From cb7fdcdcffd6117a8512199c60e434daab7bc65a Mon Sep 17 00:00:00 2001 From: JABelfiore Date: Fri, 25 Oct 2024 10:00:48 +0100 Subject: [PATCH 1/7] 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:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(AnnotationProperty())\n\n\nAnnotationAssertion( \"\")\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 Date: Fri, 25 Oct 2024 10:01:35 +0100 Subject: [PATCH 2/7] 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 7915efcd64be84385b52502314f0b442c2619345 Mon Sep 17 00:00:00 2001 From: JABelfiore Date: Thu, 14 Nov 2024 15:03:43 +0000 Subject: [PATCH 3/7] stratum spinosum of esophageal epithelium --- src/ontology/uberon-edit.obo | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 4018c5421..d4bdb83fd 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -224694,6 +224694,14 @@ is_a: UBERON:0004693 ! Peyer's patch epithelium relationship: dc-contributor https://orcid.org/0009-0005-7919-4905 property_value: dcterms-date "2024-11-07T11:44:27Z" xsd:dateTime +[Term] +id: UBERON:8700002 +name: stratum spinosum of esophageal epithelium +def: "The second deepest layer of the stratified squamous epithelium lining the esophagus, positioned directly above the stratum basale. It consists of multiple layers of keratinocytes connected by strong intercellular junctions called desmosomes, giving the cells a characteristic \"spiny\" appearance. This layer provides structural support, contributes to the epithelial barrier function, and serves as a transitional zone for keratinocytes migrating towards the luminal surface, playing a crucial role in maintaining the integrity and protective properties of the esophageal lining." [PMID:21126700, PMID:26019440] +is_a: UBERON:0010304 ! non-keratinized stratified squamous epithelium +relationship: dc-contributor https://orcid.org/0009-0005-7919-4905 +property_value: dcterms-date "2024-11-14T15:00:21Z" xsd:dateTime + [Term] id: UBERON:8850000 name: lumen of pulmonary alveolus From 89a4ba632b2bd61fc63909ec712e2e3401c20800 Mon Sep 17 00:00:00 2001 From: JABelfiore Date: Thu, 14 Nov 2024 15:24:51 +0000 Subject: [PATCH 4/7] part of relationship added --- src/ontology/uberon-edit.obo | 1 + 1 file changed, 1 insertion(+) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index d4bdb83fd..d314da4fe 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -224700,6 +224700,7 @@ name: stratum spinosum of esophageal epithelium def: "The second deepest layer of the stratified squamous epithelium lining the esophagus, positioned directly above the stratum basale. It consists of multiple layers of keratinocytes connected by strong intercellular junctions called desmosomes, giving the cells a characteristic \"spiny\" appearance. This layer provides structural support, contributes to the epithelial barrier function, and serves as a transitional zone for keratinocytes migrating towards the luminal surface, playing a crucial role in maintaining the integrity and protective properties of the esophageal lining." [PMID:21126700, PMID:26019440] is_a: UBERON:0010304 ! non-keratinized stratified squamous epithelium relationship: dc-contributor https://orcid.org/0009-0005-7919-4905 +relationship: part_of UBERON:0001043 ! esophagus property_value: dcterms-date "2024-11-14T15:00:21Z" xsd:dateTime [Term] From 32b32f08471dc36af11664a9e3435f1428f51c7e Mon Sep 17 00:00:00 2001 From: Nico Matentzoglu Date: Thu, 14 Nov 2024 18:47:32 +0200 Subject: [PATCH 5/7] Add GitHub action that assigns reviewers when equivalent class axioms are updated The main use case for this action is to provide a way to assign specific reviewers when equivalent class axioms are added or updated, but it should be easy to extend the action to other kinds of edits, hence the generic name. To achieve the above, we check the diff for changes to rows that signify a logical definition, i.e. starting with "intersection_of". If we find such a change, we set a special environment variable to "true"; if it is "true", in the next step, a reviewer is assigned. Lastly, we let the GitHub action itself make a review, which requests changes - the idea is that these need to be dismissed by a person which sufficient access to Uberon before the change is committed to the main (master) branch. Issue: https://github.com/obophenotype/uberon/issues/2020 --- .github/workflows/reviewers.yml | 47 +++++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 .github/workflows/reviewers.yml diff --git a/.github/workflows/reviewers.yml b/.github/workflows/reviewers.yml new file mode 100644 index 000000000..2ae5e3514 --- /dev/null +++ b/.github/workflows/reviewers.yml @@ -0,0 +1,47 @@ +name: Assign Reviewers for Uberon + +on: + pull_request: + types: [opened, synchronize] + paths: + - src/ontology/uberon-edit.obo + +jobs: + assign-reviewer: + runs-on: ubuntu-latest + + steps: + - name: Checkout code + uses: actions/checkout@v3 + with: + fetch-depth: 0 # Fetch the entire history for all branches + + - name: Fetch base branch + run: | + git fetch origin ${{ github.base_ref }} # Fetch base branch explicitly + + - name: Check if equivalent class axiom was edited + id: check_intersection_of + run: | + git diff origin/${{ github.base_ref }}...HEAD -- src/ontology/uberon-edit.obo > diff.txt + if grep -E '^(-|\+)intersection_of:' diff.txt; then + echo "intersection_of_found=true" >> $GITHUB_ENV + else + echo "intersection_of_found=false" >> $GITHUB_ENV + fi + + - name: Assign reviewer + if: env.intersection_of_found == 'true' + env: + GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} + run: | + gh api repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/requested_reviewers \ + --method POST \ + --field reviewers[]=cmungall + + - name: Block PR by requesting changes + if: env.intersection_of_found == 'true' + env: + GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} + run: | + gh pr review ${{ github.event.pull_request.number }} --request-changes --body "Changes detected in \`src/ontology/uberon-edit.obo\` involving \`intersection_of\`. Review by specific Uberon Core Team member is required." From 33011a49ecc9264c3463257d007b568c5c8ef79e Mon Sep 17 00:00:00 2001 From: JABelfiore Date: Fri, 15 Nov 2024 13:18:14 +0000 Subject: [PATCH 6/7] 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:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(AnnotationProperty())\n\n\nAnnotationAssertion( \"\")\n) treat-xrefs-as-has-subclass: EHDAA treat-xrefs-as-has-subclass: EV treat-xrefs-as-has-subclass: NCIT From b14aa5331421851f5e3952cb1645cc6862966ff6 Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Mon, 18 Nov 2024 17:15:26 +0000 Subject: [PATCH 7/7] Add ID range for the NDI Cloud project. Assign the ID range 8,910,000--8,919,999 to members of the NDI Cloud project, so that they can participate in creating the terms they need to cover some aspects of arthropod neuroanatomy. As discussed in Uberon call of 2024-11-18. --- src/ontology/uberon-idranges.owl | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/src/ontology/uberon-idranges.owl b/src/ontology/uberon-idranges.owl index 2dd215b32..8985f3707 100644 --- a/src/ontology/uberon-idranges.owl +++ b/src/ontology/uberon-idranges.owl @@ -261,4 +261,10 @@ Datatype: idrange:35 Annotations: allocatedto: "Tiago Lubiana" EquivalentTo: - xsd:integer[>= 8900000, <= 8909999] \ No newline at end of file + xsd:integer[>= 8900000, <= 8909999] + +Datatype: idrange:40 + Annotations: + allocatedto: "NDI Cloud" + EquivalentTo: + xsd:integer[>= 8910000, <= 8919999]