From 371cd905193df52f87ce5d636fddfe953223cf21 Mon Sep 17 00:00:00 2001 From: Dragon-AI Agent Date: Tue, 24 Mar 2026 22:46:56 +0000 Subject: [PATCH] Swap label and exact synonym for UBERON:0002346: neuroectoderm preferred Per issue #3682, 'neuroectoderm' is more common in the literature and cross-references than 'neurectoderm'. Changed the preferred label from 'neurectoderm' to 'neuroectoderm', and moved 'neurectoderm' to an EXACT synonym. Also updated the terminology_notes accordingly. References: https://github.com/obophenotype/uberon/issues/3682 Signed-off-by: @dragon-ai-agent Co-Authored-By: Claude Sonnet 4.6 --- src/ontology/uberon-edit.obo | 35 ++++++++++++++++++----------------- 1 file changed, 18 insertions(+), 17 deletions(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index a653f8d41..11eeffb07 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -2195,7 +2195,7 @@ xref: NCIT:C34309 xref: UMLS:C1515087 {source="ncithesaurus:Surface_Ectoderm"} xref: Wikipedia:External_ectoderm is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium -relationship: mutually_spatially_disjoint_with UBERON:0002346 ! neurectoderm +relationship: mutually_spatially_disjoint_with UBERON:0002346 ! neuroectoderm relationship: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0000924 {source="EHDAA2"} ! ectoderm property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1d/Ectoderm.png" xsd:anyURI @@ -25851,7 +25851,7 @@ xref: Wikipedia:Iris_sphincter_muscle is_a: UBERON:0004234 {source="BTO"} ! iris smooth muscle intersection_of: UBERON:0004590 ! sphincter muscle intersection_of: part_of UBERON:0001769 ! iris -relationship: develops_from UBERON:0002346 {source="ISBN:0781772214"} ! neurectoderm +relationship: develops_from UBERON:0002346 {source="ISBN:0781772214"} ! neuroectoderm relationship: has_muscle_antagonist UBERON:0001608 {source="dbpedia"} ! dilatator pupillae relationship: has_muscle_insertion UBERON:0001769 {notes="encircles iris", source="dbpedia"} ! iris relationship: has_muscle_origin UBERON:0001769 {notes="encircles iris", source="dbpedia"} ! iris @@ -25892,7 +25892,7 @@ xref: SCTID:280890008 xref: UMLS:C0229190 {source="ncithesaurus:Dilator_Pupillae_Muscle"} xref: Wikipedia:Iris_dilator_muscle is_a: UBERON:0004234 {source="BTO"} ! iris smooth muscle -relationship: develops_from UBERON:0002346 {source="ISBN:0781772214"} ! neurectoderm +relationship: develops_from UBERON:0002346 {source="ISBN:0781772214"} ! neuroectoderm relationship: has_muscle_antagonist UBERON:0001607 {source="dbpedia"} ! sphincter pupillae relationship: has_muscle_insertion UBERON:0001769 {notes="inner margins of iris", source="dbpedia"} ! iris relationship: has_muscle_origin UBERON:0001769 {notes="outer margins of iris", source="dbpedia"} ! iris @@ -30818,7 +30818,7 @@ xref: Wikipedia:Ciliary_body xref: XAO:0000186 is_a: UBERON:0000481 ! multi-tissue structure relationship: contributes_to_morphology_of UBERON:0011892 ! anterior uvea -relationship: develops_from UBERON:0002346 {source="ISBN:0781772214"} ! neurectoderm +relationship: develops_from UBERON:0002346 {source="ISBN:0781772214"} ! neuroectoderm relationship: has_part UBERON:0001605 ! ciliary muscle relationship: has_part UBERON:0010427 ! ciliary processes relationship: part_of UBERON:0011892 ! anterior uvea @@ -31606,7 +31606,7 @@ xref: SCTID:181170006 xref: UMLS:C0042905 {source="ncithesaurus:Vitreous_Body"} is_a: UBERON:0011825 {source="FMA"} ! loose connective tissue relationship: composed_primarily_of UBERON:0001797 ! vitreous humor -relationship: has_developmental_contribution_from UBERON:0002346 {notes="neural ectoderm of optic cup", source="ISBN:0781772214"} ! neurectoderm +relationship: has_developmental_contribution_from UBERON:0002346 {notes="neural ectoderm of optic cup", source="ISBN:0781772214"} ! neuroectoderm relationship: part_of UBERON:0001799 ! vitreous chamber of eyeball property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI property_value: editor_note "distinciton between body and humor requires more work. These may be merged in future. Note that FMA includes the hyaloid canal as part of the vitreous body" xsd:string @@ -44080,7 +44080,7 @@ xref: ZFA:0001271 is_a: UBERON:0010134 {source="MA"} ! secretory circumventricular organ relationship: capable_of GO:0001992 {source="Wikipedia"} ! regulation of systemic arterial blood pressure by vasopressin relationship: capable_of GO:0030103 {source="Wikipedia"} ! vasopressin secretion -relationship: develops_from UBERON:0002346 ! neurectoderm +relationship: develops_from UBERON:0002346 ! neuroectoderm relationship: in_taxon NCBITaxon:7742 {source="PMID:19084529"} ! Vertebrata relationship: part_of UBERON:0000007 {source="ZFA"} ! pituitary gland relationship: present_in_taxon NCBITaxon:117569 {source="Ariens, p. 1192"} ! Hyperoartia @@ -47898,7 +47898,7 @@ relationship: develops_from UBERON:0005062 {source="PMID:11523831"} ! neural fol relationship: dubious_for_taxon NCBITaxon:117565 {source="ISBN:0073040584", source="PMID:17377535"} ! Myxini relationship: existence_starts_during UBERON:0000110 {source="PMID:11523831"} ! neurula stage relationship: 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 +relationship: part_of UBERON:0002346 {source="XAO", source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! neuroectoderm 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 @@ -47946,14 +47946,14 @@ relationship: part_of UBERON:0001515 ! thoracic aorta [Term] id: UBERON:0002346 -name: neurectoderm +name: neuroectoderm def: "Embryonic ectoderm that gives rise to nervous tissue." [Wikipedia:Neuroectoderm] subset: uberon_slim subset: vertebrate_core synonym: "epithelium tubi neuralis; neuroectoderma" RELATED OMO:0003011 [Wikipedia:Neuroectoderm] synonym: "neuaral ectoderm" RELATED [] synonym: "neural ectoderm" EXACT [] -synonym: "neuroectoderm" EXACT [] +synonym: "neurectoderm" EXACT [] synonym: "presumptive central nervous system" RELATED [] synonym: "ventral neurogenic region" RELATED [VHOG:0000150] xref: AAO:0011074 @@ -47979,7 +47979,8 @@ relationship: develops_from UBERON:0000924 {source="https://github.com/obophenot relationship: has_part CL:0000133 ! neurectodermal cell property_value: has_relational_adjective "neurectodermal" xsd:string property_value: homology_notes "(...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000150", ontology="VHOG", source="DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)", source="http://bgee.unil.ch/"} -property_value: terminology_notes "we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here" xsd:string +property_value: term_tracker_item "https://github.com/obophenotype/uberon/issues/3682" xsd:string +property_value: terminology_notes "we prefer neuroectoderm to neural ectoderm since placodal ectoderm is not classified here" xsd:string [Term] id: UBERON:0002347 @@ -65252,7 +65253,7 @@ xref: Wikipedia:Nasal_placode xref: XAO:0000005 xref: ZFA:0000048 is_a: UBERON:0009955 {contradicted_by="NCBIBook:NBK53171", source="ZFA"} ! neurogenic placode -relationship: develops_from UBERON:0002346 ! neurectoderm +relationship: develops_from UBERON:0002346 ! neuroectoderm relationship: part_of UBERON:0000076 {source="EHDAA2"} ! external ectoderm relationship: part_of UBERON:0000922 ! embryo property_value: homology_notes "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (2) neurogenic placodes (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000186", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43", source="http://bgee.unil.ch/"} @@ -82168,7 +82169,7 @@ xref: XAO:0000228 xref: ZFA:0000050 is_a: UBERON:0000479 ! tissue relationship: developmentally_induced_by UBERON:0004880 ! chordamesoderm -relationship: develops_from UBERON:0002346 {source="GO-def"} ! neurectoderm +relationship: develops_from UBERON:0002346 {source="GO-def"} ! neuroectoderm relationship: develops_from UBERON:0003071 {source="ZFA"} ! eye primordium relationship: part_of UBERON:0010312 {source="ZFA"} ! immature eye property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e0/Gray863.png" xsd:anyURI @@ -102529,7 +102530,7 @@ xref: XAO:0004091 xref: ZFA:0001178 is_a: UBERON:0000479 {source="ZFA"} ! tissue relationship: develops_from UBERON:0000924 {source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! ectoderm -relationship: mutually_spatially_disjoint_with UBERON:0002346 ! neurectoderm +relationship: mutually_spatially_disjoint_with UBERON:0002346 ! neuroectoderm property_value: development_notes "After gastrulation, neural crest cells are specified at the border of the neural plate and the non-neural ectoderm." xsd:string property_value: editor_note "todo - epidermis? todo - track down EHDAA2 class in new release" xsd:string property_value: homology_notes "In the early gastrula of vertebrates, factors from the organizer (e.g. noggin, chordin, and follistatin in Xenopus) antagonize the epidermalizing factor bone morphogenetic protein 4 (BMP4), thus dividing the epiblast into neuroectoderm. In Drosophila, decapentaplegic, the homologue of BMP4, interacts similarly with the protein short gastrulation, the homologue of chordin. Thus, a comparable molecular mechanism for distinguishing non-neural ectoderm from neural ectoderm was probably present in the common ancestor of all bilaterally symmetrical animals.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001372", ontology="VHOG", source="DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)", source="http://bgee.unil.ch/"} @@ -109911,7 +109912,7 @@ xref: TAO:0000146 xref: ZFA:0000146 is_a: UBERON:0005423 ! developing anatomical structure relationship: has_potential_to_develop_into UBERON:0000955 ! brain -relationship: part_of UBERON:0002346 ! neurectoderm +relationship: part_of UBERON:0002346 ! neuroectoderm property_value: external_definition "The embryonic precursor of the brain and the set of mature brain structures that derive from it (CUMBO)" xsd:string {source="http://neurolex.org/wiki/Cumbo_terms"} [Term] @@ -120269,7 +120270,7 @@ xref: ZFA:0000063 is_a: UBERON:0016879 ! future central nervous system intersection_of: UBERON:0006598 ! presumptive structure intersection_of: has_potential_to_develop_into UBERON:0003075 ! neural plate -relationship: develops_from UBERON:0002346 ! neurectoderm +relationship: develops_from UBERON:0002346 ! neuroectoderm relationship: part_of UBERON:0004734 ! gastrula property_value: editor_note "consider merging" xsd:string property_value: external_definition "Region of the gastrula which gives rise to the neural plate.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000063", ontology="TAO", source="ZFIN:curator"} @@ -168925,7 +168926,7 @@ synonym: "presumptive central nervous system" EXACT [] intersection_of: UBERON:0006598 ! presumptive structure intersection_of: has_potential_to_develop_into UBERON:0001017 ! central nervous system relationship: develops_from UBERON:0000924 ! ectoderm -relationship: develops_from UBERON:0002346 {gci_relation="part_of", gci_filler="NCBITaxon:7742"} ! neurectoderm +relationship: develops_from UBERON:0002346 {gci_relation="part_of", gci_filler="NCBITaxon:7742"} ! neuroectoderm relationship: part_of UBERON:0016880 ! future nervous system [Term] @@ -219662,7 +219663,7 @@ synonym: "P2 iVenEp" RELATED [https://orcid.org/0000-0002-7073-9172] synonym: "venEpiP2" RELATED [] is_a: UBERON:0001048 ! primordium is_a: UBERON:6025993 ! insect ventral ectoderm derivative -relationship: develops_from UBERON:0002346 ! neurectoderm +relationship: develops_from UBERON:0002346 ! neuroectoderm relationship: part_of UBERON:0000922 ! embryo [Term]