertion(Annotation( ) "RBC") +AnnotationAssertion(Annotation( ) "RBC") AnnotationAssertion(rdfs:label "enucleate erythrocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) @@ -33684,7 +33391,6 @@ AnnotationAssertion( "NIFSTD:sao862606388") AnnotationAssertion( "projection neuron") AnnotationAssertion( "pyramidal cell") -AnnotationAssertion( "pyramidal neuron") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pyramidal neuron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -33752,7 +33458,7 @@ SubClassOf( ObjectSomeValuesFrom( "TAIR:sr") "A cell involved in transporting nutrients, minerals, water, gases and other chemicals between cells for a variety of purposes including conveying nutrition to other tissues, removing waste products from the tissues, conveying gases for respiration, distributing heat and repelling invasion of foreign substances.") AnnotationAssertion(rdfs:label "transporting cell") -SubClassOf( ) +SubClassOf( ) # Class: (supporting cell) @@ -33760,7 +33466,7 @@ AnnotationAssertion(Annotation( "BTO:0002315") AnnotationAssertion( "supportive cell") AnnotationAssertion(rdfs:label "supporting cell") -SubClassOf( ) +SubClassOf( ) # Class: (hepatic stellate cell) @@ -33824,13 +33530,12 @@ SubClassOf( ObjectSomeValuesFrom( "JB:jb") Annotation( "PMID:10495875") Annotation( "PMID:15961560") Annotation( "doi:10.23937/2572-407X.1510006") "An agranular supporting cell of the anterior pituitary (adenohypophysis) that is characterized by a star-like morphology and ability to form follicles. Folliculostellate cells communicate with each other and with endocrine cells via gap junctions.") AnnotationAssertion(Annotation( "doi:10.23937/2572-407X.1510006") "folliculo-stellate cell") AnnotationAssertion(Annotation( "PMID:34734454") "pituitary folliculostellate cell") -AnnotationAssertion(Annotation( "PMID:34734454") Annotation( ) "FS cell") -AnnotationAssertion(Annotation( "doi:10.23937/2572-407X.1510006") Annotation( ) "FSC") +AnnotationAssertion(Annotation( "PMID:34734454") Annotation( ) "FS cell") +AnnotationAssertion(Annotation( "doi:10.23937/2572-407X.1510006") Annotation( ) "FSC") AnnotationAssertion(Annotation( "PMID:34734454") "Sox2-positive stem cell") AnnotationAssertion(Annotation( "PMID:18287078") Annotation( "PMID:31620083") Annotation( "PMID:34734454") Annotation( "doi:10.23937/2572-407X.1510006") rdfs:comment "Folliculostellate cells are a heterogeneous group of cells rather than a single cell type, with different morphology and gene expression profiles. Due to this heterogeneity, it is unclear if different properties that have been attributed to folliculostellate cells (pluripotent, proliferative, phagocytic) are common in all folliculostellate cells or limited to particular subsets.") AnnotationAssertion(rdfs:label "folliculostellate cell") SubClassOf( ) -SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -33943,8 +33648,6 @@ AnnotationAssertion( "FMA:72292") AnnotationAssertion(rdfs:label "primary spermatocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) -SubClassOf( ) # Class: (secondary spermatocyte) @@ -33955,8 +33658,6 @@ AnnotationAssertion( "FMA:72293") AnnotationAssertion(rdfs:label "secondary spermatocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (fenestrated cell) @@ -33964,7 +33665,6 @@ SubClassOf( ObjectSomeValuesFrom( "window cell") AnnotationAssertion(rdfs:label "fenestrated cell") SubClassOf( ) -SubClassOf( ) # Class: (collagen secreting cell) @@ -34002,7 +33702,6 @@ AnnotationAssertion(rdfs:label "prim EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) SubClassOf(Annotation( "true") ) -SubClassOf( ) # Class: (female gamete) @@ -34028,8 +33727,6 @@ AnnotationAssertion(Annotation( "muscle precursor cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (radial glial cell) @@ -34082,10 +33779,12 @@ SubClassOf( (choroid plexus epithelial cell) AnnotationAssertion(Annotation( "GOC:add") Annotation( "GOC:tfm") Annotation( "JB:jb") Annotation( "PMID:9550134") "Specialized ependymal cell that produces the cerebrospinal fluid from the blood and secretes it into the lumen of the brain and spinal chord.") +AnnotationAssertion( ) AnnotationAssertion( "2023-08-04T08:48:30Z"^^xsd:dateTime) AnnotationAssertion(Annotation( "DOI:10.1101/2022.10.12.511898") "choroid plexus cell") AnnotationAssertion( "FMA:70549") AnnotationAssertion( "epithelial cell of choroid plexus") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "choroid plexus epithelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -34125,8 +33824,6 @@ AnnotationAssertion( "MESH:D053687") AnnotationAssertion(rdfs:label "somatic stem cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) -SubClassOf( ) # Class: (urothelial cell) @@ -34135,7 +33832,6 @@ AnnotationAssertion( "urinary tract transitional epithelial cell") AnnotationAssertion(rdfs:label "urothelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) # Class: (striated muscle cell) @@ -34177,8 +33873,8 @@ AnnotationAssertion( "MESH:D012165") AnnotationAssertion( "gangliocyte") AnnotationAssertion( "ganglion cell of retina") -AnnotationAssertion(Annotation( "doi:10.1038/s41598-020-66092-9") Annotation( ) "RGC") -AnnotationAssertion(Annotation( "doi:10.1038/s41598-020-66092-9") Annotation( ) Annotation( ) "RGCs") +AnnotationAssertion(Annotation( "doi:10.1038/s41598-020-66092-9") Annotation( ) "RGC") +AnnotationAssertion(Annotation( "doi:10.1038/s41598-020-66092-9") Annotation( ) Annotation( ) "RGCs") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "retinal ganglion cell") @@ -34191,8 +33887,8 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( "BTO:0004120") AnnotationAssertion( "horizontal cell") -AnnotationAssertion(Annotation( "doi:10.1038/s41598-020-66092-9") Annotation( ) "HC") -AnnotationAssertion(Annotation( "doi:10.1038/s41598-020-66092-9") Annotation( ) Annotation( ) "HCs") +AnnotationAssertion(Annotation( "doi:10.1038/s41598-020-66092-9") Annotation( ) "HC") +AnnotationAssertion(Annotation( "doi:10.1038/s41598-020-66092-9") Annotation( ) Annotation( ) "HCs") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "retina horizontal cell") @@ -34224,9 +33920,9 @@ SubClassOf( ObjectSomeValuesFrom( "PMID:14689473") "A bipolar neuron found in the retina and having connections with photoreceptors cells and neurons in the inner plexiform layer.") AnnotationAssertion( ) -AnnotationAssertion(Annotation( "doi:10.1038/s41598-020-66092-9") Annotation( ) "BC") -AnnotationAssertion(Annotation( "doi:10.1038/s41598-020-66092-9") Annotation( ) Annotation( ) "BCs") -AnnotationAssertion(Annotation( "GSE137537") Annotation( ) Annotation( ) "BPs") +AnnotationAssertion(Annotation( "doi:10.1038/s41598-020-66092-9") Annotation( ) "BC") +AnnotationAssertion(Annotation( "doi:10.1038/s41598-020-66092-9") Annotation( ) Annotation( ) "BCs") +AnnotationAssertion(Annotation( "GSE137537") Annotation( ) Annotation( ) "BPs") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "retinal bipolar neuron") @@ -34292,8 +33988,6 @@ SubClassOf( ObjectSomeValuesFrom( (myeloid leukocyte) AnnotationAssertion(Annotation( "GOC:add") "A cell of the monocyte, granulocyte, or mast cell lineage.") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "myeloid leukocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) @@ -34372,13 +34066,11 @@ SubClassOf(Annotation( # Class: (myeloid dendritic cell) AnnotationAssertion(Annotation( "GOC:add") Annotation( "PMID:10449155") Annotation( "PMID:17332250") Annotation( "PMID:9521319") "A dendritic cell of the myeloid lineage.") -AnnotationAssertion( ) AnnotationAssertion( "interdigitating cell") AnnotationAssertion( "veiled cell") AnnotationAssertion( "BTO:0004721") AnnotationAssertion( "CD11c+CD123- DC") AnnotationAssertion( "mDC") -AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "These cells are CD1a-negative, CD1b-positive, CD11a-positive, CD11c-positive, CD13-positive, CD14-negative, CD20-negative, CD21-negative, CD33-positive, CD40-negative, CD50-positive, CD54-positive, CD58-positive, CD68-negative, CD80-negative, CD83-negative, CD85j-positive, CD86-positive, CD89-negative, CD95-positive, CD120a-negative, CD120b-positive, CD123-negative, CD178-negative, CD206-negative, CD207-negative, CD209-negative, and TNF-alpha-negative. Upon TLR stimulation, they are capable of producing high levels of TNF-alpha, IL-6, CXCL8 (IL-8).") AnnotationAssertion(rdfs:label "myeloid dendritic cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) @@ -34742,14 +34434,12 @@ SubClassOf( "SANBI:mhl") "A skeletal muscle myoblast that differentiates into slow muscle fibers.") AnnotationAssertion(rdfs:label "slow muscle myoblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) # Class: (fast muscle myoblast) AnnotationAssertion(Annotation( "SANBI:mhl") "A skeletal muscle myoblast that differentiates into fast muscle fibers.") AnnotationAssertion(rdfs:label "fast muscle myoblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) # Class: (classical monocyte) @@ -34765,10 +34455,12 @@ SubClassOf(Annotation( # Class: (tissue-resident macrophage) AnnotationAssertion(Annotation( "GOC:ana") Annotation( "GO_REF:0000031") Annotation( "PMID:19770654") "A macrophage constitutively resident in a particular tissue under non-inflammatory conditions, and capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells.") +AnnotationAssertion( ) AnnotationAssertion( "FMA:84642") AnnotationAssertion( "FMA:84644") AnnotationAssertion( "fixed macrophage") AnnotationAssertion( "resting histiocyte") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "tissue-resident macrophage") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) @@ -34834,10 +34526,12 @@ SubClassOf( ObjectSomeValuesFrom( (early lymphoid progenitor) AnnotationAssertion(Annotation( "GOC:add") Annotation( "GOC:dsd") Annotation( "GOC:pam") Annotation( "GOC:tfm") Annotation( "GO_REF:0000031") Annotation( "PMID:19022770") "A lymphoid progenitor cell that is found in bone marrow, gives rise to B cells, T cells, natural killer cells and dendritic cells, and has the phenotype Lin-negative, Kit-positive, Sca-1-positive, FLT3-positive, CD34-positive, CD150 negative, and GlyA-negative.") +AnnotationAssertion( ) AnnotationAssertion( "lymphoid-primed multipotent progenitor") -AnnotationAssertion(Annotation( ) "ELP") -AnnotationAssertion(Annotation( "PMID:18371378") Annotation( ) "GMLP") -AnnotationAssertion(Annotation( ) "LMPP") +AnnotationAssertion(Annotation( ) "ELP") +AnnotationAssertion(Annotation( "PMID:18371378") Annotation( ) "GMLP") +AnnotationAssertion(Annotation( ) "LMPP") +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Markers are associated with mouse cells. ELP transcription factors include E2A-positive, Ikaros-positive, EBF-negative, Pax5-negative, PU.1-negative.") AnnotationAssertion(rdfs:label "early lymphoid progenitor") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) @@ -35142,8 +34836,7 @@ AnnotationAssertion( "haemopoietic cell") AnnotationAssertion( "hemopoietic cell") AnnotationAssertion(rdfs:label "hematopoietic cell") -SubClassOf( ) -SubClassOf( ) +SubClassOf( ) # Class: (conventional dendritic cell) @@ -35333,8 +35026,7 @@ AnnotationAssertion( AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "bone cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (terminally differentiated osteoblast) @@ -35387,9 +35079,9 @@ SubClassOf( "GOC:add") Annotation( "GOC:dsd") Annotation( "GOC:tfm") Annotation( "ISBN:0878932437") Annotation( "PMCID:PMC2212039") Annotation( "PMID:10724173") Annotation( "PMID:16551251") Annotation( "PMID:16647566") "A progenitor cell committed to myeloid lineage, including the megakaryocyte and erythroid lineages. These cells are CD34-positive, and express Gata1, Gata2, C/EBPa, and Pu.1.") AnnotationAssertion( "common myeloid precursor, CD34-positive") -AnnotationAssertion(Annotation( "ISBN:0878932437") Annotation( ) "CFU-GEMM") -AnnotationAssertion(Annotation( "ISBN:0878932437") Annotation( ) "CFU-S") -AnnotationAssertion(Annotation( "ISBN:0878932437") Annotation( ) "CMP") +AnnotationAssertion(Annotation( "ISBN:0878932437") Annotation( ) "CFU-GEMM") +AnnotationAssertion(Annotation( "ISBN:0878932437") Annotation( ) "CFU-S") +AnnotationAssertion(Annotation( "ISBN:0878932437") Annotation( ) "CMP") AnnotationAssertion(Annotation( "ISBN:0878932437") "colony forming unit granulocyte, erythrocyte, macrophage, and megakaryocyte") AnnotationAssertion(Annotation( "ISBN:0878932437") "multipotential myeloid stem cell") AnnotationAssertion(Annotation( "ISBN:0878932437") "myeloid stem cell") @@ -35414,8 +35106,8 @@ SubClassOf( ObjectSomeValuesFrom( "GOC:add") Annotation( "ISBN:0721601464") "A progenitor cell committed to the erythroid lineage. This cell is ter119-positive but lacks expression of other hematopoietic lineage markers (lin-negative).") AnnotationAssertion( "BTO:0004911") -AnnotationAssertion(Annotation( ) "BFU-E") -AnnotationAssertion(Annotation( ) "CFU-E") +AnnotationAssertion(Annotation( ) "BFU-E") +AnnotationAssertion(Annotation( ) "CFU-E") AnnotationAssertion( "blast forming unit erythroid") AnnotationAssertion( "burst forming unit erythroid") AnnotationAssertion( "colony forming unit erythroid") @@ -36014,7 +35706,6 @@ AnnotationAssertion( AnnotationAssertion( "FMA:69075") AnnotationAssertion(rdfs:label "endo-epithelial cell") SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (ecto-epithelial cell) @@ -36025,7 +35716,6 @@ AnnotationAssertion( AnnotationAssertion( "FMA:69074") AnnotationAssertion(rdfs:label "ecto-epithelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) # Class: (meso-epithelial cell) @@ -36036,7 +35726,6 @@ AnnotationAssertion( "epithelial mesenchymal cell") AnnotationAssertion(rdfs:label "meso-epithelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) # Class: (pancreatic ductal cell) @@ -36587,7 +36276,6 @@ AnnotationAssertion( "corneocyte") SubClassOf( ) SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -36766,7 +36454,7 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( "2010-08-30T02:00:42Z") AnnotationAssertion( "FMA:86577") -AnnotationAssertion(Annotation( "PMID:18442648") Annotation( ) "HpSC") +AnnotationAssertion(Annotation( "PMID:18442648") Annotation( ) "HpSC") AnnotationAssertion(rdfs:label "hepatic stem cell") AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/cell-ontology/issues/800") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -36807,11 +36495,9 @@ EquivalentClasses( ObjectIntersection # Class: (epithelial cell of tracheobronchial tree) AnnotationAssertion(Annotation( "GOC:tfm") "An epithelial cell of the tracheobronchial tree.") -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "2010-09-02T02:09:14Z") AnnotationAssertion( "FMA:66816") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "epithelial cell of tracheobronchial tree") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -36915,7 +36601,6 @@ AnnotationAssertion( "vertebrate lens cell") SubClassOf( ) SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (lens epithelial cell) @@ -36998,13 +36683,11 @@ SubClassOf( (pulmonary interstitial fibroblast) AnnotationAssertion(Annotation( "GOC:tfm") "A fibroblasts found in interstitial spaces in the pulmonary tract. Greater numbers of these cells are found in idiopathic pulmonary fibrosis.") -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "2010-09-07T02:29:38Z") AnnotationAssertion( "FMA:84467") AnnotationAssertion( "pulmonary myofibroblast") AnnotationAssertion( "pulmonary septal cell") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pulmonary interstitial fibroblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) @@ -37016,7 +36699,7 @@ AnnotationAssertion( "2010-09-07T03:32:33Z") AnnotationAssertion( "FMA:67513") AnnotationAssertion(rdfs:label "nucleate cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (smooth muscle cell of sphincter of pupil) @@ -37303,7 +36986,7 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( "2010-09-13T02:37:23Z") AnnotationAssertion( "FMA:72209") -AnnotationAssertion( "subcapsular thymic epithelial cell") +AnnotationAssertion(Annotation( "PMID:18194204") Annotation( "PMID:2694455") "subcapsular thymic epithelial cell") AnnotationAssertion(rdfs:label "type-1 epithelial cell of thymus") SubClassOf( ) @@ -37382,7 +37065,6 @@ SubClassOf( (endocrine-paracrine cell of prostate gland) AnnotationAssertion(Annotation( "GOC:tfm") "An ecto-epithelial cell of the prostate gland that secretes hormones.") -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "2010-09-14T03:01:58Z") AnnotationAssertion( "CALOHA:TS-1280") @@ -37390,7 +37072,6 @@ AnnotationAssertion( "FMA:86774") AnnotationAssertion( "glandular cell of prostate") AnnotationAssertion( "neuro-epithelial cell of prostate gland") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "endocrine-paracrine cell of prostate gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -37421,24 +37102,18 @@ AnnotationAssertion( AnnotationAssertion( "CALOHA:TS-2040") AnnotationAssertion( "FMA:70333") AnnotationAssertion(rdfs:label "neural cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (connective tissue cell) AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "ISBN:0618947256") "A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone.") -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "2010-09-15T03:01:54Z") AnnotationAssertion( "CALOHA:TS-2096") AnnotationAssertion( "FMA:63875") AnnotationAssertion( "MESH:D003239") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "connective tissue cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf(Annotation( "true") ) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (embryonic cell (metazoa)) @@ -37450,7 +37125,7 @@ AnnotationAssertion( "FMA:82841") AnnotationAssertion( "WBbt:0007028") AnnotationAssertion(rdfs:label "embryonic cell (metazoa)") -SubClassOf( ) +SubClassOf( ) # Class: (amniocyte) @@ -37475,21 +37150,40 @@ AnnotationAssertion(rdfs:label "myoe EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -# Class: (mammary alveolar cell) +# Class: (lactocyte) -AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "PMID:19022771") "The milk-producing cell of the alveolar unit that emerges during pregnancy.") +AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "PMID:19022771") Annotation( "PMID:28717367") Annotation( "PMID:35091553") Annotation( "PMID:35377806") Annotation( "doi:10.1177/156482659601700404") "A milk-producing glandular epithelial cell that is part of a mammary gland alveolus and differentiates from a luminal adaptive secretory precursor cell during secretory differentiation (also termed lactogenesis I). Following secretory activation (also termed lactogenesis II), a lactocyte is involved in the synthesis and/or transport of milk constituents including proteins, oligosaccharides, lactose, micronutrients, fat, hormones, immunoglobulins, and cytokines into the lumen of the lactating mammary gland.") +AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion( "2010-09-20T01:30:57Z") +AnnotationAssertion(Annotation( "PMID:19022771") "mammary alveolar cell") AnnotationAssertion( "FMA:74506") AnnotationAssertion( "FMA:79866") AnnotationAssertion( "epithelial cell of lactiferous gland") +AnnotationAssertion(Annotation( "PMID:35091553") "lactaction-associated mammary epithelial cell") +AnnotationAssertion(Annotation( "PMID:35091553") "lactation-derived mammary cell") AnnotationAssertion( "luminal cell of alveolus of lactiferous gland") AnnotationAssertion( "mammary alveolar epithelial cell") AnnotationAssertion( "mammary gland alveolar epithelial cell") -AnnotationAssertion(rdfs:label "mammary alveolar cell") +AnnotationAssertion(Annotation( "PMID:35091553") Annotation( ) "LMC") +AnnotationAssertion(rdfs:label "lactocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) SubClassOf(Annotation( "true") ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (luminal epithelial cell of mammary gland) + +AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "PMID:19022771") "A mammary epithelial cell that occurs in the lumen of the ductal and alveoli structure in the breast.") +AnnotationAssertion( ) +AnnotationAssertion( "2010-09-20T01:37:53Z") +AnnotationAssertion(Annotation( "PMID:21930782") "mature luminal cell") +AnnotationAssertion( "FMA:73280") +AnnotationAssertion(rdfs:label "luminal epithelial cell of mammary gland") +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (mammary gland epithelial cell) @@ -37501,7 +37195,6 @@ AnnotationAssertion( "mammary epithelial cell") AnnotationAssertion(rdfs:label "mammary gland epithelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) # Class: (bronchial epithelial cell) @@ -37611,7 +37304,6 @@ AnnotationAssertion( AnnotationAssertion( "pancreatic endocrine progenitor") AnnotationAssertion( "pancreatic islet progenitor cell") AnnotationAssertion(rdfs:label "progenitor cell of endocrine pancreas") -SubClassOf( ) SubClassOf( ) # Class: (gestational hematopoietic stem cell) @@ -37660,7 +37352,7 @@ AnnotationAssertion( "2010-09-22T01:40:44Z") AnnotationAssertion(Annotation( "doi:10.3389/fncir.2020.611841") "granule cell precursor") AnnotationAssertion(Annotation( "doi:10.3389/fncir.2020.611841") "granule cell progenitor") -AnnotationAssertion(Annotation( "doi:10.3389/fncir.2020.611841") Annotation( ) "GCP") +AnnotationAssertion(Annotation( "doi:10.3389/fncir.2020.611841") Annotation( ) "GCP") AnnotationAssertion(rdfs:label "cerebellar granule cell precursor") SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -37745,19 +37437,6 @@ AnnotationAssertion(rdfs:label "resp EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (somatic cell) - -AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "ISBN:0721662544") "A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell).") -AnnotationAssertion( ) -AnnotationAssertion( "2010-09-24T09:44:42Z") -AnnotationAssertion( "BTO:0001268") -AnnotationAssertion( "FMA:72300") -AnnotationAssertion( "WBbt:0008378") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "somatic cell") -SubClassOf( ) -SubClassOf( ) - # Class: (myotube) AnnotationAssertion(Annotation( "GOC:dos") Annotation( "GOC:tfm") Annotation( "ISBN:0323052908") Annotation( "PMID:22274696") "A transversely striated, synctial muscle cell, formed by the fusion of myoblasts.") @@ -37786,7 +37465,6 @@ AnnotationAssertion( AnnotationAssertion( "Schwann cell precursor cell") AnnotationAssertion(rdfs:label "Schwann cell precursor") SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (immature Schwann cell) @@ -37917,8 +37595,8 @@ AnnotationAssertion( AnnotationAssertion(Annotation( "PMID:2253328") "oligodendrocyte-type 2 astrocyte (O-2A) progenitor cell") AnnotationAssertion(Annotation( ) Annotation( "PMID:24133281") "oligodendrocyte/type-2 astrocyte progenitor cell") AnnotationAssertion( "MESH:D000073637") -AnnotationAssertion(Annotation( "PMID:24133281") Annotation( ) "O-2A/OPC") -AnnotationAssertion(Annotation( "PMID:11756508") Annotation( ) "O2A/OPC") +AnnotationAssertion(Annotation( "PMID:24133281") Annotation( ) "O-2A/OPC") +AnnotationAssertion(Annotation( "PMID:11756508") Annotation( ) "O2A/OPC") AnnotationAssertion( ) AnnotationAssertion(Annotation( "ISBN:9780702028991") Annotation( "PMID:10704434") Annotation( "PMID:2182078") rdfs:comment "This cell type can be purified from optic nerves and other regions of the embryonic, postnatal and adult rat CNS and can be differentiated in vitro to oligodendrocytes and type-2 astrocytes. Some references use the terms 'oligodendrocyte precursor cell' and 'oligodendrocyte type-2 astrocyte (O-2A) progenitor' to refer to the same entity (e.g., PMID:10704434), while others describe an oligodendrocyte type-2 astrocyte (O-2A) progenitor cell as the precurosr to oligodendrocyte- and type-2 astrocyte- progenitor cells (e.g, ISBN:9780702028991).") AnnotationAssertion(rdfs:label "oligodendrocyte precursor cell") @@ -38035,8 +37713,6 @@ AnnotationAssertion( "2010-12-03T03:17:05Z") AnnotationAssertion(rdfs:label "dermal melanocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) -SubClassOf( ) # Class: (hair follicle melanocyte) @@ -38046,7 +37722,6 @@ AnnotationAssertion( AnnotationAssertion(rdfs:label "hair follicle melanocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ) # Class: (epithelial melanocyte) @@ -38057,7 +37732,6 @@ AnnotationAssertion(rdfs:comment "Th AnnotationAssertion(rdfs:label "epithelial melanocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ) # Class: (retinal melanocyte) @@ -38067,8 +37741,6 @@ AnnotationAssertion( AnnotationAssertion( ) AnnotationAssertion(rdfs:label "retinal melanocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) -SubClassOf( ) # Class: (strial intermediate cell) @@ -38110,9 +37782,7 @@ AnnotationAssertion( "heart cell") AnnotationAssertion(rdfs:comment "From Onard of the FMA: Cardiac muscle cell or cardiac myocyte is a striated muscle cell. Cardiocyte on the other hand is any cell in the heart which includes cells other than muscle cells (e.g. endothelial cell of endocardium). Unless there is a consensus among anatomists that cardiocytes refer only to muscle cells, we will treat them as a general class of cells in the heart.") AnnotationAssertion(rdfs:label "cardiocyte") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf(Annotation( "true") ) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (spongiotrophoblast cell) @@ -38225,8 +37895,6 @@ AnnotationAssertion(Annotation( "GOC:tfm") "uterine cervix epithelial cell") AnnotationAssertion(rdfs:label "epithelial cell of cervix") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (epithelial cell of amnion) @@ -38239,8 +37907,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "epithelial cell of amnion") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) -SubClassOf(Annotation( "true") ) # Class: (amnion mesenchymal stem cell) @@ -38282,8 +37948,10 @@ EquivalentClasses( ObjectIntersection # Class: (chorionic membrane mesenchymal stem cell) AnnotationAssertion(Annotation( "GOC:tfm") "A mesenchymal stem cell of the chorionic membrane.") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "2011-02-28T03:04:35Z") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "chorionic membrane mesenchymal stem cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -38310,7 +37978,6 @@ AnnotationAssertion( AnnotationAssertion(rdfs:comment "See CL:0002619.") AnnotationAssertion(rdfs:label "embryonic blood vessel endothelial progenitor cell") SubClassOf( ) -SubClassOf( ) # Class: (fibroblast of the aortic adventitia) @@ -38369,12 +38036,10 @@ SubClassOf(Annotation( # Class: (fibroblast of lung) AnnotationAssertion(Annotation( "GOC:tfm") "A fibroblast that is part of lung.") -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "2011-02-28T05:11:03Z") AnnotationAssertion( "BTO:0000764") AnnotationAssertion( "CALOHA:TS-0575") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "fibroblast of lung") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) @@ -38409,8 +38074,10 @@ SubClassOf(Annotation( # Class: (fibroblast of pulmonary artery) AnnotationAssertion(Annotation( "GOC:tfm") "A fibroblast of pulmonary artery.") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "2011-02-28T05:22:27Z") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "fibroblast of pulmonary artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) @@ -38421,9 +38088,7 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( "2011-03-01T04:11:01Z") AnnotationAssertion(rdfs:label "hair follicle cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf(Annotation( "true") ) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (inner root sheath cell) @@ -38433,7 +38098,6 @@ AnnotationAssertion( AnnotationAssertion(rdfs:label "inner root sheath cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf(Annotation( "true") ) SubClassOf(Annotation( "true") ) # Class: (outer root sheath cell) @@ -38443,8 +38107,6 @@ AnnotationAssertion( "2011-03-01T04:29:47Z") AnnotationAssertion(rdfs:label "outer root sheath cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) -SubClassOf(Annotation( "true") ) SubClassOf(Annotation( "true") ) # Class: (hair germinal matrix cell) @@ -38553,7 +38215,6 @@ AnnotationAssertion( AnnotationAssertion(rdfs:label "placental epithelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf(Annotation( "true") ) # Class: (mesenteric preadipocyte) @@ -38631,9 +38292,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "retinal pigment epithelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (smooth muscle cell of the umbilical vein) @@ -38666,9 +38325,11 @@ SubClassOf(Annotation( # Class: (smooth muscle cell of the pulmonary artery) AnnotationAssertion(Annotation( "GOC:tfm") "A smooth muscle of the pulmonary artery.") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "2011-03-06T05:01:28Z") AnnotationAssertion( "BTO:0003336") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "smooth muscle cell of the pulmonary artery") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) @@ -38946,8 +38607,6 @@ AnnotationAssertion( "2011-03-14T12:46:28Z") AnnotationAssertion(rdfs:label "gingival epithelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) -SubClassOf(Annotation( "true") ) # Class: (prostate stromal cell) @@ -39001,8 +38660,6 @@ AnnotationAssertion( "2011-07-08T12:11:38Z") AnnotationAssertion(rdfs:label "epithelial cell of anal column") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) -SubClassOf(Annotation( "true") ) # Class: (keratinized epithelial cell of the anal canal) @@ -39098,7 +38755,7 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( "2011-07-11T03:15:38Z") AnnotationAssertion(Annotation( "PMID:17519333") Annotation( "PMID:19745164") "cardiovascular progenitor cell") -AnnotationAssertion(Annotation( "PMID:19745164") Annotation( ) "CPC") +AnnotationAssertion(Annotation( "PMID:19745164") Annotation( ) "CPC") AnnotationAssertion(rdfs:comment "Discrepancy in develops from origins prevents me from making the assertion that cardioblasts give rise to all instances of cardiocytes as we state cardiac muscle cells develop from cardiac myoblast, which in turn develop from muscle stem cell.") AnnotationAssertion(rdfs:label "cardioblast") SubClassOf( ) @@ -39149,11 +38806,11 @@ SubClassOf(Annotation( # Class: (kidney cortical cell) +AnnotationAssertion( "A cell that is part of a cortex of kidney.") AnnotationAssertion( ) AnnotationAssertion( "2011-10-25T03:49:41Z") AnnotationAssertion(rdfs:label "kidney cortical cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) # Class: (spinal cord interneuron) @@ -39166,9 +38823,10 @@ SubClassOf(Annotation( # Class: (ionocyte) AnnotationAssertion(Annotation( "PMID:17555741") Annotation( "PMID:19268451") "Specialized epithelial cells involved in the maintenance of osmotic homeostasis. They are characterized by abundant mitochondria and ion transporters. In amniotes, they are present in the renal system. In freshwater fish, ionocytes in the skin and gills help maintain osmotic homeostasis by absorbing salt from the external environment.") +AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ionocyte") SubClassOf( ) -SubClassOf( ) # Class: (macular hair cell) @@ -39190,7 +38848,7 @@ AnnotationAssertion(Annotation( "multi-ciliated cell"@en) AnnotationAssertion( "multiciliated cell"@en) AnnotationAssertion( "multiciliated epithelial cell"@en) -AnnotationAssertion(Annotation( ) "MCC"@en) +AnnotationAssertion(Annotation( ) "MCC"@en) AnnotationAssertion(rdfs:label "multi-ciliated epithelial cell") SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -39247,7 +38905,6 @@ AnnotationAssertion( AnnotationAssertion(rdfs:comment "unsure of neural crest contribution. In VSAO we have develops_from CL:0000008") AnnotationAssertion(rdfs:label "preameloblast") SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -39260,7 +38917,7 @@ AnnotationAssertion( AnnotationAssertion(Annotation( "GO_REF:0000034") "scleroblast") AnnotationAssertion(rdfs:comment "Needs logical definition. Should be capable_of skeletal system morphogenesis? or skeletal tissue development? needs to be added to GO. NOTES:a cell type of the early embryo (see also: mesenchymal cells) that will give rise to mineralized connective tissue. Scleroblasts can differentiate into osteoblasts (bone-forming cells), chondroblasts (cartilage-forming cells), odontoblasts (dentin-forming cells), ameloblasts (enamel-forming cells). The mesenchymal cells developing into osteoblasts and chondroblasts are derived from the mesoderm. Those developing into odontoblasts are neural crest cells. Those developing into ameloblasts are derived from the ectoderm. (http://www.copewithcytokines.de/cope.cgi?key=scleroblasts)") AnnotationAssertion(rdfs:label "skeletogenic cell") -SubClassOf( ) +SubClassOf( ) # Class: (precementoblast) @@ -39269,7 +38926,6 @@ AnnotationAssertion( "2012-06-15T04:37:13Z") AnnotationAssertion(rdfs:label "precementoblast") SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (preodontoblast) @@ -39279,7 +38935,6 @@ AnnotationAssertion( "2012-06-15T05:15:11Z") AnnotationAssertion(rdfs:label "preodontoblast") SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -39300,7 +38955,6 @@ AnnotationAssertion( "2012-06-27T10:44:01Z") AnnotationAssertion(rdfs:label "prechondroblast") SubClassOf( ) -SubClassOf( ) # Class: (preosteoblast) @@ -39310,7 +38964,6 @@ AnnotationAssertion( AnnotationAssertion( "osteoprogenitor cell") AnnotationAssertion(rdfs:label "preosteoblast") SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -39329,8 +38982,6 @@ SubClassOf( ObjectSomeValuesFrom( (non-striated muscle cell) AnnotationAssertion(Annotation( "GOC:DOS") "Any muscle cell in which the fibers are not organised into sarcomeres.") -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "non-striated muscle cell") SubClassOf( ) @@ -39394,23 +39045,21 @@ AnnotationAssertion(Annotation( "The vast majority of these cells develop from skeletal muscle satellite cells, although there are some reports of other origins.") AnnotationAssertion(rdfs:label "adult skeletal muscle myoblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -SubClassOf( ) # Class: (somatic muscle myoblast) AnnotationAssertion( "A myoblast that is commited to developing into a somatic muscle.") AnnotationAssertion(rdfs:label "somatic muscle myoblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) # Class: (mesenchymal cell) AnnotationAssertion( "A non-polarised cell precursor cell that is part of some mesenchyme, is associated with the cell matrix but is not connected to other cells and is capable of migration.") +AnnotationAssertion( ) AnnotationAssertion( "mesenchyme cell") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mesenchymal cell") -SubClassOf( ) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -39433,7 +39082,6 @@ AnnotationAssertion( "pancreatic endocrine cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) # Class: (noradrenergic neuron) @@ -39482,8 +39130,6 @@ AnnotationAssertion( AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mural cell"@en) -SubClassOf( ) -SubClassOf( ) SubClassOf( ) # Class: (microcirculation associated smooth muscle cell) @@ -39552,8 +39198,6 @@ AnnotationAssertion( "PMID:12021768") AnnotationAssertion(rdfs:label "compound eye retinal cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) -SubClassOf( ) -SubClassOf( ) # Class: (retinal cell) @@ -40035,11 +39679,13 @@ EquivalentClasses( ObjectIntersection # Class: (epithelial cell of endometrial gland) AnnotationAssertion(Annotation( "https://orcid.org/0000-0003-3440-1876") Annotation( "https://orcid.org/0000-0003-4183-8865") "An epithelial cell that is part of an endometrial gland.") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "2021-11-30T16:13:30Z"^^xsd:dateTime) AnnotationAssertion( "EFO:0010710") AnnotationAssertion( "endometrial glandular epithelial cell") AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "epithelial cell of endometrial gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -40143,20 +39789,34 @@ EquivalentClasses( ObjectIntersection # Class: (hepatic portal fibroblast) AnnotationAssertion(Annotation( "PMID:20209607") Annotation( "PMID:24814904") Annotation( "https://orcid.org/0000-0001-7655-4833") "A fibroblast located in the portal triad. Hepatic portal fibroblast are a non-parenchymal cell population located adjacent to bile duct epithelia in liver and are distinct from stellate cells. They differentiate into fibrogenic myofibroblasts during chronic injury states producing high levels of collagen.") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "2022-03-17T12:00:44Z"^^xsd:dateTime) AnnotationAssertion( "portal fibroblast") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "hepatic portal fibroblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (lymph node lymphatic vessel endothelial cell) AnnotationAssertion(Annotation( "https://orcid.org/0000-0001-7655-4833") "An endothelial cell located in a lymph node lymphatic vessel.") +AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lymph node lymphatic vessel endothelial cell") AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/cell-ontology/issues/1472") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +# Class: (progenitor cell of mammary luminal epithelium) + +AnnotationAssertion(Annotation( "PMID:19063729") Annotation( "PMID:20346151") Annotation( "PMID:21930782") Annotation( "https://orcid.org/0000-0003-4412-7970") "A progenitor cell with the potential to differentiate into luminal epithelial cells of mammary glands. In mouse, CD61 and c-kit were found to be coexpressed by the majority of, but not all, committed luminal progenitor cells.") +AnnotationAssertion( ) +AnnotationAssertion( "luminal progenitor cell") +AnnotationAssertion( "progenitor cell of luminal mammary epithelium") +AnnotationAssertion(rdfs:label "progenitor cell of mammary luminal epithelium") +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (stromal cell of bone marrow) AnnotationAssertion( "A stromal cell that is part_of a bone marrow.") @@ -40196,8 +39856,7 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:mtg_heart") "A specialized cardiomyocyte that transmit signals from the AV node to the cardiac Purkinje fibers.") AnnotationAssertion( "AV bundle cell") AnnotationAssertion(rdfs:label "atrioventricular bundle cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (cardiac blood vessel endothelial cell) @@ -40207,8 +39866,7 @@ EquivalentClasses( ObjectIntersection # Class: (His-Purkinje system cell) AnnotationAssertion(rdfs:label "His-Purkinje system cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (cardiac endothelial cell) @@ -40261,7 +39919,7 @@ AnnotationAssertion( "MESH:D015053") AnnotationAssertion(rdfs:label "zygote"@en) AnnotationAssertion(rdfs:seeAlso ) -SubClassOf( ) +SubClassOf( ) # Class: (cardiac glial cell) @@ -40273,7 +39931,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion( "MESH:D032386") AnnotationAssertion(rdfs:label "cardiac myoblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) # Class: (cardiac neuron) @@ -40353,8 +40010,6 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion(rdfs:label "motile sperm cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) # Class: (flagellated sperm cell) @@ -40362,7 +40017,6 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion(rdfs:label "flagellated sperm cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) # Class: (mesothelial cell of epicardium) @@ -40450,8 +40104,7 @@ SubClassOf( "GOC:dos") "A cell that, by division or terminal differentiation, can give rise to other cell types.") AnnotationAssertion(rdfs:comment "Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell.") AnnotationAssertion(rdfs:label "precursor cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (astrocyte of the forebrain) @@ -40494,9 +40147,11 @@ SubClassOf( (prostate neuroendocrine cell) AnnotationAssertion(Annotation( "PMID:33842835") Annotation( "http://orcid.org/0000-0001-7772-9578") "A neuroendocrine cell that is part of the prostate epithelium.") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "neuroendocrine cell of prostate epithelium") AnnotationAssertion( "neuroendocrine cell of the prostate") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "prostate neuroendocrine cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -40567,7 +40222,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "tracheobronchial serous cell"@en) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) # Class: (tracheobronchial chondrocyte) @@ -40584,10 +40238,12 @@ EquivalentClasses( ObjectIntersection # Class: (tracheobronchial goblet cell) AnnotationAssertion( "Any goblet cell that is part of the tracheobronchial epithelium.") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "2020-05-07T18:14:52Z"^^xsd:dateTime) AnnotationAssertion( "goblet cell of tracheobronchial tree") AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "tracheobronchial goblet cell"@en) EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -40745,8 +40401,6 @@ EquivalentClasses( ObjectIntersection # Class: (lung goblet cell) -AnnotationAssertion( ) -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lung goblet cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -40755,8 +40409,7 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "PMID:25311230") "A cell that is part of a cardiac valve.") AnnotationAssertion(Annotation( "PMID:30796046") "heart valve cell") AnnotationAssertion(rdfs:label "cardiac valve cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (growth plate cartilage chondrocyte) @@ -40773,7 +40426,7 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "PMID:33355253") Annotation( "doi:10.3109/01902148209069653") Annotation( "doi:10.7554/eLife.78216") "A neuroendocrine cell that is part of respiratory epithelium of the lung and is involved in the sensory detection of environmental stimuli, including hypoxia, nicotine and air pressure. Ultrastructurally, this cell type is characterized by the presence of cytoplasmic dense core granules, which are considered the storage sites of amine and peptide hormones. Lung neuroendocrine cells are innervated and appear as solitary cells or as clustered masses, localized at airway bifurcation sites, called neuroepithelial bodies that can release serotonin in response to hypoxia and interact with sensory nerve terminals. Lung neuroendocrine cells also function as reserve stem cells that repair the surrounding epithelium after injury.") AnnotationAssertion( ) AnnotationAssertion(Annotation( "PMID:33355253") "pulmonary neuroendocrine cell") -AnnotationAssertion(Annotation( "PMID:33355253") Annotation( ) "PNEC") +AnnotationAssertion(Annotation( "PMID:33355253") Annotation( ) "PNEC") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lung neuroendocrine cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -40803,14 +40456,12 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lung ciliated cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) # Class: (lung secretory cell) AnnotationAssertion(rdfs:label "lung secretory cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) # Class: (trophectodermal cell) @@ -40936,8 +40587,6 @@ AnnotationAssertion(Annotation( "FMA:256165") AnnotationAssertion(rdfs:label "epithelial cell of urethra") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) -SubClassOf( ) # Class: (mesothelial cell of dura mater) @@ -40946,8 +40595,6 @@ AnnotationAssertion( "FMA:256516") "squamous mesothelial cell of dura mater") AnnotationAssertion(rdfs:label "mesothelial cell of dura mater") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) -SubClassOf( ) # Class: (fibroblast of papillary layer of dermis) @@ -41171,8 +40818,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "serous cell of epithelium of trachea") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) -SubClassOf( ) # Class: (serous cell of epithelium of bronchus) @@ -41182,7 +40827,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "serous cell of epithelium of bronchus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) # Class: (serous cell of epithelium of terminal bronchiole) @@ -41190,7 +40834,6 @@ AnnotationAssertion(Annotation( "FMA:263082") AnnotationAssertion(rdfs:label "serous cell of epithelium of terminal bronchiole") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) # Class: (serous cell of epithelium of lobular bronchiole) @@ -41198,7 +40841,6 @@ AnnotationAssertion(Annotation( "FMA:263084") AnnotationAssertion(rdfs:label "serous cell of epithelium of lobular bronchiole") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) # Class: (transitional myocyte of interatrial septum) @@ -41311,7 +40953,6 @@ AnnotationAssertion(Annotation( "melanocyte of eyelid") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ) # Class: (endothelial cell of venous sinus of red pulp of spleen) @@ -41343,8 +40984,6 @@ AnnotationAssertion(Annotation( "FMA:63602") "epithelial cell of vermiform appendix") AnnotationAssertion(rdfs:label "epithelial cell of appendix") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) -SubClassOf(Annotation( "true") ) # Class: (myocyte of sinoatrial node) @@ -41352,7 +40991,6 @@ AnnotationAssertion(Annotation( "FMA:67102") AnnotationAssertion(Annotation( "FMA:67102") "SA nodal myocyte") AnnotationAssertion(Annotation( "GOC:pr") "SA node cardiac muscle cell") -AnnotationAssertion(Annotation( "FMA:67102") "myocyte of sinoatrial node") AnnotationAssertion(Annotation( "GOC:pr") "sinoatrial node cell") AnnotationAssertion( "sinoatrial node myocyte") AnnotationAssertion(Annotation( "FMA:67102") "sinuatrial node myocyte") @@ -41422,8 +41060,6 @@ AnnotationAssertion(Annotation( "FMA:67780") AnnotationAssertion(rdfs:label "epithelial cell of gallbladder") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) -SubClassOf( ) # Class: (myoepithelial cell of sweat gland) @@ -41508,7 +41144,6 @@ AnnotationAssertion( "conjunctival epithelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ) # Class: (epithelial cell of lacrimal canaliculus) @@ -41516,8 +41151,6 @@ AnnotationAssertion(Annotation( "FMA:70553") AnnotationAssertion(rdfs:label "epithelial cell of lacrimal canaliculus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) -SubClassOf( ) # Class: (epithelial cell of external acoustic meatus) @@ -41525,8 +41158,6 @@ AnnotationAssertion(Annotation( "FMA:70555") AnnotationAssertion(rdfs:label "epithelial cell of external acoustic meatus") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) -SubClassOf( ) # Class: (epithelial cell of lacrimal duct) @@ -41542,8 +41173,6 @@ AnnotationAssertion(Annotation( "FMA:70560") AnnotationAssertion(rdfs:label "epithelial cell of lacrimal sac") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) -SubClassOf( ) # Class: (epithelial cell of nasolacrimal duct) @@ -41577,8 +41206,6 @@ AnnotationAssertion(Annotation( "FMA:70615") AnnotationAssertion(rdfs:label "mesothelial cell of anterior chamber of eye") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) -SubClassOf( ) # Class: (myoepithelial cell of dilator pupillae) @@ -41603,8 +41230,6 @@ AnnotationAssertion(Annotation( "FMA:70952") AnnotationAssertion(rdfs:label "epithelial cell of sweat gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) -SubClassOf(Annotation( "true") ) # Class: (epithelial cell of nephron) @@ -41612,8 +41237,6 @@ AnnotationAssertion(Annotation( "FMA:70965") AnnotationAssertion(rdfs:label "epithelial cell of nephron") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) -SubClassOf(Annotation( "true") ) # Class: (epithelial cell of glomerular capsule) @@ -41624,8 +41247,6 @@ AnnotationAssertion( "FMA:70966") "epithelial cell of Bowman's capsule") AnnotationAssertion(rdfs:label "epithelial cell of glomerular capsule") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) -SubClassOf(Annotation( "true") ) SubClassOf( ) SubClassOf(Annotation( "true") ) @@ -41647,8 +41268,6 @@ AnnotationAssertion(Annotation( "FMA:70980") AnnotationAssertion(rdfs:label "epithelial cell of intermediate tubule") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) -SubClassOf(Annotation( "true") ) # Class: (kidney collecting duct epithelial cell) @@ -41670,8 +41289,6 @@ AnnotationAssertion(Annotation( "FMA:72142") AnnotationAssertion(rdfs:label "mesothelial cell of parietal peritoneum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) -SubClassOf(Annotation( "true") ) # Class: (mesothelial cell of visceral peritoneum) @@ -41681,8 +41298,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mesothelial cell of visceral peritoneum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) -SubClassOf(Annotation( "true") ) # Class: (melanocyte of skin) @@ -41695,7 +41310,6 @@ AnnotationAssertion( "melanocyte of skin") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) -SubClassOf( ) # Class: (chromaffin cell of ovary) @@ -41782,8 +41396,10 @@ SubClassOf(Annotation( # Class: (basal cell of urothelium) AnnotationAssertion(Annotation( "GOC:tfm") Annotation( "doi:10.1038/s41385-022-00565-0") "A basal cell that is part of the urothelium. Compared to other urothelial cell types, a basal cell of the urothelium is positioned along the basement membrane, is the most undifferentiated and serves a progenitor role.") +AnnotationAssertion( ) AnnotationAssertion( "FMA:84150") AnnotationAssertion(Annotation( "doi:10.1007/978-3-030-14366-4_8") Annotation( "doi:10.1111/cpr.13170") "urothelial basal cell") +AnnotationAssertion( ) AnnotationAssertion(Annotation( "doi:10.1038/s41385-022-00565-0") rdfs:comment "It has been noted in at least some mammalian species that the urothelial basal cell type is distinguished by expression of high levels of cytokeratin-5 (CK5), p63 and the signalling molecule Sonic hedgehog (Shh). Similar to intermediate cells, the urothelial basal cell type expresses CK17 but is negative for uroplakins (UPK) and CK20. Urothelial basal cells have also been noted to be smaller in diameter than urothelial intermediate cells.") AnnotationAssertion(rdfs:label "basal cell of urothelium") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -41829,8 +41445,6 @@ AnnotationAssertion( "FMA:86736") "peritoneal mesothelial cell") AnnotationAssertion(rdfs:label "mesothelial cell of peritoneum") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) -SubClassOf( ) # Class: (mesothelial cell of pleura) @@ -41839,8 +41453,6 @@ AnnotationAssertion( "FMA:86737") "pleural mesothelial cell") AnnotationAssertion(rdfs:label "mesothelial cell of pleura") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) -SubClassOf( ) # Class: (mesothelial cell of parietal pleura) @@ -41848,16 +41460,15 @@ AnnotationAssertion(Annotation( "FMA:86738") AnnotationAssertion(rdfs:label "mesothelial cell of parietal pleura") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) -SubClassOf(Annotation( "true") ) # Class: (mesothelial cell of visceral pleura) AnnotationAssertion(Annotation( "GOC:tfm") "A mesothelial cell that is part of the visceral pleura.") +AnnotationAssertion( ) AnnotationAssertion( "FMA:86739") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "mesothelial cell of visceral pleura") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) # Class: (nephron tubule epithelial cell) @@ -41882,44 +41493,38 @@ SubClassOf( ObjectSomeValuesFrom( (kidney cell) +AnnotationAssertion( "A cell that is part of a kidney.") AnnotationAssertion( "KUPO:0001010") AnnotationAssertion(rdfs:label "kidney cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (kidney interstitial cell) +AnnotationAssertion( "A cell that is part of kidney interstitium.") AnnotationAssertion( "KUPO:0001013") AnnotationAssertion(rdfs:label "kidney interstitial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (kidney medulla cell) +AnnotationAssertion( "A cell that is part of a renal medulla.") AnnotationAssertion( "KUPO:0001017") AnnotationAssertion(rdfs:label "kidney medulla cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (kidney pelvis cell) +AnnotationAssertion( "A cell that is part of a renal pelvis.") AnnotationAssertion( "KUPO:0001018") AnnotationAssertion(rdfs:label "kidney pelvis cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (kidney tubule cell) +AnnotationAssertion( "A cell that is part of a nephron tubule.") AnnotationAssertion( "KUPO:0001020") AnnotationAssertion(rdfs:label "kidney tubule cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (kidney glomerular epithelial cell) @@ -41931,36 +41536,33 @@ SubClassOf( ObjectSomeValuesFrom( (kidney medulla collecting duct epithelial cell) +AnnotationAssertion( "An epithelial cell that is part of a renal medulla collecting duct.") AnnotationAssertion( "KUPO:0001060") AnnotationAssertion(rdfs:label "kidney medulla collecting duct epithelial cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) -SubClassOf( ObjectSomeValuesFrom( )) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (kidney inner medulla collecting duct epithelial cell) AnnotationAssertion( "An epithelial cell that is part of some inner medullary collecting duct.") AnnotationAssertion( "KUPO:0001061") AnnotationAssertion(rdfs:label "kidney inner medulla collecting duct epithelial cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) -SubClassOf( ObjectSomeValuesFrom( )) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) # Class: (kidney outer medulla collecting duct epithelial cell) +AnnotationAssertion( "An epithelial cell that is part of an outer medullary collecting duct.") AnnotationAssertion( "KUPO:0001062") AnnotationAssertion(rdfs:label "kidney outer medulla collecting duct epithelial cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) -SubClassOf( ObjectSomeValuesFrom( )) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) # Class: (kidney cortex collecting duct epithelial cell) +AnnotationAssertion( "An epithelial cell that is part of a cortical collecting duct.") AnnotationAssertion( "KUPO:0001063") AnnotationAssertion(rdfs:label "kidney cortex collecting duct epithelial cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) -SubClassOf( ObjectSomeValuesFrom( )) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (kidney papillary duct principal epithelial cell) @@ -41993,16 +41595,14 @@ SubClassOf( ObjectSomeValuesFrom( "KUPO:0001115") AnnotationAssertion(rdfs:label "lower urinary tract cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) # Class: (ureteral cell) AnnotationAssertion( "KUPO:0001116") AnnotationAssertion(rdfs:label "ureteral cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) # Class: (kidney nerve cell) @@ -42287,7 +41887,9 @@ SubClassOf( ObjectSomeValuesFrom( (ureter smooth muscle cell) +AnnotationAssertion( ) AnnotationAssertion( "KUPO:0001118") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ureter smooth muscle cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "true") ) @@ -42673,11 +42275,11 @@ SubClassOf( (kidney collecting duct cell) +AnnotationAssertion( "A cell that is part of a collecting duct of renal tubule.") AnnotationAssertion( "KUPO:0001012") AnnotationAssertion( "Wikipedia:Kidney_collecting_duct_cell") AnnotationAssertion(rdfs:label "kidney collecting duct cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) # Class: (vasa recta descending limb cell) @@ -42725,16 +42327,14 @@ AnnotationAssertion( "KUPO:0001120") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "bladder cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) # Class: (urethra cell) AnnotationAssertion( "KUPO:0001123") AnnotationAssertion(rdfs:label "urethra cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf(Annotation( "true") ) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) # Class: (bladder urothelial cell) @@ -42834,18 +42434,18 @@ EquivalentClasses( ObjectIntersection # Class: (lung endothelial cell) -AnnotationAssertion( ) AnnotationAssertion( "endothelial cell of lung") AnnotationAssertion( "pulmonary vessel endothelial cell") -AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lung endothelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) # Class: (pulmonary artery endothelial cell) +AnnotationAssertion( ) AnnotationAssertion( "BTO:0001141") AnnotationAssertion(Annotation( "BTO:0001141") "PAEC cell") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pulmonary artery endothelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) @@ -42872,7 +42472,7 @@ SubClassOf( ObjectSomeValuesFrom( "NPX:PDR") Annotation( "https://orcid.org/0000-0001-5208-3432") "A vascular endothelial cell found in colon blood vessels.") AnnotationAssertion( "CALOHA:TS-2397") -AnnotationAssertion(Annotation( "CALOHA:TS-2397") Annotation( ) "colon endothelial cells") +AnnotationAssertion(Annotation( "CALOHA:TS-2397") Annotation( ) "colon endothelial cells") AnnotationAssertion(Annotation( "CALOHA:TS-2397") "colonic endothelial cell") AnnotationAssertion(rdfs:label "colon endothelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -43160,7 +42760,9 @@ EquivalentClasses( ObjectIntersection # Class: (articular chondrocyte) AnnotationAssertion(Annotation( "NPX:PDR") "Chondrocyte forming the hyaline cartilage found in joints.") +AnnotationAssertion( ) AnnotationAssertion( "CALOHA:TS-0056") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "articular chondrocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -43207,7 +42809,6 @@ AnnotationAssertion( "These cells are found primarily, but not exclusively, in primates including humans") AnnotationAssertion(rdfs:label "epidermal melanocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) # Class: (peripheral blood mononuclear cell) @@ -43240,8 +42841,7 @@ AnnotationAssertion( "2014-03-26T22:14:56Z") AnnotationAssertion( "CL:2000004") AnnotationAssertion(rdfs:label "pituitary gland cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (brain macroglial cell) @@ -43378,7 +42978,7 @@ AnnotationAssertion( "2014-06-24T23:16:53Z") AnnotationAssertion( "CL:2000020") AnnotationAssertion(rdfs:label "inner cell mass cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (sebaceous gland cell) @@ -43387,8 +42987,7 @@ AnnotationAssertion( "2014-06-24T23:17:00Z") AnnotationAssertion( "CL:2000021") AnnotationAssertion(rdfs:label "sebaceous gland cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (cardiac septum cell) @@ -43397,8 +42996,7 @@ AnnotationAssertion( "2014-06-24T23:17:07Z") AnnotationAssertion( "CL:2000022") AnnotationAssertion(rdfs:label "cardiac septum cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (spinal cord ventral column interneuron) @@ -43461,8 +43059,7 @@ AnnotationAssertion( "2014-06-25T01:17:50Z") AnnotationAssertion( "CL:2000030") AnnotationAssertion(rdfs:label "hypothalamus cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (lateral line ganglion neuron) @@ -43567,7 +43164,6 @@ AnnotationAssertion( AnnotationAssertion( "CL:2000045") AnnotationAssertion(rdfs:label "foreskin melanocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) # Class: (ventricular cardiac muscle cell) @@ -43662,11 +43258,9 @@ EquivalentClasses( ObjectIntersection # Class: (prostate gland microvascular endothelial cell) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any microvascular endothelial cell that is part of a prostate gland.") -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "2014-10-07T17:46:27Z") AnnotationAssertion( "CL:2000059") -AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "http://www.sciencellonline.com/site/productInformation.php?keyword=4400") AnnotationAssertion(rdfs:label "prostate gland microvascular endothelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -43689,9 +43283,11 @@ EquivalentClasses( ObjectIntersection # Class: (placental amniotic mesenchymal stromal cell) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any mesenchymal stem cell that is part of a placenta.") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "2014-10-07T17:51:11Z") AnnotationAssertion( "CL:2000061") +AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "http://www.sciencellonline.com/site/productInformation.php?keyword=7140") AnnotationAssertion(rdfs:label "placental amniotic mesenchymal stromal cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -43699,11 +43295,9 @@ EquivalentClasses( ObjectIntersection # Class: (placental villus capillary endothelial cell) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any capillary endothelial cell that is part of a placenta.") -AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "2014-10-07T17:55:56Z") AnnotationAssertion( "CL:2000062") -AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "http://www.ncbi.nlm.nih.gov/books/NBK53245/") AnnotationAssertion(rdfs:label "placental villus capillary endothelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -43895,7 +43489,6 @@ AnnotationAssertion( AnnotationAssertion( "CL:2000081") AnnotationAssertion(rdfs:label "melanocyte of skin of face") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) # Class: (melanocyte of foreskin) @@ -43905,7 +43498,6 @@ AnnotationAssertion( AnnotationAssertion( "CL:2000082") AnnotationAssertion(rdfs:label "melanocyte of foreskin") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) # Class: (hair follicle dermal papilla cell of scalp) @@ -44186,7 +43778,7 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "brain vascular cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (mammillary body neuron) @@ -44288,7 +43880,6 @@ AnnotationAssertion( "PMID:31819095") Annotation( "PMID:34082079") rdfs:comment "Cellular functions and extracellular interactions of choroidal melanocytes are distinct to skin melanocytes. They might have both neuroectodermal as well as mesectodermal origins.") AnnotationAssertion(rdfs:label "choroidal melanocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) # Class: (stromal cell of thymus) @@ -44353,6 +43944,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "kidney connecting tubule principal cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) # Class: (renal medullary fibroblast) @@ -44400,16 +43992,18 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( "2022-11-30T14:35:08Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "interstitial cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (valve interstitial cell) AnnotationAssertion(Annotation( ) Annotation( "PMID:25311230") Annotation( "https://doi.org/10.1098/rsif.2017.0580") Annotation( "https://doi.org/10.1161/ATVBAHA.120.314789") Annotation( "https://doi.org/10.1161/JAHA.117.006339") Annotation( "https://doi.org/10.2353/ajpath.2007.070251") "An interstitial cell that is part of a cardiac valve leaflet. Along with valve endothelial cells, a valve interstitial cell maintains tissue homeostasis for the function of cardiac valves through secreting biochemical signals, matrix proteins and matrix remodeling enzymes.") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "2022-12-06T14:18:45Z"^^xsd:dateTime) -AnnotationAssertion(Annotation( "PMID:25311230") Annotation( "PMID:30796046") Annotation( ) "VIC") +AnnotationAssertion(Annotation( "PMID:25311230") Annotation( "PMID:30796046") Annotation( ) "VIC") AnnotationAssertion( "cardiac valve interstitial cell") AnnotationAssertion(Annotation( "PMID:25311230") "valvular interstitial cell") +AnnotationAssertion( ) AnnotationAssertion(Annotation( "PMID:25311230") rdfs:comment "Activated valve interstitial cells undergo continual turn over into deactivated fibroblasts and other cell fates (such as apoptosis).") AnnotationAssertion(rdfs:label "valve interstitial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -44420,7 +44014,7 @@ SubClassOf( ObjectSomeValuesFrom( "PMID:25311230") "An endothelial cell that lines a surface of a cardiac valve leaflet. Along with valve interstitial cells, a valve endothelial cell maintains tissue homeostasis for the function of cardiac valves through secreting biochemical signals, matrix proteins and matrix remodeling enzymes.") AnnotationAssertion( ) AnnotationAssertion( "2022-12-09T11:58:49Z"^^xsd:dateTime) -AnnotationAssertion(Annotation( "PMID:25311230") Annotation( "PMID:30796046") Annotation( ) "VEC") +AnnotationAssertion(Annotation( "PMID:25311230") Annotation( "PMID:30796046") Annotation( ) "VEC") AnnotationAssertion(Annotation( "PMID:25311230") "valvular endothelial cell") AnnotationAssertion(Annotation( "PMID:25311230") rdfs:comment "At least in some mammalian species, a valve endothelial cell expresses CD31. Valve endothelial cells can undergo an endothelial to mesenchymal transition to acquire a fibroblast or myofibroblast phenotype that leads to changes in the microenvironmental signals and facilitates tissue regeneration.") AnnotationAssertion(rdfs:label "valve endothelial cell") @@ -44439,7 +44033,7 @@ SubClassOf( ObjectSomeValuesFrom( ) Annotation( "DOI:10.1177/154405910208100806") "A dental pulp cell that possesses stem-cell-like qualities, including self-renewal capability and multi-lineage differentiation.") AnnotationAssertion( "2023-01-10T14:02:02Z"^^xsd:dateTime) -AnnotationAssertion(Annotation( ) "DPSC") +AnnotationAssertion(Annotation( ) "DPSC") AnnotationAssertion(rdfs:label "dental pulp stem cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -44456,6 +44050,16 @@ AnnotationAssertion(Annotation( "endometrial ciliated epithelial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (ureteric bud cell) + +AnnotationAssertion(Annotation( "PMID:17133361") Annotation( "PMID:24183650") Annotation( "PMID:9374839") "An epithelial cell that is part of a ureteric bud. A ureteric bud cell has the potential to induce metanephric mesenchymal cells to proliferate and convert to epithelia that form renal tubules via: (1) the secretion of multiple diffusible growth factors that rescue renal progenitors from apoptosis and stimulate them to proliferate and (2) contact-dependent mechanisms that induce mesenchymal-epithelial conversion.") +AnnotationAssertion( "https://orcid.org/0000-0002-1425-877X") +AnnotationAssertion( "2023-10-13T11:22:42Z"^^xsd:dateTime) +AnnotationAssertion(Annotation( "PMID:24183650") Annotation( ) "UB cell") +AnnotationAssertion(rdfs:label "ureteric bud cell") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf(Annotation( "PMID:9374839") ObjectSomeValuesFrom( )) + # Class: (endothelial cell of venule of lymph node) AnnotationAssertion(Annotation( "PMID:28217126") "A(n) endothelial cell that is part of a(n) venule of lymph node.") @@ -44496,7 +44100,9 @@ EquivalentClasses( ObjectIntersection # Class: (serous secreting cell of bronchus submucosal gland) AnnotationAssertion(Annotation( "PMID:5487122") Annotation( "PMID:9651178") "A(n) serous secreting cell that is part of a(n) bronchus submucosal gland.") +AnnotationAssertion( ) AnnotationAssertion( ) +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "serous secreting cell of bronchus submucosal gland") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -44570,7 +44176,7 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "PMID:25236977") Annotation( "PMID:33796062") "A star-shaped glial cell that is part of some retina. This cell links neurons to blood vessels and may provide structural and physiological support to optic nerve head axons.") AnnotationAssertion( ) AnnotationAssertion( "2023-03-02T14:38:32Z"^^xsd:dateTime) -AnnotationAssertion(Annotation( ) Annotation( "PMID:33796062") "retinal astroglia") +AnnotationAssertion(Annotation( "PMID:33796062") Annotation( ) "retinal astroglia") AnnotationAssertion( ) AnnotationAssertion(Annotation( "PMID:32555229") Annotation( "PMID:33796062") rdfs:comment "In response to elevated intraocular pressure, a retinal astrocyte may modulate extracellular matrix remodeling. In the human retina, a retinal astrocyte is GFAP-positive, SOD3-positive and GYPC-positive.") AnnotationAssertion(rdfs:label "retinal astrocyte") @@ -44597,8 +44203,8 @@ AnnotationAssertion( "2023-03-16T11:31:23Z"^^xsd:dateTime) AnnotationAssertion(Annotation( "PMID:36524131") "lung resident megakaryocyte") AnnotationAssertion(Annotation( "PMID:36524131") "lung-resident megakaryocyte") -AnnotationAssertion(Annotation( "PMID:36524131") Annotation( ) "MKL") -AnnotationAssertion(Annotation( "PMID:33351116") Annotation( ) Annotation( ) "lung MKs") +AnnotationAssertion(Annotation( "PMID:36524131") Annotation( ) "MKL") +AnnotationAssertion(Annotation( "PMID:33351116") Annotation( ) Annotation( ) "lung MKs") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lung megakaryocyte") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -44653,10 +44259,12 @@ EquivalentClasses( ObjectIntersection # Class: (lung perichondrial fibroblast) AnnotationAssertion(Annotation( "PMID:36543915") "A perichondrial fibroblast that is part of the lung.") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "2023-03-16T16:15:39Z"^^xsd:dateTime) -AnnotationAssertion(Annotation( "PMID:36543915") Annotation( ) "PC-fibro") +AnnotationAssertion(Annotation( "PMID:36543915") Annotation( ) "PC-fibro") +AnnotationAssertion( ) AnnotationAssertion(rdfs:label "lung perichondrial fibroblast") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -44693,7 +44301,39 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( "2023-08-22T13:40:28Z"^^xsd:dateTime) AnnotationAssertion(rdfs:label "perivascular cell") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (airway submucosal gland duct ciliated cell) + +AnnotationAssertion(Annotation( "PMID:17707699") Annotation( "PMID:30864819") "A ciliated cell that is part of a ciliated duct of an airway submucosal gland.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "2023-09-08T10:32:27Z"^^xsd:dateTime) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "airway submucosal gland duct ciliated cell") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) + +# Class: (luminal adaptive secretory precursor cell of mammary gland) + +AnnotationAssertion(Annotation( "PMID:19648928") Annotation( "PMID:35617956") Annotation( "https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37368328") Annotation( "https://orcid.org/0000-0001-6677-8489") "A luminal epithelial cell of the mammary gland that can proliferate and has the potential to differentiate into a lactocyte during pregnancy. In humans, a luminal adaptive secretory precursor cell can be identified by high levels of the markers EpCAM and CD49f, and in mice it can be identified by low levels of CD29 and high levels of CD14, Kit, CD61, and Tspan8.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "2023-10-13T13:02:55Z"^^xsd:dateTime) +AnnotationAssertion(Annotation( "PMID:35617956") "alveolar cell") +AnnotationAssertion(Annotation( "PMID:26390871") "alveolar progenitor") +AnnotationAssertion(Annotation( "doi:10.1101/2023.04.21.537845") "luminal progenitor") +AnnotationAssertion(Annotation( "PMID:20346151") "luminal progenitor cell") +AnnotationAssertion(Annotation( "PMID:37380767") "luminal secretory cell") +AnnotationAssertion(Annotation( "https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37368328") "ER-negative luminal alveolar progenitor") +AnnotationAssertion(Annotation( "https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37368328") Annotation( ) "AP") +AnnotationAssertion(Annotation( "PMID:35617956") Annotation( ) "AV") +AnnotationAssertion(Annotation( "https://orcid.org/0000-0001-6677-8489") Annotation( ) "LASP") +AnnotationAssertion(Annotation( "doi:10.1101/2023.04.21.537845") Annotation( ) "LP") +AnnotationAssertion(Annotation( "PMID:37380767") Annotation( ) "LumSec") +AnnotationAssertion(rdfs:label "luminal adaptive secretory precursor cell of mammary gland") +SubClassOf( ) +SubClassOf( ) # Class: (enteroglial cell) @@ -44701,7 +44341,7 @@ AnnotationAssertion(Annotation( ) AnnotationAssertion( "2023-04-03T15:15:40Z"^^xsd:dateTime) AnnotationAssertion(Annotation( "PMID:11169131") Annotation( "PMID:25170211") "enteric glial cell") -AnnotationAssertion(Annotation( ) Annotation( "PMID:11169131") "enteric glia") +AnnotationAssertion(Annotation( "PMID:11169131") Annotation( ) "enteric glia") AnnotationAssertion(rdfs:label "enteroglial cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ObjectSomeValuesFrom( )) @@ -44718,6 +44358,17 @@ AnnotationAssertion( "fetal pre-type II pneumocyte") SubClassOf( ) +# Class: (mesenchymal stem cell of orbital adipose tissue) + +AnnotationAssertion(Annotation( ) "Any mesenchymal stem cell of adipose tissue that is part of an orbital region.") +AnnotationAssertion( ) +AnnotationAssertion( "2023-09-18T10:43:00Z"^^xsd:dateTime) +AnnotationAssertion(Annotation( "PMID:31377878") "OAMSC") +AnnotationAssertion(Annotation( "PMID:30210548") "Orbital ASCs") +AnnotationAssertion(Annotation( "PMID:31377878") "orbital adipose-derived mesenchymal stem cell") +AnnotationAssertion(rdfs:label "mesenchymal stem cell of orbital adipose tissue") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (reproduction) AnnotationAssertion(Annotation( "GOC:go_curators") Annotation( "GOC:isa_complete") Annotation( "GOC:jl") Annotation( "ISBN:0198506732") "The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms.") @@ -45091,18 +44742,8 @@ AnnotationAssertion( "GO:0001504") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "neurotransmitter uptake") -SubClassOf( ) SubClassOf( ) -# Class: (regulation of neurotransmitter levels) - -AnnotationAssertion(Annotation( "GOC:jl") "Any process that modulates levels of neurotransmitter.") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0001505") -AnnotationAssertion(rdfs:label "regulation of neurotransmitter levels") -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectAllValuesFrom( )) - # Class: (action potential) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:go_curators") Annotation( "GOC:tb") Annotation( "ISBN:978-0-07-139011-8") "A process in which membrane potential cycles through a depolarizing spike, triggered in response to depolarization above some threshold, followed by repolarization. This cycle is driven by the flow of ions through various voltage gated channels with different thresholds and ion specificities.") @@ -45591,7 +45232,6 @@ AnnotationAssertion( "GO:0001695") AnnotationAssertion(rdfs:label "histamine catabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) # Class: (gastric acid secretion) @@ -47510,7 +47150,6 @@ AnnotationAssertion(Annotation( "GO:0002263") AnnotationAssertion(rdfs:label "cell activation involved in immune response") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) # Class: (endothelial cell activation involved in immune response) @@ -47591,7 +47230,7 @@ AnnotationAssertion(Annotation( "GO:0002281") AnnotationAssertion(rdfs:label "macrophage activation involved in immune response") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (neutrophil activation involved in immune response) @@ -47937,7 +47576,6 @@ AnnotationAssertion( "leukocyte activation involved in immune response") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) # Class: (cytokine production involved in immune response) @@ -52830,7 +52468,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "chromatin binding") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) # Class: (nuclear steroid receptor activity) @@ -52924,7 +52561,21 @@ AnnotationAssertion(Annotation(rdfs:label "INF-gamma induced phosphorylation of AnnotationAssertion(Annotation(rdfs:label "IRAK1 phosphorylates Pellino") "Reactome:R-HSA-937034") AnnotationAssertion(Annotation(rdfs:label "Unknown kinase phosphorylates NICD4") "Reactome:R-HSA-9604606") AnnotationAssertion(Annotation(rdfs:label "GTP-bound RAC1 contributes to MAPK8 activation") "Reactome:R-HSA-9673284") +AnnotationAssertion(Annotation(rdfs:label "JAK1-activated RAF1 phosphorylates MAPKs") "Reactome:R-HSA-9732753") AnnotationAssertion(Annotation(rdfs:label "IRAK1 phosphorylates Pellino upon TLR7/8 or 9 activation") "Reactome:R-HSA-975139") +AnnotationAssertion(Annotation(rdfs:label "PKR dimer autophosphorylates") "Reactome:R-HSA-9833820") +AnnotationAssertion(Annotation(rdfs:label "p-PKR dimer phosphorylates eIF2-alpha") "Reactome:R-HSA-9835885") +AnnotationAssertion(Annotation(rdfs:label "p-PKR dimer phosphorylates DHX9") "Reactome:R-HSA-9836159") +AnnotationAssertion(Annotation(rdfs:label "p-PKR dimer phosphorylates CDK1") "Reactome:R-HSA-9836184") +AnnotationAssertion(Annotation(rdfs:label "p-PKR dimer phosphorylates MKK6") "Reactome:R-HSA-9836322") +AnnotationAssertion(Annotation(rdfs:label "p-PKR dimer phosphorylates TP53 tetramer") "Reactome:R-HSA-9836362") +AnnotationAssertion(Annotation(rdfs:label "p-PKR dimer phosphorylates ILF3:ILF2") "Reactome:R-HSA-9836383") +AnnotationAssertion(Annotation(rdfs:label "p-PKR dimer phosphorylates MAPT") "Reactome:R-HSA-9836404") +AnnotationAssertion(Annotation(rdfs:label "p-PKR dimer phosphorylates SNCA") "Reactome:R-HSA-9836435") +AnnotationAssertion(Annotation(rdfs:label "p-PKR dimer phosphorylates HIV tat") "Reactome:R-HSA-9836449") +AnnotationAssertion(Annotation(rdfs:label "p-PKR dimer phosphorylates PTPN2") "Reactome:R-HSA-9836515") +AnnotationAssertion(Annotation(rdfs:label "p-PKR dimer phosphorylates SPHK1") "Reactome:R-HSA-9836617") +AnnotationAssertion(Annotation(rdfs:label "p-PKR dimer phosphorylates PPP2R5A") "Reactome:R-HSA-9836664") AnnotationAssertion( "protamine kinase activity") AnnotationAssertion( "molecular_function") AnnotationAssertion( "GO:0004672") @@ -53121,7 +52772,7 @@ AnnotationAssertion(Annotation(rdfs:label "Src kinases phosphorylate VAV") "Reactome:R-HSA-5218828") AnnotationAssertion(Annotation(rdfs:label "SRC-1 phosphorylates PTK2-beta") "Reactome:R-HSA-5218830") AnnotationAssertion(Annotation(rdfs:label "p-Y402-PTK2B phosphorylates p-5Y,S732-PTK2 on Y407") "Reactome:R-HSA-5218851") -AnnotationAssertion(Annotation(rdfs:label "AXL autophosphorylates on Y772 and Y814") "Reactome:R-HSA-5357429") +AnnotationAssertion(Annotation(rdfs:label "AXL autophosphorylates on Y779 and Y821") "Reactome:R-HSA-5357429") AnnotationAssertion(Annotation(rdfs:label "1,3-beta-D-glucan:p-Y15-CLEC7A:SYK phosphorylates PLCG") "Reactome:R-HSA-5607745") AnnotationAssertion(Annotation(rdfs:label "SRC kinase phosphorylates CLEC7A:1,3-beta-D-glucan") "Reactome:R-HSA-5607750") AnnotationAssertion(Annotation(rdfs:label "LYN and FYN phosphorylate FCER1G in CLEC6A:FCERG and CLEC4E:FCERG") "Reactome:R-HSA-5621355") @@ -53216,8 +52867,8 @@ AnnotationAssertion(Annotation(rdfs:label "SRC,YES1 phosphorylate YAP1") "Reactome:R-HSA-8942607") AnnotationAssertion(Annotation(rdfs:label "p-S13, FUNDC1 is phosphorylated by CK2 at Tyr18") "Reactome:R-HSA-8948143") AnnotationAssertion(Annotation(rdfs:label "ABL1 phosphorylates YAP1") "Reactome:R-HSA-8956659") -AnnotationAssertion(Annotation(rdfs:label "G protein alpha (i)-SRC complex catalyzes SRC to p-Y416-SRC") "Reactome:R-HSA-8964242") -AnnotationAssertion(Annotation(rdfs:label "G alpha (s):GTP:SRC catalyzes SRC to p-Y416-SRC") "Reactome:R-HSA-8964252") +AnnotationAssertion(Annotation(rdfs:label "G protein alpha (i)-SRC complex catalyzes SRC to p-Y419-SRC") "Reactome:R-HSA-8964242") +AnnotationAssertion(Annotation(rdfs:label "G alpha (s):GTP:SRC catalyzes SRC to p-Y419-SRC") "Reactome:R-HSA-8964252") AnnotationAssertion(Annotation(rdfs:label "JAK2 bound to IL12RB2:IL12RB2 phosphorylate STAT4") "Reactome:R-HSA-8983872") AnnotationAssertion(Annotation(rdfs:label "Phospho-JAK2 phosphorylates EPOR") "Reactome:R-HSA-9006323") AnnotationAssertion(Annotation(rdfs:label "JAK2 transphosphorylates and is activated in response to Erythropoietin") "Reactome:R-HSA-9006332") @@ -53309,9 +52960,10 @@ AnnotationAssertion(Annotation(rdfs:label "ALK mutants phosphorylate STAT3") "Reactome:R-HSA-9712086") AnnotationAssertion(Annotation(rdfs:label "ALK fusions phosphorylate FRS") "Reactome:R-HSA-9712087") AnnotationAssertion(Annotation(rdfs:label "SRC phosphorylates RHOU") "Reactome:R-HSA-9726848") +AnnotationAssertion(Annotation(rdfs:label "JAK1-mediated phosphorylation of RAF1") "Reactome:R-HSA-9732738") AnnotationAssertion(Annotation(rdfs:label "CSF1R trans-autophosphorylates on tyrosine-561") "Reactome:R-HSA-9733314") AnnotationAssertion(Annotation(rdfs:label "Src family kinases phosphorylate CBL in CSF1 dimer:p-Y561-CSF1R dimer:CBL") "Reactome:R-HSA-9733323") -AnnotationAssertion(Annotation(rdfs:label "BACH1 is phosphorylated at tyrosine 486") "Reactome:R-HSA-9762209") +AnnotationAssertion(Annotation(rdfs:label "BACH1 is phosphorylated at tyrosine 483") "Reactome:R-HSA-9762209") AnnotationAssertion(Annotation(rdfs:label "JAK2 phosphorylation of GHR") "Reactome:R-HSA-982807") AnnotationAssertion(Annotation(rdfs:label "p-6Y-SYK phosphorylates BLNK (SLP65)") "Reactome:R-HSA-983703") AnnotationAssertion(Annotation(rdfs:label "SYK autophosphorylates at the activated BCR") "Reactome:R-HSA-983707") @@ -53647,8 +53299,6 @@ SubClassOf( "GOC:ai") Annotation( "GOC:dgf") "Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.") AnnotationAssertion( "GO:0005478") -AnnotationAssertion(Annotation(rdfs:label "Virion-associated M2 protein mediated ion infusion") "Reactome:R-HSA-168313") -AnnotationAssertion(Annotation(rdfs:label "SMAD7:SMURF1 complex is exported to the cytosol") "Reactome:R-HSA-178215") AnnotationAssertion( "molecular_function") AnnotationAssertion( "carrier") AnnotationAssertion( "GO:0005215") @@ -55724,7 +55374,6 @@ AnnotationAssertion( "GO:0006581") AnnotationAssertion(rdfs:label "acetylcholine catabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) # Class: (catecholamine metabolic process) @@ -57663,7 +57312,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "A neurotransmitter is any of a group of substances that are released on excitation from the axon terminal of a presynaptic neuron of the central or peripheral nervous system and travel across the synaptic cleft to either excite or inhibit the target cell. Among the many substances that have the properties of a neurotransmitter are acetylcholine, noradrenaline, adrenaline, dopamine, glycine, gamma-aminobutyrate, glutamic acid, substance P, enkephalins, endorphins and serotonin.") AnnotationAssertion(rdfs:label "neurotransmitter secretion") -SubClassOf( ) SubClassOf( ) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) @@ -58568,7 +58216,7 @@ AnnotationAssertion( "GO:0007560") AnnotationAssertion(rdfs:label "imaginal disc morphogenesis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -59415,7 +59063,6 @@ AnnotationAssertion( "GO:0008291") AnnotationAssertion(rdfs:label "acetylcholine metabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) # Class: (acetylcholine biosynthetic process) @@ -59428,7 +59075,6 @@ AnnotationAssertion( "GO:0008292") AnnotationAssertion(rdfs:label "acetylcholine biosynthetic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) # Class: (isoprenoid biosynthetic process) @@ -65889,7 +65535,6 @@ AnnotationAssertion( "GO:0019215") AnnotationAssertion(rdfs:label "intermediate filament binding") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) # Class: (regulation of lipid metabolic process) @@ -66496,6 +66141,14 @@ AnnotationAssertion( "isoprenoid binding") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (immunoglobulin binding) + +AnnotationAssertion(Annotation( "GOC:ma") "Binding to an immunoglobulin.") +AnnotationAssertion( "molecular_function") +AnnotationAssertion( "GO:0019865") +AnnotationAssertion(rdfs:label "immunoglobulin binding") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (outer membrane) AnnotationAssertion(Annotation( "GOC:go_curators") "The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites.") @@ -70039,6 +69692,7 @@ AnnotationAssertion( "GO:0022892") AnnotationAssertion(Annotation(rdfs:label "Egress of internalized antigen to the cytosol via sec61") "Reactome:R-HSA-1236947") AnnotationAssertion(Annotation(rdfs:label "SLC2A9 transports Fru, Glc, urate") "Reactome:R-HSA-429036") +AnnotationAssertion(Annotation(rdfs:label "MATEs mediate extrusion of xenobiotics") "Reactome:R-HSA-434650") AnnotationAssertion(Annotation(rdfs:label "Defective SLC2A9 does not transport Fru, Glc, urate") "Reactome:R-HSA-5638209") AnnotationAssertion(Annotation(rdfs:label "Fe3+ dissociates from SLC22A17:LCN2:2,5DHBA") "Reactome:R-HSA-5671707") AnnotationAssertion(Annotation(rdfs:label "An unknown carrier transports cytosolic glyoxylate to the peroxisome") "Reactome:R-HSA-6784434") @@ -71422,7 +71076,6 @@ EquivalentClasses( ObjectIntersection AnnotationAssertion(Annotation( "GOC:go_curators") "The chemical reactions and pathways resulting in the breakdown of bile acids, any of a group of steroid carboxylic acids occurring in bile.") AnnotationAssertion( "GO:0019613") -AnnotationAssertion( "MetaCyc:7ALPHADEHYDROX-PWY") AnnotationAssertion( "bile acid breakdown") AnnotationAssertion( "bile acid catabolism") AnnotationAssertion( "bile acid degradation") @@ -71460,7 +71113,6 @@ AnnotationAssertion( "A strict definition of neurotransmitter receptor activity would limit its use to receptor activity at the postsynaptic membrane as part of synaptic transmission, but we recognize that usage is often much broader than this. For the strict use case, please see 'postsynaptic neurotransmitter receptor activity'") AnnotationAssertion(rdfs:label "neurotransmitter receptor activity") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectAllValuesFrom( )) @@ -76403,6 +76055,7 @@ EquivalentClasses( ObjectIntersection # Class: (regulation of tissue remodeling) AnnotationAssertion(Annotation( "GOC:add") "Any process that modulates the frequency, rate, or extent of tissue remodeling.") +AnnotationAssertion( "regulation of tissue remodelling") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0034103") AnnotationAssertion(rdfs:label "regulation of tissue remodeling") @@ -76411,6 +76064,7 @@ EquivalentClasses( ObjectIntersection # Class: (negative regulation of tissue remodeling) AnnotationAssertion(Annotation( "GOC:add") "Any process that stops, prevents, or reduces the frequency, rate, or extent of tissue remodeling.") +AnnotationAssertion( "negative regulation of tissue remodelling") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0034104") AnnotationAssertion(rdfs:label "negative regulation of tissue remodeling") @@ -76419,6 +76073,7 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of tissue remodeling) AnnotationAssertion(Annotation( "GOC:add") "Any process that activates or increases the frequency, rate, or extent of tissue remodeling.") +AnnotationAssertion( "positive regulation of tissue remodelling") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0034105") AnnotationAssertion(rdfs:label "positive regulation of tissue remodeling") @@ -80072,49 +79727,6 @@ AnnotationAssertion( "negative regulation of T cell proliferation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (neurotransmitter metabolic process) - -AnnotationAssertion(Annotation( "GOC:jl") "The chemical reactions and pathways involving neurotransmitters, any of a group of substances that are released on excitation from the axon terminal of a presynaptic neuron of the central or peripheral nervous system and travel across the synaptic cleft to either excite or inhibit the target cell.") -AnnotationAssertion( ) -AnnotationAssertion( "neurotransmitter metabolism") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0042133") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "neurotransmitter metabolic process") -SubClassOf( ) -SubClassOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) -SubClassOf( ObjectSomeValuesFrom( ObjectComplementOf())) -DisjointClasses( ObjectSomeValuesFrom( )) - -# Class: (neurotransmitter catabolic process) - -AnnotationAssertion(Annotation( "GOC:jl") "The chemical reactions and pathways resulting in the breakdown of any of a group of substances that are released on excitation from the axon terminal of a presynaptic neuron of the central or peripheral nervous system and travel across the synaptic cleft to either excite or inhibit the target cell.") -AnnotationAssertion( "neurotransmitter breakdown") -AnnotationAssertion( "neurotransmitter catabolism") -AnnotationAssertion( "neurotransmitter degradation") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0042135") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "neurotransmitter catabolic process") -SubClassOf( ) -SubClassOf( ) - -# Class: (neurotransmitter biosynthetic process) - -AnnotationAssertion(Annotation( "GOC:jl") "The chemical reactions and pathways resulting in the formation of any of a group of substances that are released on excitation from the axon terminal of a presynaptic neuron of the central or peripheral nervous system and travel across the synaptic cleft to either excite or inhibit the target cell.") -AnnotationAssertion( "neurotransmitter biosynthesis and storage") -AnnotationAssertion( "neurotransmitter biosynthetic process and storage") -AnnotationAssertion( "neurotransmitter anabolism") -AnnotationAssertion( "neurotransmitter biosynthesis") -AnnotationAssertion( "neurotransmitter formation") -AnnotationAssertion( "neurotransmitter synthesis") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0042136") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "neurotransmitter biosynthetic process") -SubClassOf( ) -SubClassOf( ) - # Class: (lipoprotein metabolic process) AnnotationAssertion(Annotation( "ISBN:0198506732") "The chemical reactions and pathways involving any conjugated, water-soluble protein in which the covalently attached nonprotein group consists of a lipid or lipids.") @@ -80149,15 +79761,6 @@ AnnotationAssertion( "lipoprotein catabolic process") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (neurotransmitter binding) - -AnnotationAssertion(Annotation( "ISBN:0198506732") "Binding to a neurotransmitter, any chemical substance that is capable of transmitting (or inhibiting the transmission of) a nerve impulse from a neuron to another cell.") -AnnotationAssertion( "molecular_function") -AnnotationAssertion( "GO:0042165") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "neurotransmitter binding") -SubClassOf( ) - # Class: (acetylcholine binding) AnnotationAssertion(Annotation( "GOC:ai") "Binding to acetylcholine, an acetic acid ester of the organic base choline that functions as a neurotransmitter, released at the synapses of parasympathetic nerves and at neuromuscular junctions.") @@ -80165,7 +79768,6 @@ AnnotationAssertion( "GO:0042166") AnnotationAssertion(rdfs:label "acetylcholine binding") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) # Class: (nuclear outer membrane-endoplasmic reticulum membrane network) @@ -81888,7 +81490,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "ribonucleoprotein complex binding") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) # Class: (ribosome binding) @@ -82404,8 +82005,8 @@ AnnotationAssertion(Annotation( "https://github.com/geneontology/go-ontology/issues/21881"^^xsd:anyURI) AnnotationAssertion( "NIF_Subcellular:sao1456184038") AnnotationAssertion( "non-membrane-enclosed organelle") -AnnotationAssertion( "biological condensate") AnnotationAssertion( "cellular_component") +AnnotationAssertion( "biological condensate") AnnotationAssertion( "GO:0043228") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "non-membrane-bounded organelle") @@ -82596,15 +82197,16 @@ AnnotationAssertion( "response to alkaloid") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (pharyngeal muscle development) +# Class: (chordate pharyngeal muscle development) AnnotationAssertion(Annotation( "GOC:go_curators") "The process whose specific outcome is the progression of the pharyngeal muscle over time, from its formation to the mature structure. A pharyngeal muscle is any muscle that forms part of the pharynx.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/18285"^^xsd:anyURI) AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0043282") -AnnotationAssertion(rdfs:label "pharyngeal muscle development") +AnnotationAssertion(rdfs:label "chordate pharyngeal muscle development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (contractile fiber) @@ -82649,7 +82251,6 @@ AnnotationAssertion( "leukocyte degranulation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectAllValuesFrom( )) @@ -82703,9 +82304,8 @@ AnnotationAssertion( "GO:0043312") AnnotationAssertion(rdfs:label "neutrophil degranulation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) SubClassOf( ) -SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulation of neutrophil degranulation) @@ -83412,8 +83012,8 @@ EquivalentClasses( ObjectIntersection # Class: (ossification involved in bone remodeling) AnnotationAssertion(Annotation( "GOC:mtg_mpo") Annotation( "GO_REF:0000034") "The formation or growth of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone, involved in response to injury or other physical, physiological or environmental stress stimuli.") +AnnotationAssertion( "ossification involved in bone remodelling") AnnotationAssertion( "biological_process") -AnnotationAssertion( "ossification involved in bone remodelling") AnnotationAssertion( "GO:0043932") AnnotationAssertion(rdfs:label "ossification involved in bone remodeling") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -83790,20 +83390,6 @@ SubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectComplementOf())) DisjointClasses( ObjectSomeValuesFrom( )) -# Class: (dentate gyrus mossy fiber) - -AnnotationAssertion(Annotation( "NIF_Subcellular:nlx_subcell_20090601") Annotation( "PMID:17765709") "Distinctive, unmyelinated axons produced by dentate gyrus granule cells.") -AnnotationAssertion( "jl") -AnnotationAssertion( "2010-02-05T11:23:55Z") -AnnotationAssertion( "granule cell axon") -AnnotationAssertion( "NIF_Subcellular:nlx_subcell_20090601") -AnnotationAssertion( "dentate gyrus mossy fibre") -AnnotationAssertion( "cellular_component") -AnnotationAssertion( "GO:0044302") -AnnotationAssertion(rdfs:label "dentate gyrus mossy fiber") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (type B pancreatic cell proliferation) AnnotationAssertion(Annotation( "GOC:jl") Annotation( "GOC:yaf") "The multiplication or reproduction of pancreatic B cells, resulting in the expansion of an pancreatic B cell population. Pancreatic B cell are cells of the pancreas that secrete insulin.") @@ -88305,6 +87891,7 @@ SubClassOf( (regulation of bone remodeling) AnnotationAssertion(Annotation( "GOC:ai") "Any process that modulates the frequency, rate or extent of bone remodeling, the processes of bone formation and resorption that combine to maintain skeletal integrity.") +AnnotationAssertion( "regulation of bone remodelling") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0046850") AnnotationAssertion(rdfs:label "regulation of bone remodeling") @@ -88316,6 +87903,7 @@ AnnotationAssertion(Annotation( "down regulation of bone remodeling") AnnotationAssertion( "down-regulation of bone remodeling") AnnotationAssertion( "downregulation of bone remodeling") +AnnotationAssertion( "negative regulation of bone remodelling") AnnotationAssertion( "inhibition of bone remodeling") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0046851") @@ -88325,6 +87913,7 @@ EquivalentClasses( ObjectIntersection # Class: (positive regulation of bone remodeling) AnnotationAssertion(Annotation( "GOC:ai") "Any process that activates or increases the frequency, rate or extent of bone remodeling.") +AnnotationAssertion( "positive regulation of bone remodelling") AnnotationAssertion( "up regulation of bone remodeling") AnnotationAssertion( "up-regulation of bone remodeling") AnnotationAssertion( "upregulation of bone remodeling") @@ -89332,13 +88921,13 @@ SubClassOf( (animal organ development) AnnotationAssertion(Annotation( "GOC:dph") Annotation( "GOC:jid") "Development of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/25943"^^xsd:anyURI) AnnotationAssertion( "Wikipedia:Organogenesis") AnnotationAssertion( "development of an organ") AnnotationAssertion( "organogenesis") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0048513") AnnotationAssertion(rdfs:label "animal organ development") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) # Class: (blood vessel morphogenesis) @@ -89589,16 +89178,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (post-embryonic animal organ morphogenesis) - -AnnotationAssertion(Annotation( "GOC:jid") "Morphogenesis, during the post-embryonic phase, of an animal tissue or tissues that work together to perform a specific function or functions. Morphogenesis pertains to process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0048563") -AnnotationAssertion(rdfs:label "post-embryonic animal organ morphogenesis") -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (digestive tract development) AnnotationAssertion(Annotation( "GOC:go_curators") "The process whose specific outcome is the progression of the digestive tract over time, from its formation to the mature structure. The digestive tract is the anatomical structure through which food passes and is processed.") @@ -89625,16 +89204,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (post-embryonic animal organ development) - -AnnotationAssertion(Annotation( "GOC:jid") "Development, taking place during the post-embryonic phase of an animal tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.") -AnnotationAssertion( "post-embryonic animal organogenesis") -AnnotationAssertion( "biological_process") -AnnotationAssertion( "GO:0048569") -AnnotationAssertion(rdfs:label "post-embryonic animal organ development") -SubClassOf( ) -SubClassOf( ) - # Class: (notochord morphogenesis) AnnotationAssertion(Annotation( "GOC:jid") "The process in which the anatomical structures of the notochord are generated and organized. The notochord is a mesoderm-derived structure located ventral of the developing nerve cord. In vertebrates, the notochord serves as a core around which other mesodermal cells form the vertebrae. In the most primitive chordates, which lack vertebrae, the notochord persists as a substitute for a vertebral column.") @@ -90495,6 +90064,7 @@ SubClassOf( (tissue remodeling) AnnotationAssertion(Annotation( "GOC:ebc") "The reorganization or renovation of existing tissues. This process can either change the characteristics of a tissue such as in blood vessel remodeling, or result in the dynamic equilibrium of a tissue such as in bone remodeling.") +AnnotationAssertion( "tissue remodelling") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0048771") AnnotationAssertion( ) @@ -92186,6 +91756,19 @@ EquivalentClasses( ObjectIntersection SubClassOf( ) SubClassOf( ) +# Class: (ice binding) + +AnnotationAssertion(Annotation( "GOC:curators") "Binding to ice, water reduced to the solid state by cold temperature. It is a white or transparent colorless substance, crystalline, brittle, and viscoidal.") +AnnotationAssertion( "ice crystal binding") +AnnotationAssertion( "molecular_function") +AnnotationAssertion( "antifreeze activity") +AnnotationAssertion( "ice nucleation activity") +AnnotationAssertion( "ice nucleation inhibitor activity") +AnnotationAssertion( "GO:0050825") +AnnotationAssertion(rdfs:label "ice binding") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) + # Class: (defense response to fungus) AnnotationAssertion(Annotation( "GOC:ai") "Reactions triggered in response to the presence of a fungus that act to protect the cell or organism.") @@ -93093,7 +92676,7 @@ AnnotationAssertion( "molecular_function") AnnotationAssertion( "GO:0050997") AnnotationAssertion(rdfs:label "quaternary ammonium group binding") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (actin filament bundle assembly) @@ -93819,9 +93402,11 @@ SubClassOf( (establishment of localization) AnnotationAssertion(Annotation( "GOC:ai") Annotation( "GOC:dos") "Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24200"^^xsd:anyURI) AnnotationAssertion(Annotation( "GOC:mah") "establishment of localisation") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0051234") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) @@ -104122,7 +103707,6 @@ AnnotationAssertion( "GO:0070051") AnnotationAssertion(rdfs:label "fibrinogen binding") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) # Class: (extracellular exosome) @@ -111474,14 +111058,15 @@ SubClassOf( (hippocampal mossy fiber) -AnnotationAssertion(Annotation( "NIF_Subcellular:nlx_subcell_100312") Annotation( "PMID:17765709") "Axon of dentate gyrus granule cell projecting to hippocampal area CA3, characterized by expansions (mossy fiber expansions) giving the fibers a mossy appearance. These unmyelinated axons were first described by Ramon y Cajal.") +AnnotationAssertion(Annotation( "NIF_Subcellular:nlx_subcell_100312") Annotation( "PMID:17765709") Annotation( "PMID:20554881") Annotation( "PMID:24336151") "An axon of a hippocampal granule cell, including dentate gyrus granule cell and CA3 granule cell, characterized by expansions (mossy fiber expansions) giving the fibers a mossy appearance. These unmyelinated axons were first described by Ramon y Cajal.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/25796"^^xsd:anyURI) AnnotationAssertion( "pr") AnnotationAssertion( "2012-12-19T16:51:57Z") AnnotationAssertion( "NIF_Subcellular:nlx_subcell_100312") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0097457") AnnotationAssertion(rdfs:label "hippocampal mossy fiber") -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) # Class: (retinal rod cell apoptotic process) @@ -112017,7 +111602,6 @@ AnnotationAssertion( "GO:0098633") AnnotationAssertion(rdfs:label "collagen fibril binding") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) # Class: (protein complex involved in cell-cell adhesion) @@ -113973,44 +113557,48 @@ AnnotationAssertion( "positive regulation of cardiac muscle myoblast proliferation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (pharynx morphogenesis) +# Class: (nematode pharynx morphogenesis) -AnnotationAssertion(Annotation( "GOC:rz") Annotation( "PMID:20805556") "The process in which the anatomical structures of the pharynx are generated and organized.") +AnnotationAssertion(Annotation( "GOC:rz") Annotation( "PMID:20805556") "The process in which the anatomical structures of the nematode pharynx are generated and organized.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/18285"^^xsd:anyURI) AnnotationAssertion( "kmv") AnnotationAssertion( "2017-07-24T20:51:28Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0110040") -AnnotationAssertion(rdfs:label "pharynx morphogenesis") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +AnnotationAssertion(rdfs:label "nematode pharynx morphogenesis") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (regulation of pharynx morphogenesis) +# Class: (regulation of nematode pharynx morphogenesis) -AnnotationAssertion(Annotation( "GOC:rz") Annotation( "PMID:20805556") "Any process that modulates the frequency, rate or extent of pharynx morphogenesis, the process in which the anatomical structure of the pharynx is generated and organized.") +AnnotationAssertion(Annotation( "GOC:rz") Annotation( "PMID:20805556") "Any process that modulates the frequency, rate or extent of nematode pharynx morphogenesis, the process in which the anatomical structure of the pharynx is generated and organized.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/18285"^^xsd:anyURI) AnnotationAssertion( "kmv") AnnotationAssertion( "2017-07-24T21:00:20Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0110041") -AnnotationAssertion(rdfs:label "regulation of pharynx morphogenesis") +AnnotationAssertion(rdfs:label "regulation of nematode pharynx morphogenesis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (negative regulation of pharynx morphogenesis) +# Class: (negative regulation of nematode pharynx morphogenesis) -AnnotationAssertion(Annotation( "GOC:rz") Annotation( "PMID:20805556") "Any process that stops, prevents, or reduces the frequency, rate or extent of pharynx morphogenesis.") +AnnotationAssertion(Annotation( "GOC:rz") Annotation( "PMID:20805556") "Any process that stops, prevents, or reduces the frequency, rate or extent of nematode pharynx morphogenesis.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/18285"^^xsd:anyURI) AnnotationAssertion( "kmv") AnnotationAssertion( "2017-07-24T21:05:08Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0110042") -AnnotationAssertion(rdfs:label "negative regulation of pharynx morphogenesis") +AnnotationAssertion(rdfs:label "negative regulation of nematode pharynx morphogenesis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (positive regulation of pharynx morphogenesis) +# Class: (positive regulation of nematode pharynx morphogenesis) -AnnotationAssertion(Annotation( "GOC:rz") Annotation( "PMID:20805556") "Any process that activates or increases the frequency, rate or extent of pharynx morphogenesis.") +AnnotationAssertion(Annotation( "GOC:rz") Annotation( "PMID:20805556") "Any process that activates or increases the frequency, rate or extent of nematode pharynx morphogenesis.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/18285"^^xsd:anyURI) AnnotationAssertion( "kmv") AnnotationAssertion( "2017-07-24T21:09:48Z") AnnotationAssertion( "biological_process") AnnotationAssertion( "GO:0110043") -AnnotationAssertion(rdfs:label "positive regulation of pharynx morphogenesis") +AnnotationAssertion(rdfs:label "positive regulation of nematode pharynx morphogenesis") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (regulation of actin filament organization) @@ -114321,10 +113909,12 @@ EquivalentClasses( ObjectIntersection # Class: (cellular anatomical entity) AnnotationAssertion(Annotation( "GOC:kmv") "A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/24200"^^xsd:anyURI) AnnotationAssertion( "kmv") AnnotationAssertion( "2019-08-12T18:01:37Z") AnnotationAssertion( "cellular_component") AnnotationAssertion( "GO:0110165") +AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "cellular anatomical entity") SubClassOf( ) @@ -115309,6 +114899,7 @@ AnnotationAssertion(Annotation( "https://github.com/geneontology/go-ontology/issues/17073"^^xsd:anyURI) AnnotationAssertion( "pg") AnnotationAssertion( "2019-04-01T10:41:38Z") +AnnotationAssertion(Annotation(rdfs:label "M6PR transports activated ARSA to the lysosome") "Reactome:R-HSA-2248891") AnnotationAssertion(Annotation(rdfs:label "iRHOM2 transports ADAM17 from ER to the Golgi-network") "Reactome:R-HSA-9662747") AnnotationAssertion(Annotation(rdfs:label "iRHOM2 transports ADAM17:Zn2+ from Golgi to the plasma membrane") "Reactome:R-HSA-9662818") AnnotationAssertion( "molecular_function") @@ -115843,6 +115434,39 @@ AnnotationAssertion( "craniofacial suture closure") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (chordate pharynx development) + +AnnotationAssertion(Annotation( "PMID:23020903") "The process whose specific outcome is the progression of cordate pharynx over time, from its formation to the mature structure.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/18285"^^xsd:anyURI) +AnnotationAssertion( "rynl") +AnnotationAssertion( "2023-08-29T21:05:28Z") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0160093") +AnnotationAssertion(rdfs:label "chordate pharynx development") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (nematode pharynx development) + +AnnotationAssertion(Annotation( "PMID:18050503") "The process whose specific outcome is the progression of nematode pharynx over time, from its formation to the mature structure.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/18285"^^xsd:anyURI) +AnnotationAssertion( "rynl") +AnnotationAssertion( "2023-08-29T22:05:32Z") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0160094") +AnnotationAssertion(rdfs:label "nematode pharynx development") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + +# Class: (insect pharynx development) + +AnnotationAssertion(Annotation( "PMID:10952900") "The process whose specific outcome is the progression of insect pharynx over time, from its formation to the mature structure.") +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/18285"^^xsd:anyURI) +AnnotationAssertion( "rynl") +AnnotationAssertion( "2023-08-29T22:14:25Z") +AnnotationAssertion( "biological_process") +AnnotationAssertion( "GO:0160095") +AnnotationAssertion(rdfs:label "insect pharynx development") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (positive regulation of dendrite development) AnnotationAssertion(Annotation( "GOC:TermGenie") "Any process that activates or increases the frequency, rate or extent of dendrite development.") @@ -118489,7 +118113,7 @@ AnnotationAssertion( AnnotationAssertion( "molecular_function") AnnotationAssertion( "GO:1901363") AnnotationAssertion(rdfs:label "heterocyclic compound binding") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (acetate ester transport) @@ -133204,18 +132828,6 @@ AnnotationAssertion(rdfs:label "posi EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf(Annotation( "https://github.com/geneontology/go-ontology/issues/13926") ObjectSomeValuesFrom( )) -# Class: (pharyngeal gland morphogenesis) - -AnnotationAssertion(Annotation( "GOC:TermGenie") Annotation( "GO_REF:0000083") Annotation( "PMID:21868609") "The developmental process by which a pharyngeal gland is generated and organized.") -AnnotationAssertion( "rz") -AnnotationAssertion( "2017-02-03T14:39:10Z") -AnnotationAssertion(Annotation( "GOC:TermGenie") "pharynx gland morphogenesis") -AnnotationAssertion( "biological_process") -AnnotationAssertion(Annotation( "GOC:TermGenie") "glandulae pharyngeae morphogenesis") -AnnotationAssertion( "GO:1905905") -AnnotationAssertion(rdfs:label "pharyngeal gland morphogenesis") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - # Class: (regulation of calcium ion export across plasma membrane) AnnotationAssertion(Annotation( "GOC:BHF") Annotation( "GOC:BHF_miRNA") Annotation( "GOC:TermGenie") Annotation( "GOC:rph") Annotation( "GO_REF:0000058") Annotation( "PMID:22362515") "Any process that modulates the frequency, rate or extent of calcium ion export across the plasma membrane.") @@ -143434,7 +143046,6 @@ AnnotationAssertion( "quality") AnnotationAssertion( "PATO:0000001") AnnotationAssertion(rdfs:label "quality") -SubClassOf( ) # Class: (color) @@ -144049,6 +143660,16 @@ AnnotationAssertion( "haploid") SubClassOf( ) +# Class: (polyploid) + +AnnotationAssertion(Annotation( "Wikipedia:http://en.wikipedia.org/wiki/Polyploid") "A ploidy quality inhering in a bearer by virtue of the bearer's containing more than two homologous sets of chromosomes.") +AnnotationAssertion( "quality") +AnnotationAssertion( "PATO:0001377") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "polyploid") +SubClassOf( ) + # Class: (euploid) AnnotationAssertion(Annotation( "Wikipedia:http://en.wikipedia.org/wiki/Euploid") "A ploidy quality inhering in a bearer by virtue of the bearer's containing an integral multiple of the monoploid number, possibly excluding the sex-determining chromosomes.") diff --git a/src/ontology/uberon-odk.yaml b/src/ontology/uberon-odk.yaml index 74fe8513f7..678988466d 100644 --- a/src/ontology/uberon-odk.yaml +++ b/src/ontology/uberon-odk.yaml @@ -44,7 +44,8 @@ import_group: - id: cl use_base: TRUE - id: go - use_base: TRUE + make_base: TRUE + mirror_from: http://purl.obolibrary.org/obo/go/go-base.owl base_iris: - http://purl.obolibrary.org/obo/GO_ - http://purl.obolibrary.org/obo/GOREL_ From 989b5a0044625833664083f5dc45fef8bf156490 Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Thu, 26 Oct 2023 09:26:12 +0100 Subject: [PATCH 10/11] Fix composite unsats (#3099) * Remove old bogus axiom from the local CTENO mirror. The local CTENO mirror, used to produce composite-metazoan, contains several axioms coming from an old version of Uberon (CTENO has not been updated since 2016). One such axiom is 'surface groove' SubClassOf: 'surface structure' which *may* have been correct in 2016 but is clearly bogus now, since 'surface groove' (UBERON:0006846) is an immaterial anatomical entity whereas 'surface structure' (UBERON:0003102) is an anatomical structure (and thus a material anatomical entity). That single axiom is causing massive unsatisfiability issues when building composite-metazoan. * Remove bogus axiom from the local EHDAA2 mirror. The local EHDAA2 mirror, used to build composite-metazoan, contains the following axiom: 'extra embryonic coelum' SubClassOf: 'attached to' some 'coelomic cavity lumen' This is wrong as 'attached to' (RO:0002371) is range- and domain-restricted to anatomical structures, while both 'extra embryonic coelum' (EHDAA2:0004739) and 'coelomic cavity lumen' (EHDAA2:0000267) are anatomical spaces (immaterial entities). This should really be fixed in EHDAA2, but the ontology is officially marked as inactive and has not seen any really meaningful edit for the past 8 years. * Unmap 'serous sac' from EMAPA:16060 and MA:0000005. 'serous sac' (UBERON:0005906) is mapped with EMAPA:16060. This is wrong, because the Uberon term represents an entire organ, made of a serous membrane surrounding an anatomical cavity, while the EMAPA term refers to a body cavity OR the lining that surrounds it. The Uberon term is necessarily a material entity, while the EMAPA term is not committed to being either a material entity or an immaterial entity. Mapping the two terms together results, when building composite-metazoan, in the EMAPA term becoming a subclass of the Uberon term, thereby forcing the EMAPA term to be a material entity. This causes several unsatisfiability issues because there are other Uberon terms that are mapped to subclasses of the EMAPA term but represent immaterial entities. Likewise for MA:0000005. --- src/ontology/imports/local-cteno.owl | 6 ------ src/ontology/imports/local-ehdaa2.owl | 3 +-- src/ontology/uberon-edit.obo | 2 -- 3 files changed, 1 insertion(+), 10 deletions(-) diff --git a/src/ontology/imports/local-cteno.owl b/src/ontology/imports/local-cteno.owl index 6b50117eb0..d019a013ec 100644 --- a/src/ontology/imports/local-cteno.owl +++ b/src/ontology/imports/local-cteno.owl @@ -12857,12 +12857,6 @@ - - - - - surface groove - diff --git a/src/ontology/imports/local-ehdaa2.owl b/src/ontology/imports/local-ehdaa2.owl index 9400641d14..5afe4ae16e 100644 --- a/src/ontology/imports/local-ehdaa2.owl +++ b/src/ontology/imports/local-ehdaa2.owl @@ -25905,7 +25905,6 @@ SubClassOf( ObjectSomeValuesFrom( AnnotationAssertion(rdfs:label "extraembryonic coelum"^^xsd:string) SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) # Class: (urogenital sinus epithelium vesical part) @@ -26330,4 +26329,4 @@ AnnotationAssertion( "true"^^xsd:boolean) -) \ No newline at end of file +) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 9b6a1ff8a4..d806382e30 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -106778,9 +106778,7 @@ id: UBERON:0005906 name: serous sac def: "Organ with organ cavity, which has as parts a serous membrane and a serous cavity . Examples: pleural sac, pericardial sac, tendon sheath, bursa.[FMA]." [FMA:9689, https://github.com/obophenotype/uberon/issues/86] comment: See notes for serous membrane -xref: EMAPA:16060 xref: FMA:9689 -xref: MA:0000005 xref: SCTID:362890006 is_a: UBERON:0000062 ! organ relationship: has_part UBERON:0000042 ! serous membrane From 3d04ccf97b8060d423f319326c446bbc21da7ffa Mon Sep 17 00:00:00 2001 From: Anita Caron Date: Thu, 26 Oct 2023 10:43:46 +0100 Subject: [PATCH 11/11] Import OMO terms (#3092) * import OMO terms * update import with OMO:0003011 --------- Co-authored-by: Anita Caron --- docs/odk-workflows/RepositoryFileStructure.md | 1 + src/ontology/Makefile | 17 +- src/ontology/imports/merged_import.owl | 353 +++++++++++++++++- src/ontology/imports/omo_terms.txt | 5 + src/ontology/uberon-odk.yaml | 2 + 5 files changed, 370 insertions(+), 8 deletions(-) create mode 100644 src/ontology/imports/omo_terms.txt diff --git a/docs/odk-workflows/RepositoryFileStructure.md b/docs/odk-workflows/RepositoryFileStructure.md index b55918861f..aaea0d9af9 100644 --- a/docs/odk-workflows/RepositoryFileStructure.md +++ b/docs/odk-workflows/RepositoryFileStructure.md @@ -28,6 +28,7 @@ These are the current imports in UBERON | ncbitaxon | http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl | None | | nbo | http://purl.obolibrary.org/obo/nbo.owl | None | | orcidio | https://w3id.org/orcidio/orcidio.owl | None | +| omo | http://purl.obolibrary.org/obo/omo.owl | mirror | ## Components Components, in contrast to imports, are considered full members of the ontology. This means that any axiom in a component is also included in the ontology base - which means it is considered _native_ to the ontology. While this sounds complicated, consider this: conceptually, no component should be part of more than one ontology. If that seems to be the case, we are most likely talking about an import. Components are often not needed for ontologies, but there are some use cases: diff --git a/src/ontology/Makefile b/src/ontology/Makefile index f81e195d50..d650bef1c7 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -114,7 +114,7 @@ all_main: $(MAIN_FILES) # ---------------------------------------- -IMPORTS = pr cl go envo ro bspo chebi pato bfo ncbitaxon nbo orcidio +IMPORTS = pr cl go envo ro bspo chebi pato bfo ncbitaxon nbo orcidio omo IMPORT_ROOTS = $(IMPORTDIR)/merged_import IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl) @@ -339,6 +339,12 @@ $(IMPORTDIR)/%_import.owl: $(MIRRORDIR)/merged.owl $(IMPORTDIR)/%_terms_combined .PRECIOUS: $(IMPORTDIR)/%_import.owl +## Module for ontology: omo + +$(IMPORTDIR)/omo_import.owl: $(MIRRORDIR)/merged.owl $(IMPORTDIR)/omo_terms_combined.txt + if [ $(IMP) = true ]; then $(ROBOT) merge -i $< query --update ../sparql/preprocess-module.ru --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \ + $(ANNOTATE_CONVERT_FILE); fi + .PHONY: refresh-imports refresh-imports: @@ -505,6 +511,15 @@ mirror-orcidio: | $(TMPDIR) if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I https://w3id.org/orcidio/orcidio.owl -o $@.tmp.owl &&\ mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + +## ONTOLOGY: omo +.PHONY: mirror-omo +.PRECIOUS: $(MIRRORDIR)/omo.owl +mirror-omo: | $(TMPDIR) + if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/omo.owl --create-dirs -o $(MIRRORDIR)/omo.owl --retry 4 --max-time 200 &&\ + $(ROBOT) convert -i $(MIRRORDIR)/omo.owl -o $@.tmp.owl &&\ + mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + ALL_MIRRORS = $(patsubst %, $(MIRRORDIR)/%.owl, $(IMPORTS)) MERGE_MIRRORS = true diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl index fa2f60b947..4a9e67fde1 100644 --- a/src/ontology/imports/merged_import.owl +++ b/src/ontology/imports/merged_import.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2023-10-24") + +Annotation(owl:versionInfo "2023-10-25") Declaration(Class()) Declaration(Class()) @@ -9443,6 +9443,12 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -12066,6 +12072,24 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -12080,6 +12104,7 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -12087,11 +12112,13 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -12177,9 +12204,11 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -12225,54 +12254,163 @@ Declaration(AnnotationProperty() Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(Datatype(xsd:date)) ############################ # Annotation Properties ############################ # Annotation Property: (example of usage) +AnnotationAssertion( "example of usage"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold."@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "GROUP:OBI:"@en) AnnotationAssertion(rdfs:isDefinedBy ) AnnotationAssertion(rdfs:label "example of usage"@en) AnnotationAssertion(rdfs:label "example of usage") # Annotation Property: (definition) +AnnotationAssertion( "definition"@en) +AnnotationAssertion( ) +AnnotationAssertion( "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions."@en) +AnnotationAssertion( "2012-04-05: +Barry Smith + +The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. + +Can you fix to something like: + +A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. + +Alan Ruttenberg + +Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. + +On the specifics of the proposed definition: + +We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. + +Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. + +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with."@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "GROUP:OBI:"@en) AnnotationAssertion(rdfs:isDefinedBy ) AnnotationAssertion(rdfs:label "definition"@en) AnnotationAssertion(rdfs:label "definition") # Annotation Property: (editor note) +AnnotationAssertion( "editor note"@en) +AnnotationAssertion( ) +AnnotationAssertion( "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology."@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "GROUP:OBI:"@en) AnnotationAssertion(rdfs:isDefinedBy ) AnnotationAssertion(rdfs:label "editor note"@en) AnnotationAssertion(rdfs:label "editor note") +# Annotation Property: (has obsolescence reason) + +AnnotationAssertion( "has obsolescence reason"@en) +AnnotationAssertion( "Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification."@en) +AnnotationAssertion( "PERSON:Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON:Melanie Courtot"@en) +AnnotationAssertion(rdfs:label "has obsolescence reason"@en) + # Annotation Property: (curator note) +AnnotationAssertion( "curator note"@en) +AnnotationAssertion( ) +AnnotationAssertion( "An administrative note of use for a curator but of no use for a user"@en) +AnnotationAssertion( "PERSON:Alan Ruttenberg"@en) AnnotationAssertion(rdfs:isDefinedBy ) AnnotationAssertion(rdfs:label "curator note"@en) AnnotationAssertion(rdfs:label "curator note") +# Annotation Property: (term tracker item) + +AnnotationAssertion( "term tracker item"@en) +AnnotationAssertion( "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/"@en) +AnnotationAssertion( ) +AnnotationAssertion( "An IRI or similar locator for a request or discussion of an ontology term."@en) +AnnotationAssertion( "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg"@en) +AnnotationAssertion( "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:comment "The 'tracker item' can associate a tracker with a specific ontology term."@en) +AnnotationAssertion(rdfs:label "term tracker item"@en) + # Annotation Property: (expand assertion to) +AnnotationAssertion( "expand assertion to"@en) +AnnotationAssertion( "ObjectProperty: RO??? +Label: spatially disjoint from +Annotations: expand_assertion_to \"DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)\" +"@en) +AnnotationAssertion( "A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom."@en) +AnnotationAssertion( "Chris Mungall"@en) +AnnotationAssertion(rdfs:label "expand assertion to"@en) AnnotationAssertion(rdfs:label "expand assertion to") -# Annotation Property: (preferred_root) +# Annotation Property: (has ontology root term) +AnnotationAssertion( "has ontology root term"@en) +AnnotationAssertion( "Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root."@en) +AnnotationAssertion( "Nicolas Matentzoglu"@en) +AnnotationAssertion(rdfs:label "has ontology root term"@en) AnnotationAssertion(rdfs:label "preferred_root") +# Annotation Property: (scheduled for obsoletion on or after) + +AnnotationAssertion( "scheduled for obsoletion on or after"@en) +AnnotationAssertion( "Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date."@en) +AnnotationAssertion( "Chris Mungall, Jie Zheng"@en) +AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/15532"@en) +AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/32"@en) +AnnotationAssertion( "GO ontology"@en) +AnnotationAssertion(rdfs:label "scheduled for obsoletion on or after"@en) + # Annotation Property: (term replaced by) +AnnotationAssertion( "term replaced by"@en) +AnnotationAssertion( ) +AnnotationAssertion( "Use on obsolete terms, relating the term to another term that can be used as a substitute"@en) +AnnotationAssertion( "Person:Alan Ruttenberg"@en) +AnnotationAssertion( "Person:Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:comment "Add as annotation triples in the granting ontology"@en) +AnnotationAssertion(rdfs:label "term replaced by"@en) AnnotationAssertion(rdfs:label "term replaced by") -# Annotation Property: () +# Annotation Property: (abbreviation) +AnnotationAssertion( "CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation)") +AnnotationAssertion( "A synonym type for describing abbreviations or initalisms") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "2023-03-03"^^xsd:date) +AnnotationAssertion(rdfs:label "abbreviation") SubAnnotationPropertyOf( ) -# Annotation Property: () +# Annotation Property: (plural form) +AnnotationAssertion( "CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form)") +AnnotationAssertion( "A synonym type for describing pluralization synonyms") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "2023-03-03"^^xsd:date) +AnnotationAssertion(rdfs:label "plural form") SubAnnotationPropertyOf( ) +# Annotation Property: (latin term) + +AnnotationAssertion( "nasopharynx (UBERON:0001728) has the latin name \"pars nasalis pharyngis") +AnnotationAssertion( "A synonym type for describing Latin term synonyms.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( "2023-10-12"^^xsd:date) +AnnotationAssertion(rdfs:label "latin term") + # Annotation Property: (never in taxon) AnnotationAssertion( "tooth SubClassOf 'never in taxon' value 'Aves'") @@ -12653,19 +12791,34 @@ AnnotationAssertion(rdfs:label (has_broad_synonym) +AnnotationAssertion( "An alternative label for a class or property which has a more general meaning than the preferred name/primary label.") +AnnotationAssertion( ) +AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/18") +AnnotationAssertion(rdfs:label "has broad synonym"@en) AnnotationAssertion(rdfs:label "has_broad_synonym") +AnnotationAssertion(rdfs:seeAlso "https://github.com/information-artifact-ontology/ontology-metadata/issues/18") # Annotation Property: (database_cross_reference) AnnotationAssertion(rdfs:label "database_cross_reference") -# Annotation Property: (has_exact_synonym) +# Annotation Property: (has exact synonym) +AnnotationAssertion( "An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.") +AnnotationAssertion( ) +AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/20") +AnnotationAssertion(rdfs:label "has exact synonym"@en) AnnotationAssertion(rdfs:label "has_exact_synonym") +AnnotationAssertion(rdfs:seeAlso "https://github.com/information-artifact-ontology/ontology-metadata/issues/20") -# Annotation Property: (has_narrow_synonym) +# Annotation Property: (has narrow synonym) +AnnotationAssertion( "An alternative label for a class or property which has a more specific meaning than the preferred name/primary label.") +AnnotationAssertion( ) +AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/19") +AnnotationAssertion(rdfs:label "has narrow synonym"@en) AnnotationAssertion(rdfs:label "has_narrow_synonym") +AnnotationAssertion(rdfs:seeAlso "https://github.com/information-artifact-ontology/ontology-metadata/issues/19") # Annotation Property: (has_obo_format_version) @@ -12677,7 +12830,12 @@ AnnotationAssertion(rdfs:label (has_related_synonym) +AnnotationAssertion( "An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct.") +AnnotationAssertion( ) +AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/21") +AnnotationAssertion(rdfs:label "has related synonym"@en) AnnotationAssertion(rdfs:label "has_related_synonym") +AnnotationAssertion(rdfs:seeAlso "https://github.com/information-artifact-ontology/ontology-metadata/issues/21") # Annotation Property: (has_scope) @@ -137278,6 +137436,62 @@ AnnotationAssertion( "positive regulation of chromosome organization") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (data item) + +AnnotationAssertion( "data item"@en) +AnnotationAssertion(rdfs:label "data item"@en) +SubClassOf( ) + +# Class: (information content entity) + +AnnotationAssertion( "information content entity"@en) +AnnotationAssertion(rdfs:label "information content entity"@en) +SubClassOf( ) + +# Class: (curation status specification) + +AnnotationAssertion( "curation status specification"@en) +AnnotationAssertion( ) +AnnotationAssertion( "The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value."@en) +AnnotationAssertion( "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)"@en) +AnnotationAssertion( "PERSON:Bill Bug"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion( "OBI_0000266"@en) +AnnotationAssertion(rdfs:label "curation status specification"@en) +EquivalentClasses( ObjectOneOf( )) +SubClassOf( ) + +# Class: (data about an ontology part) + +AnnotationAssertion( "data about an ontology part"@en) +AnnotationAssertion( "Data about an ontology part is a data item about a part of an ontology, for example a term"@en) +AnnotationAssertion( "Person:Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "data about an ontology part"@en) +SubClassOf( ) + +# Class: (obsolescence reason specification) + +AnnotationAssertion( "obsolescence reason specification"@en) +AnnotationAssertion( ) +AnnotationAssertion( "The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value."@en) +AnnotationAssertion( "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology."@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Melanie Courtot"@en) +AnnotationAssertion(rdfs:label "obsolescence reason specification"@en) +EquivalentClasses( ObjectOneOf( )) +SubClassOf( ) + +# Class: (denotator type) + +AnnotationAssertion( "denotator type"@en) +AnnotationAssertion( "The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are \"natural kinds\" and the latter arbitrary collections of entities."@en) +AnnotationAssertion( "A denotator type indicates how a term should be interpreted from an ontological perspective."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "Barry Smith, Werner Ceusters"@en) +AnnotationAssertion(rdfs:label "denotator type"@en) +EquivalentClasses( ObjectOneOf( )) +SubClassOf( ) + # Class: (body part movement) AnnotationAssertion( "A change of place or position of part of an organism that does not involve the entire organism [NBO:SMAC]") @@ -150652,6 +150866,131 @@ AnnotationAssertion(rdfs:label "syst SubClassOf( ) +############################ +# Named Individuals +############################ + +# Individual: (example to be eventually removed) + +AnnotationAssertion( "example to be eventually removed"@en) +AnnotationAssertion(rdfs:label "example to be eventually removed"@en) + +# Individual: (failed exploratory term) + +AnnotationAssertion( "failed exploratory term"@en) +AnnotationAssertion( "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job"@en) +AnnotationAssertion( "Person:Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "failed exploratory term"@en) + +# Individual: (metadata complete) + +AnnotationAssertion( "metadata complete"@en) +AnnotationAssertion( "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete."@en) +AnnotationAssertion(rdfs:label "metadata complete"@en) + +# Individual: (organizational term) + +AnnotationAssertion( "organizational term"@en) +AnnotationAssertion( "Term created to ease viewing/sort terms for development purpose, and will not be included in a release"@en) +AnnotationAssertion(rdfs:label "organizational term"@en) + +# Individual: (ready for release) + +AnnotationAssertion( "ready for release"@en) +AnnotationAssertion( "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\""@en) +AnnotationAssertion(rdfs:label "ready for release"@en) + +# Individual: (metadata incomplete) + +AnnotationAssertion( "metadata incomplete"@en) +AnnotationAssertion( "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors."@en) +AnnotationAssertion(rdfs:label "metadata incomplete"@en) + +# Individual: (uncurated) + +AnnotationAssertion( "uncurated"@en) +AnnotationAssertion( "Nothing done yet beyond assigning a unique class ID and proposing a preferred term."@en) +AnnotationAssertion(rdfs:label "uncurated"@en) + +# Individual: (pending final vetting) + +AnnotationAssertion( "pending final vetting"@en) +AnnotationAssertion( "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor."@en) +AnnotationAssertion(rdfs:label "pending final vetting"@en) + +# Individual: (placeholder removed) + +AnnotationAssertion( "placeholder removed"@en) +AnnotationAssertion(rdfs:label "placeholder removed"@en) + +# Individual: (terms merged) + +AnnotationAssertion( "terms merged"@en) +AnnotationAssertion( "An editor note should explain what were the merged terms and the reason for the merge."@en) +AnnotationAssertion(rdfs:label "terms merged"@en) + +# Individual: (term imported) + +AnnotationAssertion( "term imported"@en) +AnnotationAssertion( "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use."@en) +AnnotationAssertion(rdfs:label "term imported"@en) + +# Individual: (term split) + +AnnotationAssertion( "term split"@en) +AnnotationAssertion( "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created."@en) +AnnotationAssertion(rdfs:label "term split"@en) + +# Individual: (universal) + +AnnotationAssertion( "universal"@en) +AnnotationAssertion( "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf"@en) +AnnotationAssertion(rdfs:label "universal"@en) + +# Individual: (defined class) + +AnnotationAssertion( "defined class"@en) +AnnotationAssertion( "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal"@en) +AnnotationAssertion( "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "defined class"@en) + +# Individual: (named class expression) + +AnnotationAssertion( "named class expression"@en) +AnnotationAssertion( "A named class expression is a logical expression that is given a name. The name can be used in place of the expression."@en) +AnnotationAssertion( "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions"@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "named class expression"@en) + +# Individual: (to be replaced with external ontology term) + +AnnotationAssertion( "to be replaced with external ontology term"@en) +AnnotationAssertion( "Terms with this status should eventually replaced with a term from another ontology."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion(rdfs:label "to be replaced with external ontology term"@en) + +# Individual: (requires discussion) + +AnnotationAssertion( "requires discussion"@en) +AnnotationAssertion( "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion(rdfs:label "requires discussion"@en) + +# Individual: (out of scope) + +AnnotationAssertion( "The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not."@en) +AnnotationAssertion( "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease."@en) +AnnotationAssertion( ) +AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/77") +AnnotationAssertion( "https://orcid.org/0000-0001-5208-3432") +AnnotationAssertion(rdfs:label "out of scope") + + EquivalentClasses(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectIntersectionOf( ObjectMinCardinality(2 ))) EquivalentClasses(ObjectIntersectionOf( ObjectComplementOf(ObjectSomeValuesFrom( ))) ObjectIntersectionOf( ObjectSomeValuesFrom( ))) EquivalentClasses(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectIntersectionOf( ObjectSomeValuesFrom( ))) diff --git a/src/ontology/imports/omo_terms.txt b/src/ontology/imports/omo_terms.txt new file mode 100644 index 0000000000..fd22180454 --- /dev/null +++ b/src/ontology/imports/omo_terms.txt @@ -0,0 +1,5 @@ +OMO:0003004 +OMO:0003000 +OMO:0003011 + + diff --git a/src/ontology/uberon-odk.yaml b/src/ontology/uberon-odk.yaml index 678988466d..2b37c24409 100644 --- a/src/ontology/uberon-odk.yaml +++ b/src/ontology/uberon-odk.yaml @@ -70,6 +70,8 @@ import_group: mirror_from: https://w3id.org/orcidio/orcidio.owl base_iris: - https://orcid.org/ + - id: omo + module_type: mirror subset_group: products: - id: appendicular-minimal