Merge branch 'master' into ro-pr-739

.github/CODEOWNERS

@@ -0,0 +1,11 @@
+# Uberon code owners (Guardians of the main branch)
+# GitHub documentation about CODEOWNERS file - https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-code-owners
+
+*       @anitacaron
+*.yaml @matentzn
+*Makefile @gouttegd
+*uberon.Makefile @gouttegd @matentzn @anitacaron
+
+
+#docs/*  [email protected] 
+#docs/*  actions-user

.github/workflows/qc.yml

@@ -19,7 +19,7 @@ jobs:
   ontology_qc:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
-    container: obolibrary/odkfull:dev
+    container: obolibrary/odkfull:v1.4.1
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:

docs/uberon-editor-sop.md

@@ -91,20 +91,23 @@ ORCID identifiers may also be used when the only available source for an asserti
 
 **Technical details of adding a cross-reference using Protégé**:
 
-For CURIEs and ORCIDs: In the "Create Annotation" window, select the annotation property **database_cross_reference**.
+For CURIEs, ORCIDs: In the "Create Annotation" window, select the annotation property [**database_cross_reference**](http://www.geneontology.org/formats/oboInOwl#hasDbXref).
+For adding URLs to text definitions or synonyms:  In the "Create Annotation" window, select the annotation property [**database_cross_reference**](http://www.geneontology.org/formats/oboInOwl#hasDbXref).
+For adding URLs to axioms that are NOT text definitions or synonyms:  In the "Create Annotation" window, select the annotation property [**source**](http://www.geneontology.org/formats/oboInOwl#source).
+
 
 For CURIEs: Enter the CURIE, using the [bioregistry OBO context](https://bioregistry.io/context/obo) prefix ([link to prefixmap](https://github.com/biopragmatics/bioregistry/blob/main/exports/contexts/obo.context.jsonld)), as a Value on the "Literal" tab. Leave Datatype empty.
 
 In cases where more than one CURIE is available for a resource, either is acceptable, but using the more semantically specific identifier is recommended. For example, when both a PMID and a doi are available for a resource, using the PMID is recommended since it indicates the cross-reference points to a paper, as opposed to a doi which could point to any digital object.
 
 For ORCIDs: Enter the ORCID as an IRI in the IRI field on the "IRI Editor" tab, for example `https://orcid.org/0000-0002-7356-1779`.
 
-For URLs: In the "Create Annotation" window, select the annotation property **'see also'** (`rdfs:seeAlso`). Enter the URL as a literal string. DO NOT use database_cross_reference with a value that is a URL. Note: In OWL-based files (like cl-edit.owl), Datatype `xsd:anyURI` is also selected; however, in OBO-based files (like uberon-edit.obo) these always become strings, so no selection needs to be made for Datatype in Uberon. Datatype selection is planned to be implemented in a future OBO revision, and updates can be checked at https://github.com/owlcollab/oboformat/issues/128.
+For URLs: Enter the URL as a literal string. Note: In OWL-based files (like cl-edit.owl), Datatype `xsd:anyURI` is also selected; however, in OBO-based files (like uberon-edit.obo) these always become strings, so no selection needs to be made for Datatype in Uberon. Datatype selection is planned to be implemented in a future OBO revision, and updates can be checked at https://github.com/owlcollab/oboformat/issues/128.
+NOTE: URLs should be avoided when a cross-reference with a CURIE is otherwise available.
 
 
-To restate, in all cases above except ORCIDs, the values are entered as literal strings. An ORCID MUST BE entered as an IRI.
 
-The above instructions apply whether the cross-reference is added to another annotation (e.g., annotating a text defintion or comment) or adding to the overall class (i.e., not an annotation of another annotation). 
+To restate, in all cases above except ORCIDs, the values are entered as literal strings. An ORCID MUST BE entered as an IRI.
 
 ## Synonyms
 

src/ontology/Makefile

@@ -42,7 +42,7 @@ REPORT_FAIL_ON =            ERROR
 REPORT_LABEL =              
 REPORT_PROFILE_OPTS =       --profile $(ROBOT_PROFILE)
 OBO_FORMAT_OPTIONS =        
-SPARQL_VALIDATION_CHECKS =  equivalent-classes owldef-self-reference illegal-annotation-property taxon-range orcid-contributor obsolete-replaced_by xrefs-mesh-pattern label-synonym-polysemy 
+SPARQL_VALIDATION_CHECKS =  equivalent-classes owldef-self-reference illegal-annotation-property taxon-range orcid-contributor obsolete-replaced_by xrefs-mesh-pattern label-synonym-polysemy id-format 
 SPARQL_EXPORTS =            basic-report 
 ODK_VERSION_MAKEFILE =      v1.4.1
 
@@ -62,7 +62,7 @@ PATTERN_RELEASE_FILES=      $(PATTERNDIR)/definitions.owl $(PATTERNDIR)/pattern.
 
 FORMATS = $(sort  owl obo json owl)
 FORMATS_INCL_TSV = $(sort $(FORMATS) tsv)
-RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-full $(ONT)-simple $(ONT)-basic ext basic composite-metazoan composite-metazoan-basic composite-vertebrate composite-vertebrate-basic common-anatomy )
+RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-full $(ONT)-simple $(ONT)-basic basic composite-metazoan composite-metazoan-basic composite-vertebrate composite-vertebrate-basic common-anatomy )
 
 # ----------------------------------------
 # Top-level targets
@@ -668,12 +668,6 @@ $(ONT)-basic.json: $(ONT)-basic.owl
 	$(ROBOT) annotate --input $< --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
 		convert --check false -f json -o $@.tmp.json &&\
 		mv $@.tmp.json $@
-ext.obo: ext.owl
-	$(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@.tmp.obo && grep -v ^owl-axioms $@.tmp.obo > $@ && rm $@.tmp.obo
-ext.json: ext.owl
-	$(ROBOT) annotate --input $< --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \
-		convert --check false -f json -o $@.tmp.json &&\
-		mv $@.tmp.json $@
 basic.obo: basic.owl
 	$(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@.tmp.obo && grep -v ^owl-axioms $@.tmp.obo > $@ && rm $@.tmp.obo
 basic.json: basic.owl
@@ -781,9 +775,6 @@ $(ONT)-basic.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(SIMPLESEED) $(KEEPRELATION
 		reduce -r ELK \
 		$(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@
 
-ext.owl:
-	echo "ERROR: You have configured a custom release artefact ($@); this release artefact needs to be define in uberon.Makefile!" && false
-
 basic.owl:
 	echo "ERROR: You have configured a custom release artefact ($@); this release artefact needs to be define in uberon.Makefile!" && false
 

src/ontology/bridge/collected-drosophila.owl

@@ -32,6 +32,6 @@
     </rdfs:comment>
     <owl:imports rdf:resource="http://purl.obolibrary.org/obo/uberon.owl"/>
     <owl:imports rdf:resource="http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-fbbt.owl"/>
-    <owl:imports rdf:resource="http://purl.obolibrary.org/obo/uberon/fbbt-nd.owl"/>
+    <owl:imports rdf:resource="http://purl.obolibrary.org/obo/fbbt.owl"/>
   </owl:Ontology>
 </rdf:RDF>

src/ontology/uberon-edit.obo

@@ -8749,8 +8749,7 @@ xref: VHOG:0000098
 xref: Wikipedia:Endocrine_system
 xref: XAO:0000158
 xref: ZFA:0001158
-intersection_of: UBERON:0015203 ! non-connected functional system
-intersection_of: capable_of GO:0050886 ! endocrine process
+is_a: UBERON:0015203 ! non-connected functional system
 disjoint_from: UBERON:0000990 ! reproductive system
 disjoint_from: UBERON:0001004 ! respiratory system
 disjoint_from: UBERON:0001007 ! digestive system
@@ -73141,6 +73140,7 @@ 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: "skin of hind limb" EXACT [OBOL:automatic]
 synonym: "skin of hindlimb" EXACT [OBOL:automatic]
 synonym: "skin of lower extremity" EXACT [OBOL:automatic]
@@ -135200,13 +135200,14 @@ id: UBERON:0010002
 name: pulmonary neuroendocrine body
 def: "Corpuscular, organoid structures composed of PNECs, found as distinctive innervated clusters only within intrapulmonary airways, where they appear concentrated at airway branch points; NEBs reach from the basement membrane to the airway lumen and are thought to function as oxygen sensors." [MP:0010921]
 subset: pheno_slim
-synonym: "NEB" EXACT [MP:0010921]
+synonym: "NEB" RELATED ABBREVIATION [MP:0010921]
 synonym: "pulmonary neuroepithelial body" EXACT [MP:0010921]
 xref: EMAPA:37943 {source="MA:th"}
 is_a: UBERON:0000061 {source="MP"} ! anatomical structure
 relationship: contributes_to_morphology_of UBERON:0000115 ! lung epithelium
-relationship: has_part CL:0000165 ! neuroendocrine cell
+relationship: has_part CL:1000223 ! lung neuroendocrine cell
 relationship: part_of UBERON:0000115 ! lung epithelium
+relationship: part_of UBERON:8600018 ! neuroendocrine system
 
 [Term]
 id: UBERON:0010005
@@ -136304,8 +136305,9 @@ subset: pheno_slim
 synonym: "neuroendocrine system gland" EXACT []
 xref: MA:0000720
 intersection_of: UBERON:0002368 ! endocrine gland
-intersection_of: part_of UBERON:0001016 ! nervous system
+intersection_of: part_of UBERON:8600018 ! neuroendocrine system
 relationship: has_part CL:0000165 ! neuroendocrine cell
+relationship: overlaps UBERON:0001016 ! nervous system
 
 [Term]
 id: UBERON:0010134
@@ -182190,8 +182192,8 @@ intersection_of: capable_of GO:0050976 ! detection of mechanical stimulus involv
 id: UBERON:0035017
 name: nociceptor nerve ending
 def: "A peripheral terminal of a peripheral, afferent sensory pain receptor cell that is sensitive to injury or pain, usually caused by extreme thermal exposures, mechanical forces, or other noxious stimuli. The nociceptor nerve ending innervates target tissue and transduces noxious stimuli to the central nervous system via some axon(s)." [MESH:D009619]
-synonym: "nociceptor" RELATED [] {http://www.w3.org/2000/01/rdf-schema#seeAlso="https://meshb.nlm.nih.gov/record/ui?ui=D009619"}
-synonym: "pain receptor" RELATED [] {http://www.w3.org/2000/01/rdf-schema#seeAlso="https://meshb.nlm.nih.gov/record/ui?ui=D009619"}
+synonym: "nociceptor" RELATED [https://meshb.nlm.nih.gov/record/ui?ui=D009619]
+synonym: "pain receptor" RELATED [https://meshb.nlm.nih.gov/record/ui?ui=D009619]
 xref: MESH:D009619
 intersection_of: UBERON:0012451 ! sensory receptor
 intersection_of: capable_of GO:0050966 ! detection of mechanical stimulus involved in sensory perception of pain
@@ -219066,12 +219068,11 @@ relationship: only_in_taxon NCBITaxon:50557 ! Insecta
 
 [Term]
 id: UBERON:60005380
-name: insect pharynx
-def: "Section of the insect foregut anterior to the esophagus." [FBbt:00005380, http://orcid.org/0000-0002-6601-2165]
-xref: FBbt:00005380
-is_a: UBERON:0004921 {source="FBbt"} ! subdivision of digestive tract
-is_a: UBERON:0006562 {notes="parent may be obsoleted"} ! pharynx
-relationship: part_of UBERON:0003929 {source="FBbt"} ! digestive tract epithelium
+name: obsolete insect pharynx
+comment: Obsoleted because the ID was minted incorrectly.
+property_value: term_tracker_item "https://github.com/obophenotype/uberon/issues/3051" xsd:anyURI
+is_obsolete: true
+replaced_by: UBERON:6005380
 
 [Term]
 id: UBERON:6001055
@@ -220223,6 +220224,15 @@ synonym: "margin" BROAD []
 is_a: UBERON:6007284 ! insect region of integument
 relationship: part_of UBERON:0000984 ! imaginal disc-derived wing
 
+[Term]
+id: UBERON:6005380
+name: insect pharynx
+def: "Section of the insect foregut anterior to the esophagus." [FBbt:00005380, http://orcid.org/0000-0002-6601-2165]
+xref: FBbt:00005380
+is_a: UBERON:0004921 {source="FBbt"} ! subdivision of digestive tract
+is_a: UBERON:0006562 {note="parent may be obsoleted"} ! pharynx
+relationship: part_of UBERON:0003929 {source="FBbt"} ! digestive tract epithelium
+
 [Term]
 id: UBERON:6005393
 name: insect embryonic/larval integumentary system
@@ -224024,6 +224034,7 @@ synonym: "anterior crural region" EXACT [FMA:24985]
 synonym: "anterior leg region" EXACT [FMA:24985]
 synonym: "anterior region of leg" EXACT [FMA:24985]
 synonym: "front of the lower leg" EXACT [https://orcid.org/0000-0002-0819-0473]
+synonym: "pretibial" RELATED [https://en.wiktionary.org/wiki/pretibial]
 synonym: "shin" EXACT [FMA:24985]
 xref: FMA:24985
 is_a: UBERON:0000061 ! anatomical structure
@@ -224208,6 +224219,51 @@ relationship: dc-contributor https://orcid.org/0000-0002-0819-0473
 relationship: located_in UBERON:0002371 ! bone marrow
 property_value: dcterms-date "2023-06-26T13:48:30Z" xsd:dateTime
 
+[Term]
+id: UBERON:8480068
+name: saphenous vein smooth muscle tissue
+def: "A portion of smooth muscle tissue that is part of a saphenous vein." [https://orcid.org/0000-0002-0819-0473]
+intersection_of: UBERON:0001135 ! smooth muscle tissue
+intersection_of: part_of UBERON:0007318 ! saphenous vein
+relationship: dc-contributor https://orcid.org/0000-0002-0819-0473
+property_value: dcterms-date "2023-08-31T11:41:09Z" xsd:dateTime
+
+[Term]
+id: UBERON:8480071
+name: skin of lobe of tail
+def: "A zone of skin that is part of the lobe tail." [https://orcid.org/0000-0002-0819-0473]
+synonym: "fluke skin" NARROW [PMID:21959845]
+intersection_of: UBERON:0000014 ! zone of skin
+intersection_of: part_of UBERON:0013131 ! lobe of tail
+relationship: dc-contributor https://orcid.org/0000-0002-0819-0473
+property_value: dcterms-date "2023-08-29T09:37:23Z" xsd:dateTime
+
+[Term]
+id: UBERON:8480072
+name: skin of shin
+def: "A zone of skin on the front hindlimb zeugopod." [https://orcid.org/0000-0002-0819-0473]
+intersection_of: UBERON:0000014 ! zone of skin
+intersection_of: part_of UBERON:8480049 ! front hindlimb zeugopod
+relationship: dc-contributor https://orcid.org/0000-0002-0819-0473
+property_value: dcterms-date "2023-08-29T09:47:32Z" xsd:dateTime
+
+[Term]
+id: UBERON:8480073
+name: skin of scapula region
+def: "A zone of skin that is above the scapula in the upper back region." [https://orcid.org/0000-0002-0819-0473]
+is_a: UBERON:0009015 ! upper back skin
+relationship: dc-contributor https://orcid.org/0000-0002-0819-0473
+property_value: dcterms-date "2023-08-29T09:53:33Z" xsd:dateTime
+
+[Term]
+id: UBERON:8480074
+name: skin of gonad
+def: "A zone of skin part of some gonad." [https://orcid.org/0000-0002-0819-0473]
+intersection_of: UBERON:0000014 ! zone of skin
+intersection_of: part_of UBERON:0000991 ! gonad
+relationship: dc-contributor https://orcid.org/0000-0002-0819-0473
+property_value: dcterms-date "2023-08-29T10:24:24Z" xsd:dateTime
+
 [Term]
 id: UBERON:8500000
 name: cranial temporal line
@@ -224440,6 +224496,18 @@ relationship: dc-contributor https://orcid.org/0000-0002-9185-3994
 relationship: part_of UBERON:0000101 ! lobe of lung
 property_value: dcterms-date "2023-07-20T12:43:29Z" xsd:dateTime
 
+[Term]
+id: UBERON:8600018
+name: neuroendocrine system
+def: "A regulatory system of the body that integrates the nervous system and the endocrine system. This system is formed by specialized neuroendocrine cells located mainly in the nervous system and neuroendocrine glands. However, they can also be found as either single cells or small clusters of cells dispersed throughout the surface epithelium of different tissues. The neuroendocrine system functions through the release of neurotransmitters and neurohormones, enabling communication between the endocrine and nervous systems to govern vitally important processes that include growth, reproduction, metabolism and energy homeostasis, electrolyte and water balance, and responses to stress." [doi:10.1016/B978-0-12-375097-6.10001-0, PMID:15481802, PMID:17003257, PMID:25905254, Wikipedia:endocrinology]
+comment: In vertebrates, the hypothalamic-pituitary-target organ axis (H-P axis), the autonomic nervous system (ANS) and the diffuse neuroendocrine or APUD system contribute to the neuroendocrine system. {xref="PMID:15481802"}
+synonym: "NES" RELATED ABBREVIATION [PMID:15481802]
+is_a: UBERON:0000467 ! anatomical system
+relationship: dc-contributor https://orcid.org/0000-0001-6677-8489
+relationship: overlaps UBERON:0000949 ! endocrine system
+relationship: overlaps UBERON:0001016 ! nervous system
+property_value: dcterms-date "2023-08-29T10:49:45Z" xsd:dateTime
+
 [Typedef]
 id: aboral_to
 name: aboral to

src/ontology/uberon-odk.yaml

@@ -20,7 +20,6 @@ release_artefacts:
   - full
   - simple
   - basic
-  - custom-ext
   - custom-basic
   - custom-composite-metazoan
   - custom-composite-metazoan-basic
@@ -109,6 +108,7 @@ robot_report:
     - obsolete-replaced_by
     - xrefs-mesh-pattern
     - label-synonym-polysemy
+    - id-format
   custom_sparql_exports:
     - basic-report
 owltools_memory: '20G'