Merge branch 'master' into 3427-epithelium-of-anorectum

Caroline-99 · web-flow · commit b3200ac47dab · 2025-03-10T13:57:49.000Z
diff --git a/.github/workflows/diff.yml b/.github/workflows/diff.yml
@@ -61,7 +61,7 @@ jobs:
     needs: [branch_status]
     if: ${{ github.event.issue.pull_request }}
     runs-on: ubuntu-latest
-    container: obolibrary/odkfull:v1.5.3
+    container: obolibrary/odkfull:v1.5.4
     steps:
       - uses: khan/pull-request-comment-trigger@v1.1.0
         id: check
@@ -94,7 +94,7 @@ jobs:
     needs: [branch_status]
     if: ${{ github.event.issue.pull_request }}
     runs-on: ubuntu-latest
-    container: obolibrary/odkfull:v1.5.3
+    container: obolibrary/odkfull:v1.5.4
     steps:
       - uses: khan/pull-request-comment-trigger@v1.1.0
         id: check
@@ -122,7 +122,7 @@ jobs:
     needs: [branch_status]
     if: ${{ github.event.issue.pull_request }}
     runs-on: ubuntu-latest
-    container: obolibrary/odkfull:v1.5.3
+    container: obolibrary/odkfull:v1.5.4
     steps:
       - uses: khan/pull-request-comment-trigger@v1.1.0
         id: check
@@ -147,7 +147,7 @@ jobs:
   diff_classification:
     needs: [classify_branch, classify_main]
     runs-on: ubuntu-latest
-    container: obolibrary/odkfull:v1.5.3
+    container: obolibrary/odkfull:v1.5.4
     steps:
       - uses: khan/pull-request-comment-trigger@v1.1.0
         id: check
diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml
@@ -23,7 +23,7 @@ jobs:
   ontology_qc:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
-    container: obolibrary/odkfull:v1.5.3
+    container: obolibrary/odkfull:v1.5.4
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml
@@ -43,7 +43,6 @@
       <uri name="http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-wbbt.owl" uri="bridge/uberon-bridge-to-wbbt.owl"/>
       <uri name="http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-wbls.owl" uri="bridge/uberon-bridge-to-wbls.owl"/>
       <uri name="http://purl.obolibrary.org/obo/uberon/bridge/uberon-bridge-to-xao.owl" uri="bridge/uberon-bridge-to-xao.owl"/>
-      <uri name="http://purl.obolibrary.org/obo/uberon/components/develops-from-chains.owl" uri="components/develops-from-chains.owl"/>
       <uri name="http://purl.obolibrary.org/obo/uberon/components/disjoint_union_over.owl" uri="components/disjoint_union_over.owl"/>
       <uri name="http://purl.obolibrary.org/obo/uberon/components/hra_depiction_3d_images.owl" uri="components/hra_depiction_3d_images.owl"/>
       <uri name="http://purl.obolibrary.org/obo/uberon/components/hra_subset.owl" uri="components/hra_subset.owl"/>
diff --git a/src/ontology/components/develops-from-chains.owl b/src/ontology/components/develops-from-chains.owl
diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo
@@ -56,7 +56,6 @@ treat-xrefs-as-equivalent: VSAO
 treat-xrefs-as-is_a: BFO
 treat-xrefs-as-is_a: VHOG
 remark: Aurelie Comte, Bill Bug, Catherine Leroy, Duncan Davidson and Trish Whetzel are also contributors. However their ORCIDs were not found.
-import: http://purl.obolibrary.org/obo/uberon/components/develops-from-chains.owl
 import: http://purl.obolibrary.org/obo/uberon/components/disjoint_union_over.owl
 import: http://purl.obolibrary.org/obo/uberon/components/hra_depiction_3d_images.owl
 import: http://purl.obolibrary.org/obo/uberon/components/hra_subset.owl
@@ -2885,13 +2884,13 @@ relationship: simultaneous_with GO:0007369 ! gastrulation
 [Term]
 id: UBERON:0000110
 name: neurula stage
-def: "Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system." [GO:0001841]
+def: "A chordate developmental stage defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system." [GO:0001841]
 xref: BilaDO:0000009
 xref: BILS:0000110
 xref: XAO:1000006
 is_a: UBERON:0000105 ! life cycle stage
 relationship: dubious_for_taxon NCBITaxon:7955 ! Danio rerio
-relationship: in_taxon NCBITaxon:6072 ! Eumetazoa
+relationship: in_taxon NCBITaxon:7711 ! Chordata
 relationship: part_of UBERON:0000068 ! embryo stage
 relationship: preceded_by UBERON:0000109 ! gastrula stage
 relationship: simultaneous_with GO:0001841 ! neural tube formation
@@ -30592,11 +30591,10 @@ xref: SCTID:280648000
 xref: UMLS:C0042160 {source="ncithesaurus:Uvea"}
 xref: Wikipedia:Uvea
 is_a: UBERON:0004923 {source="FMA"} ! organ component layer
-relationship: contributes_to_morphology_of UBERON:0000019 ! camera-type eye
 relationship: has_part UBERON:0001769 ! iris
 relationship: has_part UBERON:0001775 ! ciliary body
 relationship: has_part UBERON:0001776 ! optic choroid
-relationship: part_of UBERON:0001801 ! anterior segment of eyeball
+relationship: part_of UBERON:0000019 ! camera-type eye
 relationship: present_in_taxon NCBITaxon:7955 {source="DOI:10.1177/0192623311409597"} ! Danio rerio
 property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/eb/Gray869.png" xsd:anyURI
 property_value: editor_note "TODO - check child terms, isa vs partof. See also MA:0001284 ! tunica vasculosa plexus" xsd:string
@@ -90617,7 +90615,7 @@ property_value: external_definition "A pear shaped chamber that functions as a c
 [Term]
 id: UBERON:0004707
 name: pharyngula stage
-def: "A stage that follows the blastula, gastrula and neurula stages. At the pharyngula stage, all vertebrate embryos show remarkable similarities." [Wikipedia:Pharyngula]
+def: "A chordate developmental stage that follows the blastula, gastrula and neurula stages. At the pharyngula stage, all vertebrate embryos show remarkable similarities." [Wikipedia:Pharyngula]
 subset: efo_slim
 synonym: "pharyngula" RELATED []
 synonym: "phylotypic stage" EXACT []
@@ -90627,7 +90625,7 @@ xref: OGES:000006
 xref: Wikipedia:Pharyngula
 xref: ZFS:0000050
 is_a: UBERON:0000105 ! life cycle stage
-relationship: in_taxon NCBITaxon:6072 ! Eumetazoa
+relationship: in_taxon NCBITaxon:7711 ! Chordata
 relationship: part_of UBERON:0000111 ! organogenesis stage
 relationship: preceded_by UBERON:0000110 ! neurula stage
 property_value: taxon_notes "Corresponds to E7-E11 in Mouse (Galis et al, TREE, 2001)" xsd:string
@@ -119538,7 +119536,7 @@ is_a: UBERON:0000105 ! life cycle stage
 relationship: part_of UBERON:0000068 ! embryo stage
 relationship: preceded_by RnorDv:0000010 {gci_relation="part_of", gci_filler="NCBITaxon:10116"}
 relationship: preceded_by UBERON:0000111 ! organogenesis stage
-relationship: preceded_by UBERON:0004707 ! pharyngula stage
+relationship: preceded_by UBERON:0004707 {gci_relation="BFO:0000066", gci_filler="NCBITaxon:7711"} ! pharyngula stage
 property_value: seeAlso "https://github.com/obophenotype/uberon/issues/355" xsd:anyURI
 property_value: seeAlso "https://github.com/obophenotype/uberon/issues/565" xsd:anyURI
 
@@ -154070,7 +154068,7 @@ synonym: "secondary brain vesicle" NARROW []
 xref: NCIT:C34259
 xref: neuronames:2499
 xref: SCTID:360409004
-is_a: UBERON:0010064 {source="EHDAA2"} ! open anatomical space
+is_a: UBERON:0010000 ! multicellular anatomical structure
 relationship: part_of UBERON:0000922 ! embryo
 relationship: part_of UBERON:0005281 {source="EHDAA2"} ! ventricular system of central nervous system
 relationship: part_of UBERON:0006238 ! future brain
@@ -201999,7 +201997,7 @@ def: "Fine ridge on surface of scale, often parallel to the circumference of sca
 synonym: "circuli" EXACT OMO:0003004 [TAO:0002051]
 synonym: "crétule" EXACT [PSPUB:0000149]
 xref: ZFA:0005499
-is_a: UBERON:0006800 ! anatomical line
+is_a: UBERON:0000061 ! anatomical structure
 relationship: part_of UBERON:0007380 ! dermal scale
 property_value: provenance_notes "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string {source="http://purl.obolibrary.org/obo/tao.owl"}
 
diff --git a/src/ontology/uberon-idranges.owl b/src/ontology/uberon-idranges.owl
@@ -268,3 +268,9 @@ Datatype: idrange:40
         allocatedto: "NDI Cloud"
     EquivalentTo:
         xsd:integer[>= 8910000, <= 8919999]
+
+        Datatype: idrange:41
+    Annotations:
+        allocatedto: "Arwa Ibrahim"
+    EquivalentTo:
+        xsd:integer[>= 8920000, <= 8929999]
diff --git a/src/ontology/uberon.Makefile b/src/ontology/uberon.Makefile
@@ -117,9 +117,6 @@ $(OWLSRC): $(SRC) $(REPORTDIR)/$(SRC)-gocheck $(REPORTDIR)/$(SRC)-iconv
 			-o $@
 
 # Step 2: Reasoning.
-# For the temporary injection of property chains, see
-# <https://github.com/obophenotype/uberon/issues/2381>
-DEVELOPS_FROM_CHAIN=$(COMPONENTSDIR)/develops-from-chains.owl
 # The 'materialize' step is too resource-intensive for the GitHub
 # Action runners, so we leave it out when running online QC checks, see
 # <https://github.com/obophenotype/uberon/pull/3087#issuecomment-1755553647>
@@ -128,13 +125,11 @@ MATERIALIZE=
 else
 MATERIALIZE = materialize -T $(CONFIGDIR)/basic_properties.txt -r elk
 endif
-$(POSTPROCESS_SRC): $(OWLSRC) $(BRIDGEDIR)/uberon-bridge-to-bfo.owl $(DEVELOPS_FROM_CHAIN)
+$(POSTPROCESS_SRC): $(OWLSRC) $(BRIDGEDIR)/uberon-bridge-to-bfo.owl
 	$(ROBOT) merge -i $(OWLSRC) -i $(BRIDGEDIR)/uberon-bridge-to-bfo.owl \
-	               -i $(DEVELOPS_FROM_CHAIN) \
 	         relax $(MATERIALIZE) \
 	         reason -r elk --exclude-duplicate-axioms true \
 	                       --equivalent-classes-allowed asserted-only \
-	         unmerge -i $(DEVELOPS_FROM_CHAIN) \
 	         annotate -O $(URIBASE)/uberon.owl -V $(RELEASE)/uberon.owl -o $@
 
 # Step 3: Postprocessing. We merge some files that are derived from the
