From cb7fdcdcffd6117a8512199c60e434daab7bc65a Mon Sep 17 00:00:00 2001
From: JABelfiore <jb69@sanger.ac.uk>
Date: Fri, 25 Oct 2024 10:00:48 +0100
Subject: [PATCH 1/3] definition, synonyms, refs

---
 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 37a45d5ec..4eba15a1e 100644
--- a/src/ontology/uberon-edit.obo
+++ b/src/ontology/uberon-edit.obo
@@ -45,7 +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: 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_ 
 treat-xrefs-as-equivalent: AEO
@@ -191,6 +191,7 @@ property_value: doap-SVNRepository "https://obo.svn.sourceforge.net/svnroot/obo/
 property_value: foaf-homepage "http://uberon.org" xsd:anyURI
 property_value: has_ontology_root_term UBERON:0000104
 property_value: has_ontology_root_term UBERON:0001062
+owl-axioms: Prefix(owl:=<http://www.w3.org/2002/07/owl#>)\nPrefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)\nPrefix(xml:=<http://www.w3.org/XML/1998/namespace>)\nPrefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)\nPrefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)\n\n\nOntology(\nDeclaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym>))\n\n\nAnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/UBERON_8700000> \"\")\n)
 treat-xrefs-as-has-subclass: EHDAA
 treat-xrefs-as-has-subclass: EV
 treat-xrefs-as-has-subclass: NCIT

From 091a57c4db84e06990cc559a49e4efedf15baa51 Mon Sep 17 00:00:00 2001
From: JABelfiore <jb69@sanger.ac.uk>
Date: Fri, 25 Oct 2024 10:01:35 +0100
Subject: [PATCH 2/3] definition

---
 src/ontology/uberon-edit.obo | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo
index 4eba15a1e..85079b059 100644
--- a/src/ontology/uberon-edit.obo
+++ b/src/ontology/uberon-edit.obo
@@ -72994,8 +72994,8 @@ 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]
@@ -224670,6 +224670,14 @@ relationship: dc-contributor https://orcid.org/0000-0002-4341-3265
 relationship: dc-contributor https://orcid.org/0000-0003-2804-127X ! Sanjay Jain
 property_value: dcterms-date "2024-08-28T16:10:50Z" xsd:dateTime
 
+[Term]
+id: UBERON:8700000
+name: aorta-gonad-mesonephros
+def: "A transient organ in the developing embryo composed of the dorsal aorta, developing gonads, and embryonic kidney. This structure is located in the embryonic mesoderm and serves as the primary site for the generation of definitive hematopoietic stem cells." [PMID:25686881, PMID:25749005, PMID:31813624]
+is_a: UBERON:0002050 ! embryonic structure
+relationship: dc-contributor https://orcid.org/0009-0005-7919-4905
+property_value: dcterms-date "2024-10-25T08:42:34Z" xsd:dateTime
+
 [Term]
 id: UBERON:8850000
 name: lumen of pulmonary alveolus

From 33011a49ecc9264c3463257d007b568c5c8ef79e Mon Sep 17 00:00:00 2001
From: JABelfiore <jb69@sanger.ac.uk>
Date: Fri, 15 Nov 2024 13:18:14 +0000
Subject: [PATCH 3/3] removed empty synonym

---
 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 0a10c9974..8a8c5befc 100644
--- a/src/ontology/uberon-edit.obo
+++ b/src/ontology/uberon-edit.obo
@@ -191,7 +191,6 @@ property_value: doap-SVNRepository "https://obo.svn.sourceforge.net/svnroot/obo/
 property_value: foaf-homepage "http://uberon.org" xsd:anyURI
 property_value: has_ontology_root_term UBERON:0000104
 property_value: has_ontology_root_term UBERON:0001062
-owl-axioms: Prefix(owl:=<http://www.w3.org/2002/07/owl#>)\nPrefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)\nPrefix(xml:=<http://www.w3.org/XML/1998/namespace>)\nPrefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)\nPrefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)\n\n\nOntology(\nDeclaration(AnnotationProperty(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym>))\n\n\nAnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/UBERON_8700000> \"\")\n)
 treat-xrefs-as-has-subclass: EHDAA
 treat-xrefs-as-has-subclass: EV
 treat-xrefs-as-has-subclass: NCIT