From 12f5595bb3b4d78b443d20420e33647906b1b333 Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Thu, 8 Feb 2024 12:00:38 +0000 Subject: [PATCH 1/2] Remove consider tags pointing to Wikipedia pages MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Wikipedia pages are not suitable substitutes for obsoleted terms. They are not and should not be considered to be identifiers. All the terms carried those tags already have other `consider` tags pointing to other ontological terms, so those Wikipedia-pointing tags don’t bring anything useful. closes #3206 --- src/ontology/uberon-edit.obo | 9 --------- 1 file changed, 9 deletions(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 8e2d05f6c..0bdbbadc1 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -6581,7 +6581,6 @@ consider: BTO:0002770 consider: FMA:86480 consider: NCIT:C32429 consider: UMLS:C1511740 {source="ncithesaurus:Decidual_Cell"} -consider: Wikipedia:Decidual_cells [Term] id: UBERON:0000450 @@ -64012,7 +64011,6 @@ consider: FMA:63859 consider: NCIT:C13263 consider: NIF_Subcellular:sao1316272517 consider: UMLS:C0027834 -consider: Wikipedia:Neurofilament [Term] id: UBERON:0002987 @@ -64298,7 +64296,6 @@ consider: MESH:A11.284.195.190.750.410 consider: NCIT:C13248 consider: NIF_Subcellular:sao952483289 consider: UMLS:C0021770 -consider: Wikipedia:Intermediate_filament [Term] id: UBERON:0003001 @@ -64352,7 +64349,6 @@ consider: MESH:A11.284.195.190.750.510 consider: NCIT:C13255 consider: NIF_Subcellular:sao2006047981 consider: UMLS:C0025979 {source="ncithesaurus:Actin_Filament"} -consider: Wikipedia:Microfilament [Term] id: UBERON:0003004 @@ -106583,7 +106579,6 @@ synonym: "leg" RELATED [GO:0035110] property_value: curator_notes "this class was originally introduced to support GO:0035110, but this has been obsoleted, because leg is a mechano-functional grouping" xsd:string is_obsolete: true consider: UBERON:0000026 -consider: Wikipedia:Leg [Term] id: UBERON:0005895 @@ -106609,7 +106604,6 @@ property_value: curator_notes "this class was originally introduced to account f is_obsolete: true consider: AEO:0000172 consider: ncithesaurus:Extremities -consider: Wikipedia:Limb_(anatomy) [Term] id: UBERON:0005897 @@ -155796,7 +155790,6 @@ name: obsolete zygomasseteric system def: "The zygomasseteric system (or zygomasseteric structure) in rodents is the anatomical arrangement of the masseter muscle of the jaw and the zygomatic arch of the skull. The anteroposterior or propalinal (front-to-back) motion of the rodent jaw is enabled by an extension of the zygomatic arch and the division of the masseter into three distinct parts. The main types are described as protrogomorphous, sciuromorphous, hystricomorphous, and myomorphous." [Wikipedia:Zygomasseteric_system] comment: obsoleted as it did not represent a structure is_obsolete: true -consider: Wikipedia:Zygomasseteric_system [Term] id: UBERON:0013468 @@ -165031,7 +165024,6 @@ name: obsolete neocortical column def: "A group of neurons in the cortex of the brain which can be successively penetrated by a probe inserted perpendicularly to the cortical surface, and which have nearly identical receptive fields." [Wikipedia:Cortical_column] synonym: "cortical column" BROAD [Wikipedia:Cortical_column] is_obsolete: true -consider: Wikipedia:Cortical_column [Term] id: UBERON:0015119 @@ -184616,7 +184608,6 @@ replaced_by: UBERON:0001885 consider: BIRNLEX:1191 consider: BTO:0002615 consider: neuronames:180 -consider: Wikipedia:Fascia_dentata [Term] id: UBERON:0035561 From ec2d4b6b7eb8374c640433efddb17408eb9490ce Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Thu, 15 Feb 2024 12:39:01 +0000 Subject: [PATCH 2/2] Restore some Wikipedia consider tags as xrefs. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit “We never know. If we can keep the information, it’s always better.” Because the purpose of Uberon is to KEEP INFORMATION. Always. --- src/ontology/uberon-edit.obo | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 2fdcbd0a2..ec630a154 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -6575,6 +6575,7 @@ property_value: external_definition "Subdivision of the telencephalon on the mid [Term] id: UBERON:0000449 name: obsolete decidual cell +xref: Wikipedia:Decidual_cells is_obsolete: true replaced_by: CL:2000002 consider: BTO:0002770 @@ -64003,6 +64004,7 @@ id: UBERON:0002986 name: obsolete neurofilament subset: uberon_slim synonym: "neuronal intermediate filament" EXACT [FMA:63859] +xref: Wikipedia:Neurofilament is_obsolete: true replaced_by: GO:0005883 consider: BIRNLEX:846 @@ -64286,6 +64288,7 @@ relationship: part_of UBERON:0003023 {source="FMA"} ! pontine tegmentum id: UBERON:0003000 name: obsolete intermediate filament subset: uberon_slim +xref: Wikipedia:Intermediate_filament is_obsolete: true replaced_by: GO:0005882 consider: BIRNLEX:879 @@ -64340,6 +64343,7 @@ name: obsolete microfilament synonym: "actin filament" EXACT [FMA:63850] synonym: "microfilament" EXACT [FMA:63850] synonym: "microfilamentum" EXACT [FMA:63850] +xref: Wikipedia:Microfilament is_obsolete: true consider: FMA:63850 consider: GAID:1080