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Add HRA eye NTR template: inner/outer cortex of lens #3713

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Add HRA eye NTR template: inner/outer cortex of lens #3713

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2db0d0f
Add HRA eye NTR template: inner/outer cortex of lens
zhengj2007 May 25, 2026
740ddfe
Merge remote-tracking branch 'origin/master' into hra-eye-ntr
zhengj2007 Jun 2, 2026
9965eaf
Revert Stage 5 ODK registration for hra-eye template
zhengj2007 Jun 2, 2026
cee8838
Clean branch artifacts and keep eye NTR core changes
zhengj2007 Jun 3, 2026
a80ee32
Merge remote-tracking branch 'origin/master' into hra-eye-ntr
zhengj2007 Jun 26, 2026
05a9844
Add term_tracker_item tracker links for lens cortex terms
zhengj2007 Jun 26, 2026
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3 changes: 3 additions & 0 deletions bulk_ntr_workflow/source_data/eye.csv
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Original file line number Diff line number Diff line change
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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,
61 changes: 53 additions & 8 deletions src/ontology/uberon-edit.obo
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Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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"}
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
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