diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS index 93671487c..ae8ca7722 100644 --- a/.github/CODEOWNERS +++ b/.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/* action@github.com diff --git a/src/ontology/diffs/Makefile b/src/ontology/diffs/Makefile index ea7384c6a..c2ec34425 100644 --- a/src/ontology/diffs/Makefile +++ b/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 diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 5e5c27b86..0a10c9974 100644 --- a/src/ontology/uberon-edit.obo +++ b/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 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