diff --git a/bulk_ntr_workflow/source_data/eye.csv b/bulk_ntr_workflow/source_data/eye.csv new file mode 100644 index 000000000..7eaeec08e --- /dev/null +++ b/bulk_ntr_workflow/source_data/eye.csv @@ -0,0 +1,3 @@ +tables,as,as_label,UBERON ID,Pull Request/Issue,parents_as,parents_as_label,references +eye,https://purl.org/ccf/ASCTB-TEMP_inner-cortex,Inner cortex,,,UBERON:0000389,lens cortex, +eye,https://purl.org/ccf/ASCTB-TEMP_outer-cortex,Outer cortex,,,UBERON:0000389,lens cortex, \ No newline at end of file diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 240b86a5b..1c7d30487 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -937,7 +937,7 @@ intersection_of: has_quality PATO:0002236 ! aliform relationship: capable_of_part_of GO:0060361 ! flight relationship: in_taxon NCBITaxon:33213 ! Bilateria relationship: never_in_taxon NCBITaxon:118072 {source="bgee"} ! Coelacanthimorpha -relationship: never_in_taxon NCBITaxon:186634 {source="bgee", seeAlso="Wikipedia:Flying_fish"} ! Otomorpha +relationship: never_in_taxon NCBITaxon:186634 {seeAlso="Wikipedia:Flying_fish", source="bgee"} ! 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 @@ -22377,7 +22377,7 @@ 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", source="PMID:10220427", source="PhenoscapeRCN", seeAlso="UBERON:0012260"} +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"} [Term] id: UBERON:0001464 @@ -28046,7 +28046,7 @@ 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 {source="WP", seeAlso="https://github.com/obophenotype/uberon/issues/548"} +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"} [Term] id: UBERON:0001686 @@ -38501,7 +38501,7 @@ 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 {source="VHOG", source="Wikipedia", seeAlso="http://code.google.com/p/xenopus-anatomy-ontology/issues/detail?id=7"} ! Amphibia +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: in_taxon NCBITaxon:32523 ! Tetrapoda relationship: innervates UBERON:0001737 ! larynx relationship: innervates UBERON:3010692 {gci_relation="part_of", gci_filler="NCBITaxon:8292", source="ISBN:080184780X"} ! m. cucullaris @@ -74457,7 +74457,7 @@ 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", source="PMID:10220427", source="PhenoscapeRCN", seeAlso="UBERON:0012261"} +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"} [Term] id: UBERON:0003623 @@ -74494,7 +74494,7 @@ 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", source="PMID:10220427", source="PhenoscapeRCN", seeAlso="UBERON:0012262"} +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"} [Term] id: UBERON:0003624 @@ -138633,7 +138633,7 @@ 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 {seeAlso="https://github.com/obophenotype/mouse-anatomy-ontology/issues/117", source="MA:th"} +xref: EMAPA:37964 {source="MA:th", seeAlso="https://github.com/obophenotype/mouse-anatomy-ontology/issues/117"} xref: MA:0000754 xref: NCIT:C49776 xref: UMLS:C1710157 {source="ncithesaurus:Splenic_Marginal_Sinus"} @@ -151402,7 +151402,7 @@ 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", source="UBERON:skansa", seeAlso="UBERON:0004410"} +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"} [Term] id: UBERON:0012292 @@ -225242,6 +225242,51 @@ is_a: UBERON:0006914 ! squamous epithelium relationship: has_part CL:4030023 ! respiratory tract hillock cell relationship: part_of UBERON:0007196 ! tracheobronchial tree +[Term] +id: UBERON:8930000 +name: inner cortex of lens +def: "A zone of the lens cortex that lies immediately external to the lens nucleus and internal to the outer cortex of lens. It is composed of older, fully denucleated lens fibre cells whose lamellae remain largely intact but which are more compacted than those of the outer cortex." [PMID:10550792, PMID:20171212] +comment: Equivalent to the 'deep cortex of lens' (cortex profundus) in FMA. The boundary with the lens nucleus is a continuous gradient of fibre-cell age and compaction but is reliably visible as an optical discontinuity on Scheimpflug/slit-lamp imaging. +subset: added_by_HRA +subset: human_reference_atlas +subset: pheno_slim +synonym: "cortex profundus lentis" EXACT OMO:0003011 [FMA:280216] +synonym: "deep cortex of lens" EXACT [FMA:280216] +xref: FMA:280216 +is_a: UBERON:0034944 ! zone of organ +relationship: composed_primarily_of CL:0011004 ! lens fiber cell +relationship: dc-contributor https://orcid.org/0000-0002-2999-0103 +relationship: part_of UBERON:0000389 ! lens cortex +relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: surrounded_by UBERON:8930001 ! outer cortex of lens +relationship: surrounds UBERON:0000390 ! lens nucleus +property_value: dcterms-date "2026-05-25T00:00:00Z" xsd:dateTime +property_value: term_tracker_item "https://github.com/obophenotype/uberon/pull/3713" xsd:anyURI +created_by: dragon-ai-agent + +[Term] +id: UBERON:8930001 +name: outer cortex of lens +def: "A zone of the lens cortex that lies immediately beneath the lens capsule and epithelium and surrounds the inner cortex of lens. It is composed of the most recently differentiated lens fibre cells, added from the lens epithelium at the equator; it contains the remodelling and transition zones in which fibre cells lose their nuclei." [PMID:10550792, PMID:19357350] +comment: Equivalent to the 'superficial cortex of lens' (cortex superficialis) in FMA. The outer cortex is the site of ongoing lens fibre cell maturation, including the remodelling zone (RZ) and transition zone (TZ) described by Lim et al. 2009 (PMID:19357350). +subset: added_by_HRA +subset: human_reference_atlas +subset: pheno_slim +synonym: "cortex superficialis lentis" EXACT OMO:0003011 [FMA:280212] +synonym: "superficial cortex of lens" EXACT [FMA:280212] +xref: FMA:280212 +is_a: UBERON:0034944 ! zone of organ +relationship: adjacent_to UBERON:0001804 ! capsule of lens +relationship: adjacent_to UBERON:0005614 ! lens anterior epithelium +relationship: composed_primarily_of CL:0011004 ! lens fiber cell +relationship: dc-contributor https://orcid.org/0000-0002-2999-0103 +relationship: part_of UBERON:0000389 ! lens cortex +relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: surrounds UBERON:8930000 ! inner cortex of lens +property_value: dcterms-date "2026-05-25T00:00:00Z" xsd:dateTime +property_value: term_tracker_item "https://github.com/obophenotype/uberon/pull/3713" xsd:anyURI +created_by: dragon-ai-agent + [Typedef] id: aboral_to name: aboral to