Merge branch 'master' into 3388-aorta-gonad-mesonephros

.github/CODEOWNERS

@@ -1,10 +1,9 @@
 # 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
+*uberon.Makefile @gouttegd @matentzn
 
 
 #docs/*  [email protected] 

src/ontology/diffs/Makefile

@@ -4,9 +4,10 @@ SRC = ../../../$(ONT)-base.obo
 OWLSRC = ../../../$(ONT)-base.owl
 LAST = $(OBO)/$(ONT)/$(ONT)-base.obo
 OWLLAST = $(OBO)/$(ONT)/$(ONT)-base.owl
+REPORTDIR = ../reports
 
 #all: $(ONT)-obo-diff.html $(ONT)-def-diff.html $(ONT)-lastbuild.obo $(ONT)-combined-diff.txt $(ONT)-diff.md
-all: $(ONT)-diff.md
+all: $(ONT)-diff.md $(REPORTDIR)/diff_release_oak.md
 
 $(ONT)-combined-diff.txt: $(ONT)-def-diff.html $(ONT)-obo-diff.html
 	cat $(ONT)-def-diff.txt $(ONT)-obo-diff.txt > $@
@@ -23,3 +24,7 @@ $(ONT)-diff.md: $(ONT)-lastbuild.owl $(OWLSRC)
 $(ONT)-diff.txt: $(ONT)-lastbuild.owl $(OWLSRC)
 	robot diff --labels true -f plain -l $< -r $(OWLSRC) -o $@
 
+$(REPORTDIR)/diff_release_oak.md: $(ONT)-lastbuild.obo
+	runoak -i simpleobo:$(ONT)-lastbuild.obo \
+	       diff -X simpleobo:$(SRC) \
+	            -o $@ --output-type md

src/ontology/uberon-edit.obo

@@ -10059,7 +10059,7 @@ synonym: "oviducts" RELATED OMO:0003004 [ZFA:0000560]
 synonym: "tuba uterina" RELATED [BTO:0000980]
 synonym: "tuba uterinae" RELATED [BTO:0000980]
 synonym: "tubular parts of female reproductive system" RELATED [http://orcid.org/0000-0002-6601-2165]
-synonym: "uterine tube" EXACT []
+synonym: "uterine tube" NARROW []
 xref: AAO:0010533
 xref: BSA:0000083
 xref: BTO:0000980
@@ -39577,6 +39577,7 @@ xref: XAO:0000119
 is_a: UBERON:0000171 ! respiration organ
 relationship: contributes_to_morphology_of UBERON:0001004 ! respiratory system
 relationship: develops_from UBERON:0000118 ! lung bud
+relationship: has_part UBERON:0002185 ! bronchus
 relationship: in_lateral_side_of UBERON:0000170 ! pair of lungs
 relationship: in_taxon NCBITaxon:7776 ! Gnathostomata <vertebrates>
 relationship: located_in UBERON:0002224 ! thoracic cavity
@@ -78433,9 +78434,9 @@ def: "Initial section of the oviduct through which the ova pass from the ovary t
 subset: efo_slim
 subset: pheno_slim
 subset: uberon_slim
-synonym: "fallopian tubes" RELATED []
+synonym: "fallopian tubes" RELATED OMO:0003004 []
 synonym: "female paramesonephric duct" RELATED [EHDAA2:0000504]
-synonym: "mammalian oviduct" EXACT [https://sourceforge.net/p/geneontology/ontology-requests/8397/]
+synonym: "mammalian oviduct" BROAD [https://sourceforge.net/p/geneontology/ontology-requests/8397/]
 synonym: "paramesonephric duct of female" RELATED [EMAPA:35660]
 synonym: "salpinges" BROAD OMO:0003004 []
 synonym: "salpinx" BROAD []
@@ -90443,9 +90444,9 @@ intersection_of: part_of UBERON:0005928 ! external naris
 [Term]
 id: UBERON:0004693
 name: Peyer's patch epithelium
-def: "The specialized epithelium of the Peyer's patch." [ISBN:0-8153-1691-7, MGI:cwg, MP:0002388]
+def: "The specialized epithelial layer covering the entire Peyer's patch, including both the follicular and interfollicular areas and forming part of the gut-associated lymphoid tissue." [ISBN:0-8153-1691-7, MGI:cwg, MP:0002388]
 subset: pheno_slim
-synonym: "Peyer's patch epithelium" EXACT [MA:0000731]
+synonym: "Peyer's patch epithelium" EXACT [MA:0000731, PMID:31813624]
 xref: EMAPA:36506
 xref: MA:0000731
 intersection_of: UBERON:0000483 ! epithelium
@@ -152081,12 +152082,18 @@ relationship: overlaps UBERON:0005022 ! mucosa of nasopharynx
 [Term]
 id: UBERON:0012331
 name: mesosalpinx
-def: "The mesosalpinx is part of the lining of the abdominal cavity in higher vertebrates, specifically the portion of the broad ligament that stretches from the uterine tube to the level of the ovary." [Wikipedia:Mesosalpinx]
+def: "A serous layer that is part of the peritoneal lining of the abdominal cavity in higher vertebrates, specifically the portion of the broad ligament that stretches from the uterine (fallopian) tube to the ovary. It is made up of epithelial cells of mesothelium and a mesh of serous membrane lining." [doi:10.1016/B978-0-12-801238-3.64401-X, PMID:29763118, Wikipedia:Mesosalpinx]
+synonym: "fallopian tube mesosalpinx" EXACT []
+synonym: "mesentery of fallopian tube" EXACT [PMID:29763118]
+synonym: "mesentery of uterine tube" EXACT [PMID:29763118]
+synonym: "serous layer of fallopian tube" EXACT [doi:10.1016/B978-0-12-801238-3.64401-X]
 xref: FMA:19808
 xref: SCTID:279900000
 xref: Wikipedia:Mesosalpinx
+is_a: UBERON:0000042 ! serous membrane
 is_a: UBERON:0002095 ! mesentery
 relationship: part_of UBERON:0012332 ! broad ligament of uterus
+relationship: surrounds UBERON:0003889 ! fallopian tube
 
 [Term]
 id: UBERON:0012332
@@ -224687,6 +224694,15 @@ 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:8700001
+name: follicle associated epithelium
+def: "A specialized epithelial layer overlying the luminal surface of lymphoid follicles in gut-associated lymphoid tissue. It is found in Peyer's patches of the small intestine and appendix in humans and in the intestine and caecal patches in mice. This layer contains specialised M cells and has fewer goblet cells compared to surrounding tissue. This layer plays a crucial role in mucosal immune surveillance." [DOI:10.1007/s00702-022-02561-x, DOI:10.4061/2010/823710]
+synonym: "FAE" EXACT [DOI:10.1007/s00702-022-02561-x]
+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:8850000
 name: lumen of pulmonary alveolus