From e29800cac102323c840b7bdd3ddf4de4bf723167 Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Wed, 12 Jun 2024 11:17:25 -0300 Subject: [PATCH 1/6] Add sensory corpuscle Adds sensory corpuscle and positions Meissner, Pacinian, Ruffini and Herbst's under it. --- src/ontology/uberon-edit.obo | 42 +++++++++++++++++++++++------------- 1 file changed, 27 insertions(+), 15 deletions(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 70bbdae5f4..1313f21701 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -7007,8 +7007,8 @@ consider: FBbt:00007012 consider: FMA:86454 consider: GO:0044464 consider: HAO:0000014 +consider: http://purl.obolibrary.org/obo/NIF_Subcellular_sao-1337158144 consider: NCIT:C34070 -consider: NIF_Subcellular:sao-1337158144 consider: OpenCyc:Mx4rwQwkcZwpEbGdrcN5Y29ycA consider: TGMA:0001834 consider: UMLS:C1178969 {source="ncithesaurus:Cell_Part"} @@ -11048,7 +11048,7 @@ is_obsolete: true consider: FBbt:00005107 consider: FMA:67301 consider: GO:0043025 -consider: NIF_Subcellular:sao1044911821 +consider: http://purl.obolibrary.org/obo/NIF_Subcellular_sao1044911821 [Term] id: UBERON:0001023 @@ -11063,9 +11063,9 @@ consider: FBbt:00005110 consider: FMA:67314 consider: GAID:749 consider: GO:0030425 +consider: http://purl.obolibrary.org/obo/NIF_Subcellular_sao1211023249 consider: MESH:A08.663.256 consider: NCIT:C32447 -consider: NIF_Subcellular:sao1211023249 consider: OpenCyc:Mx4rviIdspwpEbGdrcN5Y29ycA consider: TGMA:0001373 consider: UMLS:C0011305 @@ -11082,8 +11082,8 @@ consider: FBbt:00005113 consider: FMA:61814 consider: GAID:751 consider: GO:0043005 +consider: http://purl.obolibrary.org/obo/NIF_Subcellular_sao-867568886 consider: MESH:A08.663.256.500 -consider: NIF_Subcellular:sao-867568886 [Term] id: UBERON:0001025 @@ -11099,9 +11099,9 @@ consider: FBbt:00005114 consider: FMA:67408 consider: GAID:766 consider: GO:0045202 +consider: http://purl.obolibrary.org/obo/NIF_Subcellular_sao914572699 consider: MESH:A08.850 consider: NCIT:C13281 -consider: NIF_Subcellular:sao914572699 consider: SCTID:362298009 consider: UMLS:C0039062 @@ -11161,8 +11161,8 @@ replaced_by: GO:0031594 consider: FBbt:00005142 consider: FMA:61803 consider: GAID:809 +consider: http://purl.obolibrary.org/obo/NIF_Subcellular_sao1124888485 consider: MESH:D009469 -consider: NIF_Subcellular:sao1124888485 [Term] id: UBERON:0001030 @@ -11172,7 +11172,7 @@ is_obsolete: true consider: FBbt:00005143 consider: FMA:67107 consider: GO:0048788 -consider: NIF_Subcellular:sao1884931180 +consider: http://purl.obolibrary.org/obo/NIF_Subcellular_sao1884931180 [Term] id: UBERON:0001031 @@ -63902,8 +63902,8 @@ is_obsolete: true replaced_by: GO:0005883 consider: BIRNLEX:846 consider: FMA:63859 +consider: http://purl.obolibrary.org/obo/NIF_Subcellular_sao1316272517 consider: NCIT:C13263 -consider: NIF_Subcellular:sao1316272517 consider: UMLS:C0027834 [Term] @@ -64187,9 +64187,9 @@ replaced_by: GO:0005882 consider: BIRNLEX:879 consider: FMA:63851 consider: GAID:1079 +consider: http://purl.obolibrary.org/obo/NIF_Subcellular_sao952483289 consider: MESH:A11.284.195.190.750.410 consider: NCIT:C13248 -consider: NIF_Subcellular:sao952483289 consider: UMLS:C0021770 [Term] @@ -64241,9 +64241,9 @@ is_obsolete: true consider: FMA:63850 consider: GAID:1080 consider: GO:0005884 +consider: http://purl.obolibrary.org/obo/NIF_Subcellular_sao2006047981 consider: MESH:A11.284.195.190.750.510 consider: NCIT:C13255 -consider: NIF_Subcellular:sao2006047981 consider: UMLS:C0025979 {source="ncithesaurus:Actin_Filament"} [Term] @@ -76936,7 +76936,7 @@ xref: NIF_Subcellular:FMA_83604 xref: SCTID:37419002 xref: Wikipedia:File\:Gray935.png xref: Wikipedia:Lamellar_corpuscle -is_a: UBERON:0012449 {source="Wikipedia"} ! mechanoreceptor +is_a: UBERON:8900000 {source="Wikipedia"} ! sensory corpuscle relationship: part_of UBERON:0002067 {notes="may also be located in organs - check"} ! dermis property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/52/Gray935.png" xsd:anyURI property_value: external_ontology_notes "FMA treats pacinia and G-M as distinct" xsd:string {external_ontology="FMA"} @@ -152842,7 +152842,7 @@ def: "The Corpuscles of Herbst or Herbst corpuscles are a nerve-ending similar t synonym: "corpuscles of Herbst" RELATED [Wikipedia:Corpuscles_of_Herbst] synonym: "Herbst corpuscle" RELATED [Wikipedia:Corpuscles_of_Herbst] xref: Wikipedia:Corpuscles_of_Herbst -is_a: UBERON:0012449 {source="Wikipedia"} ! mechanoreceptor +is_a: UBERON:8900000 {source="Wikipedia"} ! sensory corpuscle relationship: only_in_taxon NCBITaxon:8782 ! Aves [Term] @@ -152877,7 +152877,7 @@ xref: NCIT:C13171 xref: SCTID:41421000 xref: UMLS:C0205831 {source="ncithesaurus:Meissner_Corpuscle"} xref: Wikipedia:Meissner%27s_corpuscle -is_a: UBERON:0012449 {source="Wikipedia"} ! mechanoreceptor +is_a: UBERON:8900000 {source="Wikipedia"} ! sensory corpuscle relationship: part_of UBERON:0002199 ! integument [Term] @@ -152945,7 +152945,7 @@ xref: NCIT:C13175 xref: SCTID:53140000 xref: UMLS:C0035943 {source="ncithesaurus:Ruffinis_Corpuscle"} xref: Wikipedia:Bulbous_corpuscle -is_a: UBERON:0012449 {source="FMA"} ! mechanoreceptor +is_a: UBERON:8900000 {source="FMA"} ! sensory corpuscle relationship: part_of UBERON:0002199 ! integument property_value: curator_notes "there is some debate as to its existence[ISBN:9780849388118]" xsd:string property_value: external_ontology_notes "MP says subcutaneous tissue of digits; NCITA says hypodermis" xsd:string {external_ontology="MP"} @@ -177321,7 +177321,7 @@ alt_id: UBERON:0025487 synonym: "regional part of gustatory epithelium" EXACT HUMAN_PREFERRED [BIRNLEX:4100] is_obsolete: true consider: BIRNLEX:4100 -consider: http://uri.neuinfo.org/nif/nifstd/nifext_13 +consider: nifext:13 [Term] id: UBERON:0025236 @@ -224513,6 +224513,18 @@ relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 ! Aleix Puig- relationship: located_in UBERON:8600025 ! intervillous space property_value: dcterms-date "2024-04-15T10:05:35Z" xsd:dateTime +[Term] +id: UBERON:8900000 +name: sensory corpuscle +def: "A mechanosensory complex in the terminal end of some nerves that forms a corpuscle. It consists of one or more neuronal terminations and associated non-neuronal cells." [PMID:35356056] +synonym: "COEC" EXACT [PMID:35356056] +synonym: "cutaneous end-organ complex" EXACT [PMID:35356056] +xref: http://www.wikidata.org/entity/Q126363978 +is_a: UBERON:0005162 ! multi cell part structure +is_a: UBERON:0012449 ! mechanoreceptor +property_value: http://purl.org/dc/elements/1.1/date "2024-06-12T13:51:05Z" xsd:dateTime +created_by: https://orcid.org/0000-0003-2473-2313 + [Typedef] id: aboral_to name: aboral to From db50cb757ff6f2249d48a424635a807b2048570a Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Wed, 12 Jun 2024 11:38:27 -0300 Subject: [PATCH 2/6] Change date relation to dcterms-date --- 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 1313f21701..1b9b37438b 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -224522,7 +224522,7 @@ synonym: "cutaneous end-organ complex" EXACT [PMID:35356056] xref: http://www.wikidata.org/entity/Q126363978 is_a: UBERON:0005162 ! multi cell part structure is_a: UBERON:0012449 ! mechanoreceptor -property_value: http://purl.org/dc/elements/1.1/date "2024-06-12T13:51:05Z" xsd:dateTime +property_value: dcterms-date "2024-06-12T13:51:05Z" xsd:string created_by: https://orcid.org/0000-0003-2473-2313 [Typedef] From 575cbb4e4da4ef921bb2931724d90739e8ae079c Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Wed, 12 Jun 2024 14:06:38 -0300 Subject: [PATCH 3/6] Change synonym type and remove superclass --- 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 1b9b37438b..8f2af2c6ec 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -72993,8 +72993,8 @@ 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] @@ -224517,10 +224517,9 @@ property_value: dcterms-date "2024-04-15T10:05:35Z" xsd:dateTime id: UBERON:8900000 name: sensory corpuscle def: "A mechanosensory complex in the terminal end of some nerves that forms a corpuscle. It consists of one or more neuronal terminations and associated non-neuronal cells." [PMID:35356056] -synonym: "COEC" EXACT [PMID:35356056] +synonym: "COEC" RELATED OMO:0003000 [PMID:35356056] synonym: "cutaneous end-organ complex" EXACT [PMID:35356056] xref: http://www.wikidata.org/entity/Q126363978 -is_a: UBERON:0005162 ! multi cell part structure is_a: UBERON:0012449 ! mechanoreceptor property_value: dcterms-date "2024-06-12T13:51:05Z" xsd:string created_by: https://orcid.org/0000-0003-2473-2313 From 3947dfe885ecc464c52da85259e28f85edc4a640 Mon Sep 17 00:00:00 2001 From: Anita Caron Date: Tue, 25 Jun 2024 16:00:41 +0100 Subject: [PATCH 4/6] define idspace for NIF_Subcellular MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit With new OWL API 4.5.29 we can now define idspaces for NIF_Subcellular. Its terms were mistakenly changed to the OBO namespace when using Protégé 5.6.5. This commit fixes that. --- src/ontology/uberon-edit.obo | 21 +++++++++++---------- 1 file changed, 11 insertions(+), 10 deletions(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 8f2af2c6ec..fa1ce776d2 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -45,6 +45,7 @@ synonymtypedef: PENDING_REVIEW "expert consultation and attribution required" synonymtypedef: SENSU "taxonomic disambiguation" synonymtypedef: SYSTEMATIC "a systematic synonym used as the base name for design patterns" default-namespace: uberon +idspace: NIF_Subcellular http://www.neurolex.org/wiki/ treat-xrefs-as-equivalent: AEO treat-xrefs-as-equivalent: BILA treat-xrefs-as-equivalent: BSPO @@ -7007,8 +7008,8 @@ consider: FBbt:00007012 consider: FMA:86454 consider: GO:0044464 consider: HAO:0000014 -consider: http://purl.obolibrary.org/obo/NIF_Subcellular_sao-1337158144 consider: NCIT:C34070 +consider: NIF_Subcellular:sao-1337158144 consider: OpenCyc:Mx4rwQwkcZwpEbGdrcN5Y29ycA consider: TGMA:0001834 consider: UMLS:C1178969 {source="ncithesaurus:Cell_Part"} @@ -11048,7 +11049,7 @@ is_obsolete: true consider: FBbt:00005107 consider: FMA:67301 consider: GO:0043025 -consider: http://purl.obolibrary.org/obo/NIF_Subcellular_sao1044911821 +consider: NIF_Subcellular:sao1044911821 [Term] id: UBERON:0001023 @@ -11063,9 +11064,9 @@ consider: FBbt:00005110 consider: FMA:67314 consider: GAID:749 consider: GO:0030425 -consider: http://purl.obolibrary.org/obo/NIF_Subcellular_sao1211023249 consider: MESH:A08.663.256 consider: NCIT:C32447 +consider: NIF_Subcellular:sao1211023249 consider: OpenCyc:Mx4rviIdspwpEbGdrcN5Y29ycA consider: TGMA:0001373 consider: UMLS:C0011305 @@ -11082,8 +11083,8 @@ consider: FBbt:00005113 consider: FMA:61814 consider: GAID:751 consider: GO:0043005 -consider: http://purl.obolibrary.org/obo/NIF_Subcellular_sao-867568886 consider: MESH:A08.663.256.500 +consider: NIF_Subcellular:sao-867568886 [Term] id: UBERON:0001025 @@ -11099,9 +11100,9 @@ consider: FBbt:00005114 consider: FMA:67408 consider: GAID:766 consider: GO:0045202 -consider: http://purl.obolibrary.org/obo/NIF_Subcellular_sao914572699 consider: MESH:A08.850 consider: NCIT:C13281 +consider: NIF_Subcellular:sao914572699 consider: SCTID:362298009 consider: UMLS:C0039062 @@ -11161,8 +11162,8 @@ replaced_by: GO:0031594 consider: FBbt:00005142 consider: FMA:61803 consider: GAID:809 -consider: http://purl.obolibrary.org/obo/NIF_Subcellular_sao1124888485 consider: MESH:D009469 +consider: NIF_Subcellular:sao1124888485 [Term] id: UBERON:0001030 @@ -11172,7 +11173,7 @@ is_obsolete: true consider: FBbt:00005143 consider: FMA:67107 consider: GO:0048788 -consider: http://purl.obolibrary.org/obo/NIF_Subcellular_sao1884931180 +consider: NIF_Subcellular:sao1884931180 [Term] id: UBERON:0001031 @@ -63902,8 +63903,8 @@ is_obsolete: true replaced_by: GO:0005883 consider: BIRNLEX:846 consider: FMA:63859 -consider: http://purl.obolibrary.org/obo/NIF_Subcellular_sao1316272517 consider: NCIT:C13263 +consider: NIF_Subcellular:sao1316272517 consider: UMLS:C0027834 [Term] @@ -64187,9 +64188,9 @@ replaced_by: GO:0005882 consider: BIRNLEX:879 consider: FMA:63851 consider: GAID:1079 -consider: http://purl.obolibrary.org/obo/NIF_Subcellular_sao952483289 consider: MESH:A11.284.195.190.750.410 consider: NCIT:C13248 +consider: NIF_Subcellular:sao952483289 consider: UMLS:C0021770 [Term] @@ -64241,9 +64242,9 @@ is_obsolete: true consider: FMA:63850 consider: GAID:1080 consider: GO:0005884 -consider: http://purl.obolibrary.org/obo/NIF_Subcellular_sao2006047981 consider: MESH:A11.284.195.190.750.510 consider: NCIT:C13255 +consider: NIF_Subcellular:sao2006047981 consider: UMLS:C0025979 {source="ncithesaurus:Actin_Filament"} [Term] From bf9f4ae5aebf4430b11b6ce52c6aa430396f9232 Mon Sep 17 00:00:00 2001 From: Anita Caron Date: Tue, 2 Jul 2024 11:24:32 +0100 Subject: [PATCH 5/6] declare idspace `NIFEXT` that is not OBO URI --- src/ontology/uberon-edit.obo | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index fa1ce776d2..0b4460826e 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -46,6 +46,7 @@ synonymtypedef: SENSU "taxonomic disambiguation" synonymtypedef: SYSTEMATIC "a systematic synonym used as the base name for design patterns" default-namespace: uberon idspace: NIF_Subcellular http://www.neurolex.org/wiki/ +idspace: NIFEXT http://uri.neuinfo.org/nif/nifstd/nifext_ treat-xrefs-as-equivalent: AEO treat-xrefs-as-equivalent: BILA treat-xrefs-as-equivalent: BSPO @@ -177322,7 +177323,7 @@ alt_id: UBERON:0025487 synonym: "regional part of gustatory epithelium" EXACT HUMAN_PREFERRED [BIRNLEX:4100] is_obsolete: true consider: BIRNLEX:4100 -consider: nifext:13 +consider: NIFEXT:13 [Term] id: UBERON:0025236 From 81dcf6c239aab35f236fc4c546c916251dcaf120 Mon Sep 17 00:00:00 2001 From: Anita Caron Date: Wed, 14 Aug 2024 15:02:55 +0100 Subject: [PATCH 6/6] use `terms:contributor` instead of `created_by` --- src/ontology/uberon-edit.obo | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 13c2b3e2af..82e7202995 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -45,9 +45,9 @@ synonymtypedef: PENDING_REVIEW "expert consultation and attribution required" synonymtypedef: SENSU "taxonomic disambiguation" synonymtypedef: SYSTEMATIC "a systematic synonym used as the base name for design patterns" default-namespace: uberon -idspace: EFO http://www.ebi.ac.uk/efo/EFO_ +idspace: EFO http://www.ebi.ac.uk/efo/EFO_ idspace: NIF_Subcellular http://www.neurolex.org/wiki/ -idspace: NIFEXT http://uri.neuinfo.org/nif/nifstd/nifext_ +idspace: NIFEXT http://uri.neuinfo.org/nif/nifstd/nifext_ treat-xrefs-as-equivalent: AEO treat-xrefs-as-equivalent: BILA treat-xrefs-as-equivalent: BSPO @@ -72997,8 +72997,8 @@ 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] @@ -224555,8 +224555,8 @@ synonym: "COEC" RELATED OMO:0003000 [PMID:35356056] synonym: "cutaneous end-organ complex" EXACT [PMID:35356056] xref: http://www.wikidata.org/entity/Q126363978 is_a: UBERON:0012449 ! mechanoreceptor +relationship: dc-contributor https://orcid.org/0000-0003-2473-2313 property_value: dcterms-date "2024-06-12T13:51:05Z" xsd:string -created_by: https://orcid.org/0000-0003-2473-2313 [Typedef] id: aboral_to