From fcc9edf9ecd91e14e759ca6269b51fd89364a098 Mon Sep 17 00:00:00 2001 From: Chris Mungall Date: Mon, 23 Sep 2024 14:39:03 -0700 Subject: [PATCH 1/4] Adding gross anatomical part. Fixes #2921 --- src/ontology/uberon-edit.obo | 17 ++++++++++++----- 1 file changed, 12 insertions(+), 5 deletions(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 6ec4cd4499..b9afd324f5 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -233,6 +233,13 @@ relationship: present_in_taxon NCBITaxon:33090 ! Viridiplantae relationship: present_in_taxon NCBITaxon:33208 ! Metazoa relationship: present_in_taxon NCBITaxon:4751 ! Fungi +[Term] +id: UBERON:0000001 ! gross anatomical part +name: gross anatomical part +def: "Anatomical structure that is part of a multicellular organism and is at the gross anatomical level, e.g. above the level of a cell. Included are portions of organism substances such as blood, multi-cell-part structures such as axon tracts, acellular anatomical structures such as hair, and organism subdivisions such as head. Excluded is the whole organism and more granular parts of the organism, such as atoms, molecules, macromolecular complexes and cells." [CARO:0001008] +xref: CARO:0001008 +is_a: UBERON:0000465 ! material anatomical entity + [Term] id: UBERON:0000002 name: uterine cervix @@ -6813,7 +6820,7 @@ xref: TGMA:0001824 xref: VHOG:0001726 xref: XAO:0004001 xref: ZFA:0001487 -is_a: UBERON:0000465 ! material anatomical entity +is_a: UBERON:0000001 ! gross anatomical part relationship: has_quality PATO:0002198 ! quality of a substance relationship: part_of UBERON:0000468 {notes="this relationship may be too strong and may be weakened in future"} ! multicellular organism relationship: present_in_taxon NCBITaxon:33090 ! Viridiplantae @@ -7227,7 +7234,7 @@ xref: TAO:0000382 xref: TGMA:0001841 xref: XAO:0003162 xref: ZFA:0000382 -is_a: UBERON:0000061 ! anatomical structure +is_a: UBERON:0000001 ! gross anatomical part disjoint_from: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure relationship: present_in_taxon NCBITaxon:33090 ! Viridiplantae relationship: present_in_taxon NCBITaxon:33208 ! Metazoa @@ -101229,7 +101236,7 @@ xref: CALOHA:TS-2122 xref: EHDAA2:0003125 xref: FMA:292313 xref: MIAA:0000019 -is_a: UBERON:0000465 ! material anatomical entity +is_a: UBERON:0000001 ! gross anatomical part relationship: capable_of GO:0032502 ! developmental process relationship: present_in_taxon NCBITaxon:33090 ! Viridiplantae relationship: present_in_taxon NCBITaxon:33208 ! Metazoa @@ -187335,7 +187342,7 @@ def: "Material anatomical entity that forms the outermost boundary of an anatomi subset: common_anatomy xref: AAO:0010270 xref: ZFA:0005594 -is_a: UBERON:0000465 ! material anatomical entity +is_a: UBERON:0000001 ! gross anatomical part relationship: bounding_layer_of UBERON:0000061 ! anatomical structure relationship: present_in_taxon NCBITaxon:33090 ! Viridiplantae relationship: present_in_taxon NCBITaxon:33208 ! Metazoa @@ -220291,7 +220298,7 @@ relationship: in_taxon NCBITaxon:50557 ! Insecta id: UBERON:6040005 name: insect synaptic neuropil def: "The part of the neuropil consisting largely of synapsing neuron projections." [FlyBase:FBrf0224194] -is_a: UBERON:0000465 ! material anatomical entity +is_a: UBERON:0000001 ! gross anatomical part relationship: in_taxon NCBITaxon:50557 ! Insecta relationship: part_of UBERON:0002606 ! neuropil From 78c1dbf95387f7bb55ac73aa31bbbb74754bbc4a Mon Sep 17 00:00:00 2001 From: Chris Mungall Date: Mon, 23 Sep 2024 14:52:13 -0700 Subject: [PATCH 2/4] axioms --- 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 b9afd324f5..fef687e543 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -238,7 +238,11 @@ id: UBERON:0000001 ! gross anatomical part name: gross anatomical part def: "Anatomical structure that is part of a multicellular organism and is at the gross anatomical level, e.g. above the level of a cell. Included are portions of organism substances such as blood, multi-cell-part structures such as axon tracts, acellular anatomical structures such as hair, and organism subdivisions such as head. Excluded is the whole organism and more granular parts of the organism, such as atoms, molecules, macromolecular complexes and cells." [CARO:0001008] xref: CARO:0001008 +disjoint_from: GO:0005623 ! cell +disjoint_from: GO:0110165 ! cellular anatomical entity +disjoint_from: UBERON:0000468 ! multicellular organism is_a: UBERON:0000465 ! material anatomical entity +relationship: in_taxon NCBITaxon:2759 ! Eukaryota [Term] id: UBERON:0000002 From 1a338fef25db3bd092988b8c431e1e498f46627d Mon Sep 17 00:00:00 2001 From: Chris Mungall Date: Thu, 17 Oct 2024 14:27:28 -0700 Subject: [PATCH 3/4] fix unsat --- src/ontology/uberon-edit.obo | 1 - 1 file changed, 1 deletion(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index fef687e543..9082a279bb 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -156110,7 +156110,6 @@ synonym: "midline birth canal" RELATED [] intersection_of: UBERON:0000996 ! vagina intersection_of: connected_to UBERON:0013523 ! lateral vaginal canal intersection_of: intersects_midsagittal_plane_of UBERON:0003975 ! internal female genitalia -relationship: channel_for UBERON:0000922 ! embryo relationship: in_taxon NCBITaxon:9263 {editor="cjm"} ! Metatheria [Term] From 852bb4abfa70a8c5286255ee86c5c9313dde4b02 Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Thu, 15 Jan 2026 11:35:37 +0200 Subject: [PATCH 4/4] Update taxon relationship to 'present_in_taxon' in OBO file Changed the relationship from 'in_taxon' to 'present_in_taxon' for NCBITaxon:2759 (Eukaryota) in the uberon-edit.obo ontology file to reflect updated ontology standards. --- 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 3ef462b357..8878e15fb5 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -238,7 +238,7 @@ disjoint_from: GO:0005623 ! cell disjoint_from: GO:0110165 ! cellular anatomical entity disjoint_from: UBERON:0000468 ! multicellular organism is_a: UBERON:0000465 ! material anatomical entity -relationship: in_taxon NCBITaxon:2759 ! Eukaryota +relationship: present_in_taxon NCBITaxon:2759 ! Eukaryota [Term] id: UBERON:0000002