From 205c56010deaf64829a8a7cdb8c72c03c76f6c96 Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Wed, 6 Dec 2023 22:45:07 +0000 Subject: [PATCH 1/7] Use a SSSOM/T-OWL ruleset to generate the mappings component. Use a custom SSSOM/T-OWL ruleset to generate the components of cross-references representing the mappings. This allows to annotate the cross-reference annotations with some metadata indicating the provenance of the mapping. This requires the latest version of the SSSOM plugin, which we update here. --- src/ontology/uberon.Makefile | 7 +++---- src/scripts/mappings-to-xrefs.rules | 19 +++++++++++++++++++ 2 files changed, 22 insertions(+), 4 deletions(-) create mode 100644 src/scripts/mappings-to-xrefs.rules diff --git a/src/ontology/uberon.Makefile b/src/ontology/uberon.Makefile index c10ecb9876..fcac9bdeae 100644 --- a/src/ontology/uberon.Makefile +++ b/src/ontology/uberon.Makefile @@ -124,7 +124,7 @@ export ROBOT_PLUGINS_DIRECTORY # Make sure the SSSOM plugin for ROBOT is available. $(TMPDIR)/plugins/sssom.jar: mkdir -p $(TMPDIR)/plugins - curl -L -o $@ https://github.com/gouttegd/sssom-java/releases/download/sssom-java-0.6.1/sssom-robot-plugin-0.6.1.jar + curl -L -o $@ https://github.com/gouttegd/sssom-java/releases/download/sssom-java-0.6.2/sssom-robot-plugin-0.6.2.jar # Ditto for the specific Uberon plugin $(TMPDIR)/plugins/uberon.jar: @@ -1429,9 +1429,8 @@ $(COMPONENTSDIR)/hra_depiction_3d_images.owl: $(TMPDIR)/hra_depiction_3d_images. $(COMPONENTSDIR)/mappings.owl: $(SRC) $(EXTERNAL_SSSOM_SETS) $(TMPDIR)/plugins/sssom.jar $(ROBOT) sssom:inject -i $< \ $(foreach set, $(EXTERNAL_SSSOM_SETS), --sssom $(set)) \ - --invert --only-subject-in UBERON \ - --check-subject --drop-duplicate-objects \ - --hasdbxref --no-merge --bridge-file $@ \ + --ruleset $(SCRIPTSDIR)/mappings-to-xrefs.rules \ + --no-merge --bridge-file $@ \ --bridge-iri http://purl.obolibrary.org/obo/uberon/components/mappings.owl diff --git a/src/scripts/mappings-to-xrefs.rules b/src/scripts/mappings-to-xrefs.rules new file mode 100644 index 0000000000..c437fd88ad --- /dev/null +++ b/src/scripts/mappings-to-xrefs.rules @@ -0,0 +1,19 @@ +prefix UBERON: +prefix oboInOwl: + +# Make sure UBERON classes, and only UBERON classes, are on the object side +subject==UBERON:* -> invert(); +!object==UBERON:* -> stop(); + +# Ignore any mapping to an inexistent or obsolete UBERON class. +predicate==* -> check_object_existence(); + +# Ignore any mapping where the same foreign term is mapped to more than one UBERON class. +!cardinality==*:1 -> stop(); + +# Create the hasDbXref annotation and annotate it with a subset of the mapping metadata +object==UBERON:* -> annotate_object(oboInOwl:hasDbXref, "%subject_curie", + "direct:mapping_justification, + author_id, + creator_id, + mapping_provider"); From b0837f0e97d282ca16089c0c58c3f894b849e564 Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Wed, 6 Dec 2023 22:47:42 +0000 Subject: [PATCH 2/7] Add Biomappings as an external SSSOM provider. When fetching mappings from remote sources, include the Biomappings set. --- src/ontology/uberon.Makefile | 20 +++++++++++++++++++- 1 file changed, 19 insertions(+), 1 deletion(-) diff --git a/src/ontology/uberon.Makefile b/src/ontology/uberon.Makefile index fcac9bdeae..414ed5cd41 100644 --- a/src/ontology/uberon.Makefile +++ b/src/ontology/uberon.Makefile @@ -1266,7 +1266,7 @@ composites: composite-metazoan.obo composite-vertebrate.obo # them and store them into mappings/ONT-mappings.ssom.tsv. # The following ontologies publish their own mapping sets. -EXTERNAL_SSSOM_PROVIDERS = fbbt cl zfa +EXTERNAL_SSSOM_PROVIDERS = fbbt cl zfa biomappings # All the sets coming from the above ontologies. EXTERNAL_SSSOM_SETS = $(foreach provider, $(EXTERNAL_SSSOM_PROVIDERS), mappings/$(provider)-mappings.sssom.tsv) @@ -1282,6 +1282,24 @@ ifeq ($(strip $(IMP)),true) mappings/%-mappings.sssom.tsv: %-mappings wget -O $@ http://purl.obolibrary.org/obo/$*/$*-mappings.sssom.tsv +# Special case for the Biomappings set which is provided with the +# metadata in a separate file. We assemble a single YAML+TSV file and +# we also filter out anything that has nothing to do with Uberon: the +# set is quite large and we commit it to the repository, so we want to +# keep it to the minimum stuff we actually need. +# (We do the filtering with sed because "sssom dosql" is WAY too slow +# for what it does.) +mappings/biomappings-mappings.sssom.tsv: $(TMPDIR)/biomappings.sssom.tsv \ + $(TMPDIR)/biomappings.sssom.yml + sed 's/^/#/' $(TMPDIR)/biomappings.sssom.yml > $@ + sed -n '1p; /UBERON:/p' $(TMPDIR)/biomappings.sssom.tsv >> $@ + +$(TMPDIR)/biomappings.sssom.tsv: + wget -O $@ https://w3id.org/biopragmatics/biomappings/sssom/biomappings.sssom.tsv + +$(TMPDIR)/biomappings.sssom.yml: + wget -O $@ https://w3id.org/biopragmatics/biomappings/sssom/biomappings.sssom.yml + # Special cases for ontologies that do no provide a ready-to-use set # ------------------------------------------------------------------ From cf56ae93471ea7128eada9e9090e3a15a4d659d2 Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Wed, 6 Dec 2023 22:53:57 +0000 Subject: [PATCH 3/7] Revert "Add xrefs curated in Biomappings (#2950)" This reverts commit 2494303464a3bfe08fa1a798e686ea1e6bbe602b. That commit manually introduced Biomappings-provided cross-references directly in the -edit file, but we are now importing those cross-references automatically using the Biomappings SSSOM set. --- src/ontology/uberon-edit.obo | 61 ------------------------------------ 1 file changed, 61 deletions(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 4a025c5d76..1558815734 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -786,7 +786,6 @@ synonym: "Komplexauge" RELATED [BTO:0001921] synonym: "zusammengesetztes Auge" RELATED [BTO:0001921] xref: BTO:0001921 xref: HAO:0000217 -xref: IDOMAL:0002421 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: TGMA:0000024 xref: Wikipedia:Compound_eye intersection_of: UBERON:0000970 ! eye @@ -2177,7 +2176,6 @@ def: "The surface (external) layer of ectoderm which begins to proliferate short subset: pheno_slim synonym: "surface (external) ectoderm" EXACT [] synonym: "surface ectoderm" EXACT [MP:0012532] -xref: BTO:0006242 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: EHDAA2:0001968 xref: EHDAA:1494 xref: EHDAA:350 @@ -2818,7 +2816,6 @@ xref: BILS:0000106 xref: EFO:0001322 xref: EHDAA:27 xref: FBdv:00005288 -xref: IDOMAL:0000302 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: NCIT:C12601 xref: PdumDv:0000100 xref: VHOG:0000745 @@ -4994,7 +4991,6 @@ property_value: taxon_notes "In humans it is a tendon-like structure that has de id: UBERON:0000353 name: parenchyma def: "Functional part of an organ in the body. This is in contrast to the stroma, which refers to the structural tissue of organs, being exactly, connective tissues." [Wikipedia:Parenchyma] -xref: BTO:0001539 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: EHDAA:3015 xref: EHDAA:3905 xref: EHDAA:3999 @@ -6934,7 +6930,6 @@ xref: EV:0100000 xref: FMA:7149 xref: galen:AnatomicalSystem xref: HAO:0000011 -xref: IDOMAL:0002460 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: MA:0000003 xref: NCIT:C12919 xref: SCTID:278195005 @@ -7250,7 +7245,6 @@ name: anatomical cluster def: "Anatomical group whose component anatomical structures lie in close proximity to each other." [FBbt:00007277] subset: common_anatomy subset: upper_level -xref: IDOMAL:0002461 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: VHOG:0001737 is_a: UBERON:0034923 ! disconnected anatomical group relationship: present_in_taxon NCBITaxon:33090 ! Viridiplantae @@ -7341,7 +7335,6 @@ xref: BILA:0000054 xref: CARO:0000054 xref: EHDAA2:0003054 xref: HAO:0000054 -xref: IDOMAL:0002459 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: TAO:0001512 xref: TGMA:0001846 xref: VHOG:0001724 @@ -7980,7 +7973,6 @@ xref: EMAPA:16039 xref: FMA:69068 xref: GAID:963 xref: http://neurolex.org/wiki/Category\:Embryonic_organism -xref: IDOMAL:0000646 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: MAT:0000226 xref: MESH:D004622 xref: MIAA:0000019 @@ -35979,7 +35971,6 @@ synonym: "nucleus preopticus lateralis" RELATED LATIN [NeuroNames:381] xref: BAMS:LPO xref: BIRNLEX:1722 xref: BM:Die-Hy-LPO -xref: BTO:0006166 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: DHBA:10471 xref: EMAPA:35483 xref: FMA:62326 @@ -36605,7 +36596,6 @@ xref: BAMS:R xref: BAMS:RN xref: BIRNLEX:1478 xref: BM:MB-RN -xref: BTO:0006329 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: DHBA:12247 xref: EHDAA2:0004706 xref: EMAPA:35724 @@ -39184,7 +39174,6 @@ synonym: "nucleus praeopticus medialis" RELATED LATIN [NeuroNames:380] synonym: "nucleus preopticus medialis" RELATED LATIN [NeuroNames:380] xref: BAMS:MPO xref: BIRNLEX:706 -xref: BTO:0006167 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: DHBA:10470 xref: DMBA:15604 xref: EMAPA:35549 @@ -42499,7 +42488,6 @@ xref: FMA:72429 xref: HBA:9021 xref: MA:0001020 xref: MBA:1052 -xref: mesh:D045042 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: neuronames:504 {source="BIRNLEX:1437"} xref: UMLS:C0262306 {source="BIRNLEX:1437"} xref: Wikipedia:Pedunculopontine_tegmental_nucleus @@ -44783,7 +44771,6 @@ def: "Group of neurons situated on the ventral surface of the fornix at the leve subset: uberon_slim synonym: "organum subfornicale" RELATED LATIN [Wikipedia:Subfornical_organ] xref: BAMS:SFO -xref: BTO:0006266 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: DHBA:12104 xref: EMAPA:35830 xref: FMA:75260 @@ -45935,7 +45922,6 @@ def: "The celiac ganglia are two large irregularly shaped masses of nerve tissue subset: uberon_slim synonym: "coeliac ganglion" EXACT [FMA:77570] xref: BAMS:GCE -xref: BTO:0006296 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: EHDAA2:0000266 xref: EHDAA:8946 xref: EMAPA:19321 @@ -50333,7 +50319,6 @@ subset: vertebrate_core synonym: "vertebra bone" EXACT [] synonym: "vertebrae" EXACT OMO:0003004 [PHENOSCAPE:ad] xref: AAO:0000691 -xref: BTO:0006196 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: CALOHA:TS-2352 xref: EFO:0001371 xref: EMAPA:32740 @@ -50878,7 +50863,6 @@ xref: BAMS:LH xref: BAMS:LHA xref: BIRNLEX:4037 xref: BM:Die-Hy-HLA -xref: BTO:0006481 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: EMAPA:35480 xref: FMA:62030 xref: GAID:640 @@ -55682,7 +55666,6 @@ xref: BAMS:MEPO xref: BAMS:MnPO xref: BIRNLEX:1208 xref: BM:MPO -xref: BTO:0006168 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: DHBA:13063 xref: FMA:62323 xref: HBA:4548 @@ -57243,7 +57226,6 @@ xref: BAMS:OV xref: BAMS:SoC xref: BAMS:VOLT xref: BIRNLEX:1400 -xref: BTO:0006268 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: DHBA:12106 xref: DMBA:15582 xref: EMAPA:37742 {source="MA:th"} @@ -57758,7 +57740,6 @@ xref: BAMS:P xref: BIRNLEX:1464 xref: BM:CST xref: BM:Me-PyT -xref: BTO:0006132 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: DHBA:12776 xref: DMBA:17756 xref: EMAPA:36600 @@ -58012,7 +57993,6 @@ synonym: "tractus rubrospinalis" RELATED LATIN [Wikipedia:Rubrospinal_tract] xref: BAMS:rs xref: BAMS:rust xref: BIRNLEX:1476 -xref: BTO:0006159 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: DHBA:12782 xref: DMBA:17792 xref: FMA:72640 @@ -58924,7 +58904,6 @@ synonym: "lateral occipitotemporal gyrus (heimer-83)" EXACT [] xref: BAMS:ITG xref: BIRNLEX:1577 xref: BM:Tel-ITG -xref: BTO:0006175 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: DHBA:12142 xref: FMA:61907 xref: HBA:4147 @@ -58950,7 +58929,6 @@ synonym: "tractus olivocerebellaris" RELATED LATIN [NeuroNames:804] xref: BAMS:oc xref: BAMS:oct xref: BIRNLEX:1579 -xref: BTO:0006157 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: DHBA:12747 xref: FMA:72638 xref: MBA:404 @@ -59402,7 +59380,6 @@ synonym: "gyrus temporalis superior" RELATED LATIN [Wikipedia:Superior_temporal_ xref: BAMS:STG xref: BIRNLEX:1648 xref: BM:Tel-STG -xref: BTO:0006177 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: DHBA:12140 xref: EFO:0001944 xref: FMA:61905 @@ -59454,7 +59431,6 @@ synonym: "medial temporal gyrus" RELATED [Wikipedia:Middle_temporal_gyrus] synonym: "middle (medial) temporal gyrus" RELATED [BAMS:MTG] xref: BAMS:MTG xref: BIRNLEX:1653 -xref: BTO:0006176 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: DHBA:12141 xref: EFO:0002466 xref: FMA:61906 @@ -65477,7 +65453,6 @@ synonym: "olfactory placodes" EXACT OMO:0003004 [] synonym: "placoda nasalis" EXACT LATIN [] synonym: "placoda olfactoria" EXACT LATIN [] xref: AAO:0011076 -xref: BTO:0006222 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: EFO:0003420 xref: EHDAA2:0001232 xref: EHDAA:1504 @@ -65638,7 +65613,6 @@ synonym: "epitrichium" RELATED [MP:0013530] synonym: "EVL" RELATED [ZFA:0001185] synonym: "periderm" RELATED [] synonym: "skin periderm" EXACT [EHDAA2:0001846] -xref: BTO:0003377 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: EHDAA2:0001846 xref: EHDAA:6538 xref: FMA:295662 @@ -65748,7 +65722,6 @@ synonym: "archinephric duct" RELATED [VHOG:0000082] synonym: "ductus pronephricus" RELATED LATIN [Wikipedia:Pronephric_duct] synonym: "pronephric ducts" RELATED OMO:0003004 [ZFA:0000150] xref: AAO:0011088 -xref: BTO:0005991 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: NCIT:C34279 xref: SCTID:361406002 xref: TAO:0000150 @@ -66173,7 +66146,6 @@ synonym: "Leydig's duct" RELATED [Wikipedia:Wolffian_duct] synonym: "renal duct" RELATED [] synonym: "Wolffian duct" EXACT [GOC:yaf, Wikipedia:Wolffian_duct, ZFA:0000546] xref: AAO:0000637 -xref: BTO:0005990 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: EHDAA2:0001243 xref: EHDAA:1590 xref: EMAPA:16577 @@ -66579,7 +66551,6 @@ synonym: "sclerotomes" EXACT OMO:0003004 [TAO:0001080] synonym: "sclerotomus" RELATED LATIN [Wikipedia:Sclerotome] xref: AAO:0010571 xref: AEO:0000212 -xref: BTO:0006255 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: EHDAA2:0003439 xref: EMAPA:31159 xref: FMA:295652 @@ -76196,7 +76167,6 @@ synonym: "floor of mouth" EXACT [FMA:86592] synonym: "floor of oval cavity" EXACT [] synonym: "floor of the oval cavity" EXACT [] synonym: "sublingual region" NARROW [GAID:1283] -xref: BTO:0006184 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: CALOHA:TS-2207 xref: EFO:0001923 xref: EMAPA:37911 {source="MA:th"} @@ -76367,7 +76337,6 @@ comment: Design pattern notes: check whether this fits the foramen design patter subset: pheno_slim subset: vertebrate_core xref: AAO:0010826 -xref: BTO:0006035 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: EMAPA:37868 {source="MA:th"} xref: FMA:75306 xref: GAID:228 @@ -79015,7 +78984,6 @@ synonym: "choroid plexus epithelial tissue" EXACT [OBOL:automatic] synonym: "epithelial tissue of chorioid plexus of cerebral hemisphere" EXACT [OBOL:automatic] synonym: "epithelial tissue of choroid plexus" EXACT [OBOL:automatic] synonym: "epithelium of choroid plexus" EXACT [FMA:242811] -xref: BTO:0006008 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: EMAPA:36608 xref: FMA:242811 xref: MA:0000824 @@ -79435,7 +79403,6 @@ synonym: "gland of reproductive system" EXACT [OBOL:automatic] synonym: "reproductive gland" EXACT [MA:0001751] synonym: "reproductive system gland" EXACT [OBOL:automatic] synonym: "sex gland" EXACT [MP:0000653] -xref: BTO:0006162 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: MA:0001751 intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0000990 ! reproductive system @@ -80677,7 +80644,6 @@ synonym: "epimere mesoderm" RELATED [] synonym: "mesenchyma dermatomiale" RELATED LATIN [Wikipedia:Dermatomal_mesenchyme] xref: AAO:0011028 xref: AEO:0001017 -xref: BTO:0006248 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: EHDAA2_RETIRED:0003428 xref: EHDAA:1719 xref: EHDAA:1725 @@ -89537,7 +89503,6 @@ synonym: "otic region" RELATED [] synonym: "periotic" RELATED [] synonym: "periotic capsule" RELATED [VHOG:0000854] xref: AAO:0010143 -xref: BTO:0005981 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: SCTID:361515007 xref: VHOG:0000854 is_a: UBERON:0010363 ! endochondral element @@ -101114,7 +101079,6 @@ subset: pheno_slim synonym: "circumventricular organ" EXACT [NLXANAT:20090312] synonym: "circumventricular organ of neuraxis" EXACT [FMA:84081] synonym: "CVO" EXACT OMO:0003000 [NLXANAT:20090312] -xref: BTO:0006267 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: EMAPA:35243 xref: FMA:84081 xref: MA:0002942 @@ -102882,7 +102846,6 @@ def: "Multi-tissue structure that arises from the heart rudiment and will become subset: vertebrate_core synonym: "early primitive heart tube" NARROW [EMAPA:16208] synonym: "primitive heart tube" EXACT [EMAPA:16215] -xref: BTO:0006179 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: EHDAA2:0001512 xref: EHDAA:424 xref: EHDAA:436 @@ -122848,7 +122811,6 @@ name: spinothalamic tract def: "A tract that originates from neurons in the spinal central gray and projects to various somatosensory nuclei of the thalamus. It is formed in the medulla by merger of the anterior spinothalamic tract and lateral spinothalamic tract (adapted from Braininfo.org)." [NLXANAT:1010017] xref: BAMS:spth xref: BAMS:stt -xref: BTO:0006128 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: DHBA:12789 xref: MBA:871 xref: MESH:D013133 @@ -128676,7 +128638,6 @@ synonym: "lateral line organ" BROAD [ZFA:0000243] synonym: "neuromast organ" EXACT [PHENOSCAPE:wd] synonym: "neuromasts" EXACT OMO:0003004 [ZFA:0000243] xref: AAO:0001004 -xref: BTO:0006219 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: EFO:0003513 xref: TAO:0000243 xref: ZFA:0000243 @@ -130647,7 +130608,6 @@ name: epibranchial ganglion def: "Cranial ganglion which develops from an epibranchial placode." [PMID:20133851, ZFIN:curator] comment: Epibranchial ganglia orchestrate the development of the cranial neurogenic crest synonym: "epibranchial ganglia" EXACT OMO:0003004 [ZFA:0001555] -xref: BTO:0006250 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: TAO:0001555 xref: ZFA:0001555 is_a: UBERON:0001714 {source="ZFA"} ! cranial ganglion @@ -143035,7 +142995,6 @@ def: "A cartilage element that is part of a splanchnocranium." [OBOL:automatic] subset: efo_slim synonym: "pharyngeal arch cartilages" EXACT OMO:0003004 [ZFA:0001460] synonym: "splanchnocranium cartilage" EXACT [ZFA:0001460] -xref: BTO:0006051 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: EFO:0003689 xref: TAO:0001460 xref: ZFA:0001460 @@ -149127,7 +149086,6 @@ id: UBERON:0011895 name: endomysium def: "A layer of connective tissue that ensheaths a muscle fiber and is composed mostly from reticular fibers. It also contains capillaries, nerves and lymphatics. The term cardiac skeleton is sometimes considered synonymous with endomysium, but sometimes it refers to the combination of the endomysium and perimysium." [Wikipedia:Endomysium] synonym: "fascia of muscle fiber" EXACT [FMA:9729] -xref: BTO:0006241 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: FMA:9729 xref: NCIT:C32517 xref: SCTID:91739007 @@ -149228,7 +149186,6 @@ def: "Plantaris is a vestigial structure and one of the superficial muscles of t subset: efo_slim synonym: "musculus plantaris" EXACT LATIN [] synonym: "plantaris" EXACT [FMA:22543] -xref: BTO:0006312 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: EFO:0001979 xref: EMAPA:36254 xref: FMA:22543 @@ -155131,7 +155088,6 @@ synonym: "rete mirabilia" RELATED [Wikipedia:Rete_mirabile] synonym: "rete mirabilis" RELATED [Wikipedia:Rete_mirabile] synonym: "retie mirabilia" RELATED OMO:0003004 [Wikipedia:Rete_mirabile] synonym: "wonderful net" RELATED [Wikipedia:Rete_mirabile] -xref: BTO:0006363 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: FMA:76728 xref: Wikipedia:Rete_mirabile is_a: UBERON:0002049 ! vasculature @@ -158608,7 +158564,6 @@ subset: pheno_slim synonym: "arterial blood" EXACT [FMA:83066] synonym: "blood in artery" EXACT [FMA:83066] synonym: "portion of arterial blood" EXACT [FMA:83066] -xref: BTO:0006188 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: FMA:83066 intersection_of: UBERON:0000178 ! blood intersection_of: located_in UBERON:0001637 ! artery @@ -158620,7 +158575,6 @@ def: "A blood that is part of a vein." [OBOL:automatic] synonym: "blood in vein" EXACT [FMA:83067] synonym: "portion of venous blood" EXACT [FMA:83067] synonym: "venous blood" EXACT [FMA:83067] -xref: BTO:0006187 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: FMA:83067 intersection_of: UBERON:0000178 ! blood intersection_of: located_in UBERON:0001638 ! vein @@ -165533,7 +165487,6 @@ def: "Light reflecting layer found in a variety of different types of eye." [htt subset: functional_classification synonym: "tapetal layer" EXACT [] synonym: "tapetum layer" EXACT [] -xref: BTO:0001350 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: SPD:0000343 is_a: UBERON:0000479 ! tissue relationship: has_quality PATO:0001297 ! reflectivity @@ -181789,7 +181742,6 @@ def: "One of several small clusters of chemoreceptors, baroreceptors, and suppor synonym: "aortic bodies" RELATED OMO:0003004 [Wikipedia:Aortic_body] synonym: "aortic glands" RELATED OMO:0003004 [Wikipedia:Aortic_body] synonym: "Zuckerkandl's body" RELATED [Wikipedia:Aortic_body] -xref: BTO:0006193 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: MESH:D001016 xref: NCIT:C97112 xref: SCTID:75061007 @@ -182397,7 +182349,6 @@ is_a: UBERON:0000058 ! duct [Term] id: UBERON:0035053 name: interlobular duct of salivary gland -xref: BTO:0006341 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: FMA:60053 intersection_of: UBERON:0014716 ! interlobular duct intersection_of: part_of UBERON:0001044 ! saliva-secreting gland @@ -187773,7 +187724,6 @@ name: vaginal fluid def: "Fluid that lines the vaginal walls that consists of multiple secretions that collect in the vagina from different glands." [http://www.bumc.bu.edu/sexualmedicine/physicianinformation/female-genital-anatomy/] synonym: "vaginal discharge" RELATED [] synonym: "vaginal secretion" RELATED [] -xref: BTO:0003084 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} intersection_of: UBERON:0006314 ! bodily fluid intersection_of: located_in UBERON:0000996 ! vagina @@ -191575,7 +191525,6 @@ property_value: provenance_notes "This class was sourced from an external ontolo [Term] id: UBERON:2000293 name: synencephalon -xref: BTO:0006476 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: ZFA:0000293 is_a: UBERON:0000481 ! multi-tissue structure relationship: part_of UBERON:0001894 ! diencephalon @@ -191608,7 +191557,6 @@ property_value: provenance_notes "This class was sourced from an external ontolo [Term] id: UBERON:2000298 name: vent -xref: BTO:0006431 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: ZFA:0000298 is_a: UBERON:0003102 ! surface structure 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"} @@ -191859,7 +191807,6 @@ synonym: "branchiospine" EXACT [PSPUB:0000164] synonym: "gill rakers" EXACT OMO:0003004 [TAO:0000356] synonym: "gill-raker" EXACT [TAO:0000356] synonym: "gillraker" EXACT [TAO:0000356] -xref: BTO:0002149 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: ZFA:0000356 is_a: UBERON:0008907 ! dermal bone relationship: never_in_taxon NCBITaxon:40674 {source="https://github.com/obophenotype/uberon/issues/2050"} ! Mammalia @@ -211953,7 +211900,6 @@ property_value: provenance_notes "This class was sourced from an external ontolo id: UBERON:3010489 name: muscular artery def: "Part of the external carotid which delivers blood to the mm rectus cervicis and interhyoideus posterior." [AAO:BJB] -xref: BTO:0004724 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} is_a: UBERON:0001637 ! artery relationship: part_of UBERON:0001070 ! external carotid artery relationship: supplies UBERON:3010654 ! rectus cervicis @@ -212279,7 +212225,6 @@ property_value: provenance_notes "This class was sourced from an external ontolo id: UBERON:3010586 name: vasa efferentia def: "Sperm travel through these 4 or 5 fine ducts which pass through the mesorchium from the testis to the sexual kidney." [AAO:BMZ] -xref: BTO:0002254 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} is_a: UBERON:0006946 ! efferent duct property_value: provenance_notes "This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string {source="http://purl.obolibrary.org/obo/aao.owl"} @@ -214022,7 +213967,6 @@ def: "Median fin that is located posterior to the anus." [TAO:curator] synonym: "nageoire anale" EXACT [PSPUB:0000164] synonym: "proctoptère" EXACT [PSPUB:0000136] synonym: "proctoptérygie" EXACT [PAPUB:0000142, PSPUB:0000140] -xref: BTO:0004652 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: ZFA:0001162 intersection_of: UBERON:0008897 ! fin intersection_of: has_skeleton UBERON:4000166 ! anal fin skeleton @@ -214038,7 +213982,6 @@ synonym: "tail" RELATED [VSAO:0000164] synonym: "tail fin" RELATED [VSAO:0000164] synonym: "uroptère" EXACT [PSPUB:0000135] synonym: "uroptérygie" EXACT [PSPUB:0000140] -xref: BTO:0001827 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: ZFA:0001058 intersection_of: UBERON:0008897 ! fin intersection_of: has_skeleton UBERON:4000167 ! caudal fin skeleton @@ -217038,7 +216981,6 @@ relationship: dc-contributor https://orcid.org/0000-0003-3162-7490 ! Wasila M Da id: UBERON:4300194 name: photophore def: "A light-emitting organ which appears as luminous spots on various marine animals, including fish and cephalopods." [PHENOSCAPE] {comment="https://en.wikipedia.org/wiki/Photophore"} -xref: BTO:0001477 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} is_a: UBERON:0000062 ! organ relationship: dc-contributor https://orcid.org/0000-0003-3162-7490 ! Wasila M Dahdul relationship: never_in_taxon NCBITaxon:314146 ! Euarchontoglires @@ -222816,7 +222758,6 @@ name: cerebral nuclei def: "One of three components of the cerebrum that is a composite structure of the endbrain defined on the basis of origin from the ventricular ridge of the embryonic Encephalon. It consists of the extended striatum and the extended pallidum." [neuronames:2677] comment: This was added as a more precise mapping to the Allen brain atlas (as opposed to collection of basal ganglia) synonym: "CNU" EXACT [MBA:623] -xref: BTO:0006534 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} xref: DHBA:10331 xref: HBA:4275 xref: MBA:623 @@ -223470,7 +223411,6 @@ property_value: seeAlso "https://github.com/obophenotype/uberon/issues/476" xsd: id: UBERON:8450002 name: excretory system def: "An anatomical system that eliminates waste products that arise as a result of metabolic activity." [GO:0007588] -xref: BTO:0006338 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} intersection_of: UBERON:0000467 ! anatomical system intersection_of: capable_of GO:0046903 ! secretion created_by: http://orcid.org/0000-0002-6095-8718 @@ -223882,7 +223822,6 @@ property_value: dcterms-date "2022-11-22T09:15:50Z" xsd:dateTime id: UBERON:8480040 name: ovarian fluid def: "Fish ovary secretion released with eggs." [PMID:8526977] -xref: BTO:0004569 {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0003-4423-4370"} is_a: UBERON:0006537 ! female reproductive gland secretion relationship: dc-contributor https://orcid.org/0000-0002-0819-0473 ! Paula Duek Roggli relationship: in_taxon NCBITaxon:7898 ! Actinopterygii From 9c43406067f9bc2136148fbe11146dbf138dec50 Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Wed, 6 Dec 2023 23:02:42 +0000 Subject: [PATCH 4/7] Commit generated files. Commit the imported mapping set from Biomappings and the re-generated mappings component. --- src/ontology/components/mappings.owl | 7032 ++++++++++++++--- .../mappings/biomappings-mappings.sssom.tsv | 371 + 2 files changed, 6327 insertions(+), 1076 deletions(-) create mode 100644 src/ontology/mappings/biomappings-mappings.sssom.tsv diff --git a/src/ontology/components/mappings.owl b/src/ontology/components/mappings.owl index a9df9c5fb2..431f9e5ff9 100644 --- a/src/ontology/components/mappings.owl +++ b/src/ontology/components/mappings.owl @@ -1,1078 +1,5958 @@ - - - - FBbt:00000001 - - - FBbt:00000002 - - - FBbt:00000003 - - - FBbt:00000004 - - - FBbt:00000005 - - - FBbt:00000006 - - - FBbt:00000007 - - - FBbt:00000008 - - - FBbt:00000009 - - - FBbt:00000011 - - - FBbt:00000014 - - - FBbt:00000015 - - - FBbt:00000016 - - - FBbt:00000017 - - - FBbt:00000018 - - - FBbt:00000019 - - - FBbt:00000020 - - - FBbt:00000021 - - - FBbt:00000029 - - - FBbt:00000030 - - - FBbt:00000038 - - - FBbt:00000042 - - - FBbt:00000046 - - - FBbt:00000052 - - - FBbt:00000093 - - - FBbt:00000095 - - - FBbt:00000096 - - - FBbt:00000097 - - - FBbt:00000104 - - - FBbt:00000110 - - - FBbt:00000111 - - - FBbt:00000112 - - - FBbt:00000119 - - - FBbt:00000123 - - - FBbt:00000125 - - - FBbt:00000126 - - - FBbt:00000128 - - - FBbt:00000130 - - - FBbt:00000136 - - - FBbt:00000137 - - - FBbt:00000154 - - - FBbt:00000155 - - - FBbt:00000157 - - - FBbt:00000158 - - - FBbt:00000160 - - - FBbt:00000162 - - - FBbt:00000165 - - - FBbt:00000166 - - - FBbt:00000167 - - - FBbt:00000168 - - - FBbt:00000169 - - - FBbt:00000170 - - - FBbt:00000171 - - - FBbt:00000172 - - - FBbt:00000180 - - - FBbt:00000181 - - - FBbt:00000186 - - - FBbt:00000439 - - - FBbt:00001055 - - - FBbt:00001056 - - - FBbt:00001057 - - - FBbt:00001059 - - - FBbt:00001060 - - - FBbt:00001135 - - - FBbt:00001648 - - - FBbt:00001649 - - - FBbt:00001650 - - - FBbt:00001652 - - - FBbt:00001653 - - - FBbt:00001655 - - - FBbt:00001656 - - - 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FBbt:00007248 - - - FBbt:00007276 - - - FBbt:00007277 - - - FBbt:00007278 - - - FBbt:00007280 - - - FBbt:00007284 - - - FBbt:00007285 - - - FBbt:00007288 - - - FBbt:00007289 - - - FBbt:00007330 - - - FBbt:00007331 - - - FBbt:00007373 - - - FBbt:00007410 - - - FBbt:00007424 - - - FBbt:00007474 - - - FBbt:00007692 - - - FBbt:00016022 - - - FBbt:00040003 - - - FBbt:00040005 - - - FBbt:00040007 - - - FBbt:00041000 - - - FBbt:00047153 - - - FBbt:00047166 - - - FBbt:00057001 - - - FBbt:00058291 - - - FBbt:00100152 - - - FBbt:00100153 - - - FBbt:00100313 - - - FBbt:00100314 - - - FBbt:00100315 - - - FBbt:00100316 - - - FBbt:00100317 - - - FBbt:00110636 - - - FBbt:00110746 - - - FBbt:00110811 - - - FBbt:10000000 - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + FBbt:00005157 + + + + + FBbt:00005157 + + + + FBbt:00005098 + + + + + FBbt:00005098 + + + + https://meshb.nlm.nih.gov/record/ui?ui=D007515 + + + + + https://meshb.nlm.nih.gov/record/ui?ui=D007515 + + 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orcid:0000-0002-1216-4761 +#- orcid:0000-0002-2046-6145 +#- orcid:0000-0002-2627-0696 +#- orcid:0000-0002-6601-2165 +#- orcid:0000-0003-1307-2508 +#- orcid:0000-0003-4423-4370 +#curie_map: +# AGRO: http://purl.obolibrary.org/obo/AGRO_ +# APOLLO_SV: http://purl.obolibrary.org/obo/APOLLO_SV_ +# BFO: http://purl.obolibrary.org/obo/BFO_ +# BTO: http://purl.obolibrary.org/obo/BTO_ +# CARO: http://purl.obolibrary.org/obo/CARO_ +# CHEBI: http://purl.obolibrary.org/obo/CHEBI_ +# CHMO: http://purl.obolibrary.org/obo/CHMO_ +# CIDO: http://purl.obolibrary.org/obo/CIDO_ +# CL: http://purl.obolibrary.org/obo/CL_ +# CLO: http://purl.obolibrary.org/obo/CLO_ +# DOID: http://purl.obolibrary.org/obo/DOID_ +# DRON: http://purl.obolibrary.org/obo/DRON_ +# EFO: http://www.ebi.ac.uk/efo/EFO_ +# ENVO: http://purl.obolibrary.org/obo/ENVO_ +# FMA: http://purl.org/sig/ont/fma/fma +# GO: http://purl.obolibrary.org/obo/GO_ +# HP: http://purl.obolibrary.org/obo/HP_ +# IAO: http://purl.obolibrary.org/obo/IAO_ +# IDO: http://purl.obolibrary.org/obo/IDO_ +# IDOMAL: http://purl.obolibrary.org/obo/IDOMAL_ +# MAXO: http://purl.obolibrary.org/obo/MAXO_ +# MI: http://purl.obolibrary.org/obo/MI_ +# MIAPA: http://purl.obolibrary.org/obo/MIAPA_ +# MIRO: http://purl.obolibrary.org/obo/MIRO_ +# MONDO: http://purl.obolibrary.org/obo/MONDO_ +# MPATH: http://purl.obolibrary.org/obo/MPATH_ +# NBO: http://purl.obolibrary.org/obo/NBO_ +# NCBIProtein: https://www.ncbi.nlm.nih.gov/protein/ +# NCBITaxon: http://purl.obolibrary.org/obo/NCBITaxon_ +# NCIT: http://purl.obolibrary.org/obo/NCIT_ +# OAE: http://purl.obolibrary.org/obo/OAE_ +# OBI: http://purl.obolibrary.org/obo/OBI_ +# OGG: http://purl.obolibrary.org/obo/OGG_ +# OGMS: http://purl.obolibrary.org/obo/OGMS_ +# OPMI: http://purl.obolibrary.org/obo/OPMI_ +# PATO: http://purl.obolibrary.org/obo/PATO_ +# PCO: http://purl.obolibrary.org/obo/PCO_ +# PR: http://purl.obolibrary.org/obo/PR_ +# RO: http://purl.obolibrary.org/obo/RO_ +# STATO: http://purl.obolibrary.org/obo/STATO_ +# UBERON: http://purl.obolibrary.org/obo/UBERON_ +# VO: http://purl.obolibrary.org/obo/VO_ +# agrovoc: http://aims.fao.org/aos/agrovoc/c_ +# aio: https://w3id.org/aio/ +# ccle: https://www.cbioportal.org/patient?studyId=ccle_broad_2019&caseId= +# cellosaurus: https://www.cellosaurus.org/CVCL_ +# cemo: https://biopragmatics.github.io/providers/cemo/ +# commoncoreontology: http://www.ontologyrepository.com/CommonCoreOntologies/ +# cpt: https://www.aapc.com/codes/cpt-codes/ +# cvx: https://biopragmatics.github.io/providers/cvx/ +# dc: http://purl.org/dc/elements/1.1/ +# debio: https://biopragmatics.github.io/debio/ +# depmap: https://depmap.org/portal/cell_line/ +# drugbank: http://www.drugbank.ca/drugs/ +# fplx: https://sorgerlab.github.io/famplex/ +# hgnc: https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/ +# idocovid19: http://purl.obolibrary.org/obo/COVIDO_ +# interpro: http://purl.obolibrary.org/obo/IPR_ +# ito: https://bioportal.bioontology.org/ontologies/ITO/?p=classes&conceptid=https://identifiers.org/ito:ITO_ +# kegg.pathway: https://www.kegg.jp/entry/ +# kestrelo: http://purl.obolibrary.org/obo/kestrelo_ +# mesh: https://meshb.nlm.nih.gov/record/ui?ui= +# ndfrt: https://evs.nci.nih.gov/ftp1/NDF-RT/NDF-RT.owl# +# obo: http://purl.obolibrary.org/obo/ +# oboInOwl: http://www.geneontology.org/formats/oboInOwl# +# orcid: https://orcid.org/ +# pfam: https://www.ebi.ac.uk/interpro/entry/pfam/ +# pubchem.compound: https://pubchem.ncbi.nlm.nih.gov/compound/ +# reactome: https://reactome.org/content/detail/ +# skos: http://www.w3.org/2004/02/skos/core# +# umls: http://linkedlifedata.com/resource/umls/id/ +# uniprot: https://purl.uniprot.org/uniprot/ +# uniprot.chain: http://purl.uniprot.org/annotation/ +# vido: http://purl.obolibrary.org/obo/VIDO_ +# vsmo: http://purl.obolibrary.org/obo/VSMO_ +# wikipathways: http://www.wikipathways.org/instance/ +#license: https://creativecommons.org/publicdomain/zero/1.0/ +#mapping_provider: https://github.com/biopragmatics/biomappings +#mapping_set_description: Biomappings is a repository of community curated and predicted +# equivalences and related mappings between named biological entities that are not +# available from primary sources. It's also a place where anyone can contribute curations +# of predicted mappings or their own novel mappings. +#mapping_set_id: https://w3id.org/biopragmatics/biomappings/sssom/biomappings.sssom.tsv +#mapping_set_title: Biomappings +#mapping_set_version: 0.3.7.dev0 +subject_id subject_label predicate_id predicate_modifier object_id object_label mapping_justification author_id confidence mapping_tool +IDOMAL:0000302 zygote stage skos:exactMatch UBERON:0000106 zygote stage semapv:ManualMappingCuration orcid:0000-0003-4423-4370 +IDOMAL:0000646 embryo skos:exactMatch UBERON:0000922 embryo semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.7777777777777778 mira +IDOMAL:0002421 compound eye skos:exactMatch UBERON:0000018 compound eye semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.7777777777777778 mira +IDOMAL:0002459 anatomical group skos:exactMatch UBERON:0000480 anatomical group semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.7777777777777778 mira +IDOMAL:0002460 anatomical system skos:exactMatch UBERON:0000467 anatomical system semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.7777777777777778 mira +IDOMAL:0002461 anatomical cluster skos:exactMatch UBERON:0000477 anatomical cluster semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.7777777777777778 mira +UBERON:0000017 exocrine pancreas skos:exactMatch mesh:D046790 Pancreas, Exocrine semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0000076 external ectoderm skos:exactMatch BTO:0006242 external ectoderm semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.9 generate_uberon_bto_mappings.py +UBERON:0000105 life cycle stage skos:exactMatch mesh:D008018 Life Cycle Stages semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0000120 blood brain barrier skos:exactMatch mesh:D001812 Blood-Brain Barrier semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0000127 facial nucleus skos:exactMatch mesh:D065828 Facial Nucleus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0000159 anal canal skos:exactMatch mesh:D001003 Anal Canal semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0000175 pleural effusion skos:exactMatch mesh:D010996 Pleural Effusion semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0000220 atlanto-occipital joint skos:exactMatch mesh:D001269 Atlanto-Occipital Joint semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0000353 parenchyma skos:exactMatch BTO:0001539 parenchyma semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.9 generate_uberon_bto_mappings.py +UBERON:0000387 meniscus skos:exactMatch mesh:D000072600 Meniscus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0000569 ileocecal valve skos:exactMatch mesh:D007080 Ileocecal Valve semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0000939 imaginal disc skos:exactMatch mesh:D060227 Imaginal Discs semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0001049 neural tube skos:exactMatch mesh:D054259 Neural Tube semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0001156 ascending colon skos:exactMatch mesh:D044682 Colon, Ascending semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0001157 transverse colon skos:exactMatch mesh:D044684 Colon, Transverse semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0001158 descending colon skos:exactMatch mesh:D044683 Colon, Descending semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0001347 white adipose tissue skos:exactMatch mesh:D052436 Adipose Tissue, White semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0001473 lymphatic vessel skos:exactMatch mesh:D042601 Lymphatic Vessels semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0001642 superior sagittal sinus skos:exactMatch mesh:D054063 Superior Sagittal Sinus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0001715 oculomotor nuclear complex skos:exactMatch mesh:D065838 Oculomotor Nuclear Complex semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0001806 sympathetic ganglion skos:exactMatch mesh:D005728 Ganglia, Sympathetic semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0001808 parasympathetic ganglion skos:exactMatch mesh:D005726 Ganglia, Parasympathetic semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0001823 nasal cartilage skos:exactMatch mesh:D055171 Nasal Cartilages semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0001856 semicircular duct skos:exactMatch mesh:D054776 Semicircular Ducts semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0001862 vestibular labyrinth skos:exactMatch mesh:D014722 Vestibule, Labyrinth semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0001863 scala vestibuli skos:exactMatch mesh:D054738 Scala Vestibuli semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0001883 olfactory tubercle skos:exactMatch mesh:D066208 Olfactory Tubercle semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0001907 zona incerta skos:exactMatch mesh:D065820 Zona Incerta semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0001931 lateral preoptic nucleus skos:exactMatch BTO:0006166 nucleus preopticus lateralis semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.556 https://github.com/biomappings/biomappings/blob/530a1b/scripts/generate_uberon_bto_mappings.py +UBERON:0001944 pretectal region skos:exactMatch mesh:D066250 Pretectal Region semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0001947 red nucleus skos:exactMatch BTO:0006329 red nucleus semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.9 generate_uberon_bto_mappings.py +UBERON:0001977 blood serum skos:exactMatch mesh:D044967 Serum semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0001995 fibrocartilage skos:exactMatch mesh:D051445 Fibrocartilage semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002020 gray matter skos:exactMatch mesh:D066128 Gray Matter semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002035 medial preoptic nucleus skos:exactMatch BTO:0006167 nucleus preopticus medialis semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.556 https://github.com/biomappings/biomappings/blob/530a1b/scripts/generate_uberon_bto_mappings.py +UBERON:0002043 dorsal raphe nucleus skos:exactMatch mesh:D065847 Dorsal Raphe Nucleus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002062 endocardial cushion skos:exactMatch mesh:D054089 Endocardial Cushions semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002120 pronephros skos:exactMatch mesh:D060910 Pronephros semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002128 superior olivary complex skos:exactMatch mesh:D065832 Superior Olivary Complex semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002142 pedunculopontine tegmental nucleus skos:exactMatch mesh:D045042 Pedunculopontine Tegmental Nucleus semapv:ManualMappingCuration orcid:0000-0003-4423-4370 +UBERON:0002145 interpeduncular nucleus skos:exactMatch mesh:D066268 Interpeduncular Nucleus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002152 middle cerebellar peduncle skos:exactMatch mesh:D065837 Middle Cerebellar Peduncle semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002156 nucleus raphe magnus skos:exactMatch mesh:D065846 Nucleus Raphe Magnus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002157 nucleus raphe pallidus skos:exactMatch mesh:D065848 Nucleus Raphe Pallidus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002186 bronchiole skos:exactMatch mesh:D055745 Bronchioles semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002219 subfornical organ skos:exactMatch BTO:0006266 subfornical organ semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.9 generate_uberon_bto_mappings.py +UBERON:0002236 costal cartilage skos:exactMatch mesh:D066186 Costal Cartilage semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002242 nucleus pulposus skos:exactMatch mesh:D000070614 Nucleus Pulposus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002262 celiac ganglion skos:exactMatch BTO:0006296 celiac ganglion semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.9 generate_uberon_bto_mappings.py +UBERON:0002316 white matter skos:exactMatch mesh:D066127 White Matter semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002373 palatine tonsil skos:exactMatch mesh:D014066 Palatine Tonsil semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002396 vomer skos:exactMatch mesh:D055172 Vomer semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002409 pericardial fluid skos:exactMatch mesh:D000069236 Pericardial Fluid semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002412 vertebra skos:exactMatch BTO:0006196 vertebra semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.9 generate_uberon_bto_mappings.py +UBERON:0002430 lateral hypothalamic area skos:exactMatch BTO:0006481 lateral hypothalamus semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.556 https://github.com/biomappings/biomappings/blob/530a1b/scripts/generate_uberon_bto_mappings.py +UBERON:0002469 esophagus mucosa skos:exactMatch mesh:D000071041 Esophageal Mucosa semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002493 uterine artery skos:exactMatch mesh:D055988 Uterine Artery semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002540 lateral line system skos:exactMatch mesh:D053403 Lateral Line System semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002548 larva skos:exactMatch mesh:D007814 Larva semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002600 limbic lobe skos:exactMatch mesh:D065726 Limbic Lobe semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002623 cerebral peduncle skos:exactMatch mesh:D065850 Cerebral Peduncle semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002625 median preoptic nucleus skos:exactMatch BTO:0006168 nucleus preopticus medianus semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.556 https://github.com/biomappings/biomappings/blob/530a1b/scripts/generate_uberon_bto_mappings.py +UBERON:0002631 cerebral crus skos:exactMatch mesh:D065843 Cerebral Crus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002639 midbrain reticular formation skos:exactMatch mesh:D066265 Midbrain Reticular Formation semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002682 abducens nucleus skos:exactMatch mesh:D065827 Abducens Nucleus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002684 nucleus raphe obscurus skos:exactMatch mesh:D065849 Nucleus Raphe Obscurus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002689 supraoptic crest skos:exactMatch BTO:0006268 organum vasculosum laminae terminalis semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.556 https://github.com/biomappings/biomappings/blob/530a1b/scripts/generate_uberon_bto_mappings.py +UBERON:0002707 corticospinal tract skos:exactMatch BTO:0006132 corticospinal tract semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.9 generate_uberon_bto_mappings.py +UBERON:0002714 rubrospinal tract skos:exactMatch BTO:0006159 rubrospinal tract semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.9 generate_uberon_bto_mappings.py +UBERON:0002743 basal forebrain skos:exactMatch mesh:D066187 Basal Forebrain semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002751 inferior temporal gyrus skos:exactMatch BTO:0006175 inferior temporal gyrus semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.9 generate_uberon_bto_mappings.py +UBERON:0002752 olivocerebellar tract skos:exactMatch BTO:0006157 olivocerebellar fiber system semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.556 https://github.com/biomappings/biomappings/blob/530a1b/scripts/generate_uberon_bto_mappings.py +UBERON:0002769 superior temporal gyrus skos:exactMatch BTO:0006177 superior temporal gyrus semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.9 generate_uberon_bto_mappings.py +UBERON:0002771 middle temporal gyrus skos:exactMatch BTO:0006176 middle temporal gyrus semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.9 generate_uberon_bto_mappings.py +UBERON:0002883 central amygdaloid nucleus skos:exactMatch mesh:D066274 Central Amygdaloid Nucleus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002894 olfactory cortex skos:exactMatch mesh:D066194 Olfactory Cortex semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0002932 trapezoid body skos:exactMatch mesh:D065833 Trapezoid Body semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0003023 pontine tegmentum skos:exactMatch mesh:D065821 Pontine Tegmentum semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0003044 uncinate fasciculus skos:exactMatch mesh:D000083382 Uncinate Fasciculus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0003050 olfactory placode skos:exactMatch BTO:0006222 olfactory placode semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.9 generate_uberon_bto_mappings.py +UBERON:0003055 periderm skos:exactMatch BTO:0003377 periderm semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.9 generate_uberon_bto_mappings.py +UBERON:0003060 pronephric duct skos:exactMatch BTO:0005991 pronephric duct semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.9 generate_uberon_bto_mappings.py +UBERON:0003074 mesonephric duct skos:exactMatch BTO:0005990 mesonephric duct semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.9 generate_uberon_bto_mappings.py +UBERON:0003075 neural plate skos:exactMatch mesh:D054258 Neural Plate semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0003089 sclerotome skos:exactMatch BTO:0006255 sclerotome semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.9 generate_uberon_bto_mappings.py +UBERON:0003143 pupa skos:exactMatch mesh:D011679 Pupa semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0003209 blood nerve barrier skos:exactMatch mesh:D049428 Blood-Nerve Barrier semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0003460 arm bone skos:exactMatch mesh:D050280 Arm Bones semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0003462 facial bone skos:exactMatch mesh:D005147 Facial Bones semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0003679 mouth floor skos:exactMatch BTO:0006184 mouth floor semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.9 generate_uberon_bto_mappings.py +UBERON:0003687 foramen magnum skos:exactMatch BTO:0006035 foramen magnum semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.9 generate_uberon_bto_mappings.py +UBERON:0003881 CA1 field of hippocampus skos:exactMatch mesh:D056547 CA1 Region, Hippocampal semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0003882 CA2 field of hippocampus skos:exactMatch mesh:D056651 CA2 Region, Hippocampal semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0003883 CA3 field of hippocampus skos:exactMatch mesh:D056654 CA3 Region, Hippocampal semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0003911 choroid plexus epithelium skos:exactMatch BTO:0006008 choroid plexus epithelium semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.9 generate_uberon_bto_mappings.py +UBERON:0003937 reproductive gland skos:exactMatch BTO:0006162 reproductive gland semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.9 generate_uberon_bto_mappings.py +UBERON:0004016 dermatome skos:exactMatch BTO:0006248 dermatome semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.9 generate_uberon_bto_mappings.py +UBERON:0004341 primitive streak skos:exactMatch mesh:D054240 Primitive Streak semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0004637 otic capsule skos:exactMatch BTO:0005981 auditory capsule semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.556 https://github.com/biomappings/biomappings/blob/530a1b/scripts/generate_uberon_bto_mappings.py +UBERON:0004676 spinal cord lateral horn skos:exactMatch mesh:D066152 Spinal Cord Lateral Horn semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0004720 cerebellar vermis skos:exactMatch mesh:D065814 Cerebellar Vermis semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0004725 piriform cortex skos:exactMatch mesh:D066195 Piriform Cortex semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0004749 blastodisc skos:exactMatch mesh:D054239 Blastodisc semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0005290 myelencephalon skos:exactMatch mesh:D054024 Myelencephalon semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0005335 chorioallantoic membrane skos:exactMatch mesh:D049033 Chorioallantoic Membrane semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0005403 ventral striatum skos:exactMatch mesh:D066328 Ventral Striatum semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0005408 circumventricular organ skos:exactMatch BTO:0006267 circumventricular organ semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.9 generate_uberon_bto_mappings.py +UBERON:0005408 circumventricular organ skos:exactMatch mesh:D066280 Circumventricular Organs semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0005438 coronary sinus skos:exactMatch mesh:D054326 Coronary Sinus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0005456 jugular foramen skos:exactMatch mesh:D000080869 Jugular Foramina semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0005498 primitive heart tube skos:exactMatch BTO:0006179 cardiac tube semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.556 https://github.com/biomappings/biomappings/blob/530a1b/scripts/generate_uberon_bto_mappings.py +UBERON:0005631 extraembryonic membrane skos:exactMatch mesh:D005321 Extraembryonic Membranes semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0005742 adventitia skos:exactMatch mesh:D063194 Adventitia semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0005777 glomerular basement membrane skos:exactMatch mesh:D050533 Glomerular Basement Membrane semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0006083 perirhinal cortex skos:exactMatch mesh:D000071039 Perirhinal Cortex semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0006108 corticomedial nuclear complex skos:exactMatch mesh:D066276 Corticomedial Nuclear Complex semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0006444 annulus fibrosus skos:exactMatch mesh:D000070616 Annulus Fibrosus semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0006562 pharynx skos:exactMatch 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Tracts semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0008266 periodontal ligament skos:exactMatch mesh:D010513 Periodontal Ligament semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0008269 nacre skos:exactMatch mesh:D060734 Nacre semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0008826 pulmonary surfactant skos:exactMatch mesh:D011663 Pulmonary Surfactants semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0008904 neuromast skos:exactMatch BTO:0006219 neuromast semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.9 generate_uberon_bto_mappings.py +UBERON:0008974 apocrine gland skos:exactMatch mesh:D001050 Apocrine Glands semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0009127 epibranchial ganglion skos:exactMatch BTO:0006250 epibranchial ganglion semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.9 generate_uberon_bto_mappings.py +UBERON:0009755 spermaceti skos:exactMatch mesh:C009301 spermaceti semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0009757 ambergris skos:exactMatch mesh:D018648 Ambergris semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0010264 hepatopancreas skos:exactMatch mesh:D043143 Hepatopancreas semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0010361 synostosis skos:exactMatch mesh:D013580 Synostosis semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0010725 accessory navicular bone skos:exactMatch mesh:C536002 Accessory navicular bone semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0011004 pharyngeal arch cartilage skos:exactMatch BTO:0006051 pharyngeal arch cartilage semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.9 generate_uberon_bto_mappings.py +UBERON:0011119 carpometacarpal joint skos:exactMatch mesh:D052737 Carpometacarpal Joints semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0011166 patellofemoral joint skos:exactMatch mesh:D057071 Patellofemoral Joint semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0011390 pudendal nerve skos:exactMatch mesh:D060525 Pudendal Nerve semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0011895 endomysium skos:exactMatch BTO:0006241 endomysium semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.9 generate_uberon_bto_mappings.py +UBERON:0011905 plantaris skos:exactMatch BTO:0006312 plantaris muscle semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.556 https://github.com/biomappings/biomappings/blob/530a1b/scripts/generate_uberon_bto_mappings.py +UBERON:0012245 silk skos:exactMatch mesh:D047011 Silk semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0013218 rete mirabile skos:exactMatch BTO:0006363 rete mirabile semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.9 generate_uberon_bto_mappings.py +UBERON:0013422 infratemporal fossa skos:exactMatch mesh:D000080884 Infratemporal Fossa semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0013755 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+UBERON:0016884 shoulder joint skos:exactMatch mesh:D012785 Shoulder Joint semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0018144 cervical rib skos:exactMatch mesh:D057070 Cervical Rib semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0018388 cercaria skos:exactMatch mesh:D058487 Cercaria semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0034971 aortic body skos:exactMatch BTO:0006193 aortic body semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.9 generate_uberon_bto_mappings.py +UBERON:0034971 aortic body skos:exactMatch mesh:D001016 Aortic Bodies semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0035032 abdominal oblique muscle skos:exactMatch mesh:D000071596 Abdominal Oblique Muscles semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:0035050 excretory duct skos:exactMatch BTO:0006341 excretory duct semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.9 generate_uberon_bto_mappings.py +UBERON:0035618 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orcid:0000-0003-4423-4370 0.556 https://github.com/biomappings/biomappings/blob/530a1b/scripts/generate_uberon_bto_mappings.py +UBERON:4200215 suture skos:exactMatch mesh:D013537 Sutures semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +UBERON:4300194 photophore skos:exactMatch BTO:0001477 photophore semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.9 generate_uberon_bto_mappings.py +UBERON:8440012 cerebral nuclei skos:exactMatch BTO:0006534 cerebral nucleus semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.556 https://github.com/biomappings/biomappings/blob/530a1b/scripts/generate_uberon_bto_mappings.py +UBERON:8450002 excretory system skos:exactMatch BTO:0006338 excretory system semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.9 generate_uberon_bto_mappings.py +UBERON:8480040 ovarian fluid skos:exactMatch BTO:0004569 ovarian fluid semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.9 generate_uberon_bto_mappings.py +UBERON:0000104 life cycle 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Peripheral Arterial Disease semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +VO:0010896 Ssb skos:exactMatch Not UBERON:0004199 S-shaped body semapv:ManualMappingCuration orcid:0000-0003-4423-4370 +VO:0010971 SurA skos:exactMatch Not UBERON:0003823 hindlimb zeugopod semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.5209235209235209 mira +VO:0011021 CP skos:exactMatch Not UBERON:0001886 choroid plexus semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.5555555555555556 mira +VO:0011021 CP skos:exactMatch Not UBERON:0005343 cortical plate semapv:ManualMappingCuration orcid:0000-0003-4423-4370 0.5555555555555556 mira +VO:0011276 SP skos:exactMatch Not UBERON:0004035 cortical subplate semapv:ManualMappingCuration orcid:0000-0003-4423-4370 +VO:0012403 Rib skos:exactMatch Not UBERON:0002228 rib semapv:ManualMappingCuration orcid:0000-0003-4423-4370 +IDOMAL:0000443 gravid skos:exactMatch UBERON:0009097 gravid organism semapv:LexicalMatching 0.5555555555555556 mira +IDOMAL:0001253 adult stage skos:exactMatch UBERON:0000066 fully formed stage semapv:LexicalMatching 0.5555555555555556 mira +IDOMAL:0001253 adult stage skos:exactMatch UBERON:0000113 post-juvenile adult stage semapv:LexicalMatching 0.5555555555555556 mira +IDOMAL:0002126 visceral nervous system skos:exactMatch UBERON:0002410 autonomic nervous system semapv:LexicalMatching 0.5555555555555556 mira +IDOMAL:0002461 anatomical cluster skos:exactMatch UBERON:0034921 multi organ part structure semapv:LexicalMatching 0.5555555555555556 mira +UBERON:0000016 endocrine pancreas skos:exactMatch mesh:D007515 Islets of Langerhans semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0000044 dorsal root ganglion skos:exactMatch mesh:D005727 Ganglia, Spinal semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0000167 oral cavity skos:exactMatch mesh:D009055 Mouth semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0000341 throat skos:exactMatch mesh:D010614 Pharynx semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0000990 reproductive system skos:exactMatch mesh:D005835 Genitalia semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0001009 circulatory system skos:exactMatch mesh:D002319 Cardiovascular System semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0001173 biliary tree skos:exactMatch mesh:D001659 Biliary Tract semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0001268 peritoneal fluid skos:exactMatch mesh:D001202 Ascitic Fluid semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0001377 quadriceps femoris skos:exactMatch mesh:D052097 Quadriceps Muscle semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0001439 compact bone tissue skos:exactMatch mesh:D000071538 Cortical Bone semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0001555 digestive tract skos:exactMatch mesh:D041981 Gastrointestinal Tract semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0001601 extra-ocular muscle skos:exactMatch mesh:D009801 Oculomotor Muscles semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0001683 jugal bone skos:exactMatch mesh:D015050 Zygoma semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0001742 epiglottic cartilage skos:exactMatch mesh:D004825 Epiglottis semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0001797 vitreous humor skos:exactMatch mesh:D014822 Vitreous Body semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0001870 frontal cortex skos:exactMatch mesh:D005625 Frontal Lobe semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0001943 midbrain tegmentum skos:exactMatch mesh:D013681 Tegmentum Mesencephali semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0001965 substantia nigra pars compacta skos:exactMatch mesh:D065842 Pars Compacta semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0001966 substantia nigra pars reticulata skos:exactMatch mesh:D065841 Pars Reticulata semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0002072 hypodermis skos:exactMatch mesh:D040521 Subcutaneous Tissue semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0002090 postcranial axial skeleton skos:exactMatch mesh:D013131 Spine semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0002101 limb skos:exactMatch mesh:D005121 Extremities semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0002141 parvocellular oculomotor nucleus skos:exactMatch mesh:D065839 Edinger-Westphal Nucleus semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0002190 subcutaneous adipose tissue skos:exactMatch mesh:D015434 Panniculitis semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0002207 xiphoid process skos:exactMatch mesh:D014989 Xiphoid Bone semapv:LexicalMatching 0.9 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generate_uberon_mesh_mappings.py +UBERON:0002705 midline nuclear group skos:exactMatch mesh:D020644 Midline Thalamic Nuclei semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0002726 cervical spinal cord skos:exactMatch mesh:D066193 Cervical Cord semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0002754 predorsal bundle skos:exactMatch mesh:D065844 Tectospinal Fibers semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0002776 ventral nuclear group skos:exactMatch mesh:D020651 Ventral Thalamic Nuclei semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0002895 secondary olfactory cortex skos:exactMatch mesh:D018728 Entorhinal Cortex semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0002967 cingulate gyrus skos:exactMatch mesh:D006179 Gyrus Cinguli semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0003011 facial motor nucleus skos:exactMatch mesh:D065828 Facial Nucleus semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0003128 cranium skos:exactMatch mesh:D012886 Skull semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0004550 gastroesophageal sphincter skos:exactMatch mesh:D049630 Esophageal Sphincter, Lower semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0005343 cortical plate skos:exactMatch mesh:D002540 Cerebral Cortex semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0005366 olfactory lobe skos:exactMatch mesh:D066194 Olfactory Cortex semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0005902 occipital region skos:exactMatch mesh:D009778 Occipital Lobe semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0006098 basal nuclear complex skos:exactMatch mesh:D001479 Basal Ganglia semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0006514 pallidum skos:exactMatch mesh:D005917 Globus Pallidus semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0006657 glenoid fossa skos:exactMatch mesh:D061165 Glenoid Cavity semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0006692 vertebral canal skos:exactMatch mesh:D013115 Spinal Canal semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0006810 olecranon skos:exactMatch mesh:D056740 Olecranon Process semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0007251 preoptic nucleus skos:exactMatch mesh:D011301 Preoptic Area semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0007380 dermal scale skos:exactMatch mesh:D000075342 Animal Scales semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0007381 epidermal scale skos:exactMatch mesh:D000075342 Animal Scales semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0007641 trigeminal nuclear complex skos:exactMatch mesh:D014278 Trigeminal Nuclei semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0008275 carapace skos:exactMatch mesh:D060105 Animal Shells semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0008969 dental follicle skos:exactMatch mesh:D003795 Dental Sac semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0009040 deep circumflex iliac artery skos:exactMatch mesh:D007083 Iliac Artery semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0009951 main olfactory bulb skos:exactMatch mesh:D009830 Olfactory Bulb semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0011117 superior tibiofibular joint skos:exactMatch mesh:D007719 Knee Joint semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0011132 intercarpal joint skos:exactMatch mesh:D050824 Carpal Joints semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0014621 cervical spinal cord ventral horn skos:exactMatch mesh:D066151 Spinal Cord Ventral Horn semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0016435 chest wall skos:exactMatch mesh:D035441 Thoracic Wall semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0016530 parietal cortex skos:exactMatch mesh:D010296 Parietal Lobe semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0016538 temporal cortex skos:exactMatch mesh:D013702 Temporal Lobe semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:0018141 anterior perforated substance skos:exactMatch mesh:D066208 Olfactory Tubercle semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:2000006 ball skos:exactMatch mesh:D015452 Precursor B-Cell Lymphoblastic Leukemia-Lymphoma semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:2000188 corpus cerebelli skos:exactMatch mesh:D002531 Cerebellum semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:3011045 gasserian ganglion skos:exactMatch mesh:D012668 Trigeminal Ganglion semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py +UBERON:3011048 genital system skos:exactMatch mesh:D005835 Genitalia semapv:LexicalMatching 0.9 generate_uberon_mesh_mappings.py From e2b83149eaecb3c6c602dbbe49ac254b51ddffb5 Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Mon, 11 Dec 2023 21:57:27 +0000 Subject: [PATCH 5/7] Update SSSOM plugin to version 0.7.1. --- src/ontology/uberon.Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ontology/uberon.Makefile b/src/ontology/uberon.Makefile index ceeb0d8bfc..da4f6836eb 100644 --- a/src/ontology/uberon.Makefile +++ b/src/ontology/uberon.Makefile @@ -124,7 +124,7 @@ export ROBOT_PLUGINS_DIRECTORY # Make sure the SSSOM plugin for ROBOT is available. $(TMPDIR)/plugins/sssom.jar: mkdir -p $(TMPDIR)/plugins - curl -L -o $@ https://github.com/gouttegd/sssom-java/releases/download/sssom-java-0.6.2/sssom-robot-plugin-0.6.2.jar + curl -L -o $@ https://github.com/gouttegd/sssom-java/releases/download/sssom-java-0.7.1/sssom-robot-plugin-0.7.1.jar # Ditto for the specific Uberon plugin $(TMPDIR)/plugins/uberon.jar: From 46c8488375a84dd9c62c72e4f3f4f7a65da5a875 Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Tue, 12 Dec 2023 23:51:43 +0000 Subject: [PATCH 6/7] Make sure all cross-references use CURIEs. When generating the mappings component, make sure all cross-references are only ever written in CURIE form. We do that by: * using the new option --error-on-unshortenable-iris, to force the command to error out if any IRI cannot be shortened for lack of a suitable prefix declaration; * declare the "http://id.nlm.nih.gov/mesh/" prefix so that any identifier in that namespace can be shortened; * rename subject IDs that use the bogus prefix "https://meshb.nlm.nih.gov/record/ui?ui=" to force them to use the correct prefix. In the future, the last step should ideally be performed earlier in the pipeline, just after fetching the Biomappings set and saving it to the mappings directory. But this will require the "sssom-cli" tool which is not part of the ODK yet. --- src/ontology/uberon.Makefile | 4 +++- src/scripts/mappings-to-xrefs.rules | 11 +++++++++-- 2 files changed, 12 insertions(+), 3 deletions(-) diff --git a/src/ontology/uberon.Makefile b/src/ontology/uberon.Makefile index da4f6836eb..fe8fb2153d 100644 --- a/src/ontology/uberon.Makefile +++ b/src/ontology/uberon.Makefile @@ -124,7 +124,7 @@ export ROBOT_PLUGINS_DIRECTORY # Make sure the SSSOM plugin for ROBOT is available. $(TMPDIR)/plugins/sssom.jar: mkdir -p $(TMPDIR)/plugins - curl -L -o $@ https://github.com/gouttegd/sssom-java/releases/download/sssom-java-0.7.1/sssom-robot-plugin-0.7.1.jar + curl -L -o $@ https://github.com/gouttegd/sssom-java/releases/download/sssom-java-0.7.2/sssom-robot-plugin-0.7.2.jar # Ditto for the specific Uberon plugin $(TMPDIR)/plugins/uberon.jar: @@ -1380,6 +1380,7 @@ $(TMPDIR)/bridges: $(SRC) $(IMPORTDIR)/local-cl.owl $(TMPDIR)/uberon-mappings.ss sssom:inject --sssom $(TMPDIR)/uberon-mappings.sssom.tsv \ $(foreach set, $(EXTERNAL_SSSOM_SETS), --sssom $(set)) \ --ruleset $(TMPDIR)/bridges.rules \ + --exclude-rule xrefs \ --dispatch-table $(BRIDGEDIR)/bridges.dispatch && \ touch $@ @@ -1457,6 +1458,7 @@ $(COMPONENTSDIR)/mappings.owl: $(SRC) $(EXTERNAL_SSSOM_SETS) $(TMPDIR)/plugins/s $(ROBOT) sssom:inject -i $< \ $(foreach set, $(EXTERNAL_SSSOM_SETS), --sssom $(set)) \ --ruleset $(SCRIPTSDIR)/mappings-to-xrefs.rules \ + --error-on-unshortenable-iris \ --no-merge --bridge-file $@ \ --bridge-iri http://purl.obolibrary.org/obo/uberon/components/mappings.owl diff --git a/src/scripts/mappings-to-xrefs.rules b/src/scripts/mappings-to-xrefs.rules index c437fd88ad..baedfb452d 100644 --- a/src/scripts/mappings-to-xrefs.rules +++ b/src/scripts/mappings-to-xrefs.rules @@ -1,5 +1,7 @@ -prefix UBERON: -prefix oboInOwl: +prefix UBERON: +prefix oboInOwl: +prefix bogusmesh: +prefix MESH: # Make sure UBERON classes, and only UBERON classes, are on the object side subject==UBERON:* -> invert(); @@ -11,6 +13,11 @@ predicate==* -> check_object_existence(); # Ignore any mapping where the same foreign term is mapped to more than one UBERON class. !cardinality==*:1 -> stop(); +# Fix bogus MESH IRIs +subject==bogusmesh:* -> replace("subject_id", + "https://meshb.nlm.nih.gov/record/ui[?]ui=", + "http://id.nlm.nih.gov/mesh/"); + # Create the hasDbXref annotation and annotate it with a subset of the mapping metadata object==UBERON:* -> annotate_object(oboInOwl:hasDbXref, "%subject_curie", "direct:mapping_justification, From 9c02b5a4765f678b72fce37c99746bb0f4bad386 Mon Sep 17 00:00:00 2001 From: Damien Goutte-Gattat Date: Wed, 13 Dec 2023 00:03:27 +0000 Subject: [PATCH 7/7] Commit re-generated mappings component. --- src/ontology/components/mappings.owl | 732 +++++++++++++-------------- 1 file changed, 366 insertions(+), 366 deletions(-) diff --git a/src/ontology/components/mappings.owl b/src/ontology/components/mappings.owl index 431f9e5ff9..028ea7a966 100644 --- a/src/ontology/components/mappings.owl +++ b/src/ontology/components/mappings.owl @@ -74,22 +74,22 @@ - https://meshb.nlm.nih.gov/record/ui?ui=D007515 + MESH:D007515 - https://meshb.nlm.nih.gov/record/ui?ui=D007515 + MESH:D007515 https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D046790 + MESH:D046790 - https://meshb.nlm.nih.gov/record/ui?ui=D046790 + MESH:D046790 https://github.com/biopragmatics/biomappings @@ -131,12 +131,12 @@ - https://meshb.nlm.nih.gov/record/ui?ui=D005727 + MESH:D005727 - https://meshb.nlm.nih.gov/record/ui?ui=D005727 + MESH:D005727 https://github.com/biopragmatics/biomappings @@ -190,12 +190,12 @@ https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D001812 + MESH:D001812 - https://meshb.nlm.nih.gov/record/ui?ui=D001812 + MESH:D001812 https://github.com/biopragmatics/biomappings @@ -210,12 +210,12 @@ - https://meshb.nlm.nih.gov/record/ui?ui=D001003 + MESH:D001003 - https://meshb.nlm.nih.gov/record/ui?ui=D001003 + MESH:D001003 https://github.com/biopragmatics/biomappings @@ -230,22 +230,22 @@ - https://meshb.nlm.nih.gov/record/ui?ui=D009055 + MESH:D009055 - https://meshb.nlm.nih.gov/record/ui?ui=D009055 + MESH:D009055 https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D010996 + MESH:D010996 - https://meshb.nlm.nih.gov/record/ui?ui=D010996 + MESH:D010996 https://github.com/biopragmatics/biomappings @@ -269,12 +269,12 @@ - https://meshb.nlm.nih.gov/record/ui?ui=D001269 + MESH:D001269 - https://meshb.nlm.nih.gov/record/ui?ui=D001269 + MESH:D001269 https://github.com/biopragmatics/biomappings @@ -309,12 +309,12 @@ https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D000072600 + MESH:D000072600 - https://meshb.nlm.nih.gov/record/ui?ui=D000072600 + MESH:D000072600 https://github.com/biopragmatics/biomappings @@ -484,12 +484,12 @@ - https://meshb.nlm.nih.gov/record/ui?ui=D007080 + MESH:D007080 - https://meshb.nlm.nih.gov/record/ui?ui=D007080 + MESH:D007080 https://github.com/biopragmatics/biomappings @@ -604,7 +604,7 @@ FBbt:00001761 - https://meshb.nlm.nih.gov/record/ui?ui=D060227 + MESH:D060227 @@ -615,7 +615,7 @@ - https://meshb.nlm.nih.gov/record/ui?ui=D060227 + MESH:D060227 https://github.com/biopragmatics/biomappings @@ -694,7 +694,7 @@ FBbt:00004857 - https://meshb.nlm.nih.gov/record/ui?ui=D005835 + MESH:D005835 @@ -705,7 +705,7 @@ - https://meshb.nlm.nih.gov/record/ui?ui=D005835 + MESH:D005835 https://github.com/biopragmatics/biomappings @@ -764,12 +764,12 @@ - https://meshb.nlm.nih.gov/record/ui?ui=D002319 + MESH:D002319 - https://meshb.nlm.nih.gov/record/ui?ui=D002319 + MESH:D002319 https://github.com/biopragmatics/biomappings @@ -900,12 +900,12 @@ - https://meshb.nlm.nih.gov/record/ui?ui=D054259 + MESH:D054259 - https://meshb.nlm.nih.gov/record/ui?ui=D054259 + MESH:D054259 https://github.com/biopragmatics/biomappings @@ -974,45 +974,45 @@ - https://meshb.nlm.nih.gov/record/ui?ui=D044682 + MESH:D044682 - https://meshb.nlm.nih.gov/record/ui?ui=D044682 + MESH:D044682 https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D044684 + MESH:D044684 - https://meshb.nlm.nih.gov/record/ui?ui=D044684 + MESH:D044684 https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D044683 + MESH:D044683 - https://meshb.nlm.nih.gov/record/ui?ui=D044683 + MESH:D044683 https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D001659 + MESH:D001659 - https://meshb.nlm.nih.gov/record/ui?ui=D001659 + MESH:D001659 https://github.com/biopragmatics/biomappings @@ -1037,60 +1037,60 @@ https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D001202 + MESH:D001202 - https://meshb.nlm.nih.gov/record/ui?ui=D001202 + MESH:D001202 https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D052436 + MESH:D052436 - https://meshb.nlm.nih.gov/record/ui?ui=D052436 + MESH:D052436 https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D052097 + MESH:D052097 - https://meshb.nlm.nih.gov/record/ui?ui=D052097 + MESH:D052097 https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D000071538 + MESH:D000071538 - https://meshb.nlm.nih.gov/record/ui?ui=D000071538 + MESH:D000071538 https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D042601 + MESH:D042601 - https://meshb.nlm.nih.gov/record/ui?ui=D042601 + MESH:D042601 https://github.com/biopragmatics/biomappings FBbt:00003125 - https://meshb.nlm.nih.gov/record/ui?ui=D041981 + MESH:D041981 @@ -1101,155 +1101,155 @@ - https://meshb.nlm.nih.gov/record/ui?ui=D041981 + MESH:D041981 https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D009801 + MESH:D009801 - https://meshb.nlm.nih.gov/record/ui?ui=D009801 + MESH:D009801 https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D054063 + MESH:D054063 - https://meshb.nlm.nih.gov/record/ui?ui=D054063 + MESH:D054063 https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D015050 + MESH:D015050 - https://meshb.nlm.nih.gov/record/ui?ui=D015050 + MESH:D015050 https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D065838 + MESH:D065838 - https://meshb.nlm.nih.gov/record/ui?ui=D065838 + MESH:D065838 https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D004825 + MESH:D004825 - https://meshb.nlm.nih.gov/record/ui?ui=D004825 + MESH:D004825 https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D014822 + MESH:D014822 - https://meshb.nlm.nih.gov/record/ui?ui=D014822 + MESH:D014822 https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D005728 + MESH:D005728 - https://meshb.nlm.nih.gov/record/ui?ui=D005728 + MESH:D005728 https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D005726 + MESH:D005726 - https://meshb.nlm.nih.gov/record/ui?ui=D005726 + MESH:D005726 https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D055171 + MESH:D055171 - https://meshb.nlm.nih.gov/record/ui?ui=D055171 + MESH:D055171 https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D054776 + MESH:D054776 - https://meshb.nlm.nih.gov/record/ui?ui=D054776 + MESH:D054776 https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D014722 + MESH:D014722 - https://meshb.nlm.nih.gov/record/ui?ui=D014722 + MESH:D014722 https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D054738 + MESH:D054738 - https://meshb.nlm.nih.gov/record/ui?ui=D054738 + MESH:D054738 https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D005625 + MESH:D005625 - https://meshb.nlm.nih.gov/record/ui?ui=D005625 + MESH:D005625 https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D065820 + MESH:D065820 - https://meshb.nlm.nih.gov/record/ui?ui=D065820 + MESH:D065820 https://github.com/biopragmatics/biomappings @@ -1266,22 +1266,22 @@ https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D013681 + MESH:D013681 - https://meshb.nlm.nih.gov/record/ui?ui=D013681 + MESH:D013681 https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D066250 + MESH:D066250 - https://meshb.nlm.nih.gov/record/ui?ui=D066250 + MESH:D066250 https://github.com/biopragmatics/biomappings @@ -1298,54 +1298,54 @@ https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D065842 + MESH:D065842 - https://meshb.nlm.nih.gov/record/ui?ui=D065842 + MESH:D065842 https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D065841 + MESH:D065841 - https://meshb.nlm.nih.gov/record/ui?ui=D065841 + MESH:D065841 https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D044967 + MESH:D044967 - https://meshb.nlm.nih.gov/record/ui?ui=D044967 + MESH:D044967 https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D051445 + MESH:D051445 - https://meshb.nlm.nih.gov/record/ui?ui=D051445 + MESH:D051445 https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D066128 + MESH:D066128 - https://meshb.nlm.nih.gov/record/ui?ui=D066128 + MESH:D066128 https://github.com/biopragmatics/biomappings @@ -1362,12 +1362,12 @@ https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D065847 + MESH:D065847 - https://meshb.nlm.nih.gov/record/ui?ui=D065847 + MESH:D065847 https://github.com/biopragmatics/biomappings @@ -1382,161 +1382,161 @@ - https://meshb.nlm.nih.gov/record/ui?ui=D054089 + MESH:D054089 - https://meshb.nlm.nih.gov/record/ui?ui=D054089 + MESH:D054089 https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D040521 + MESH:D040521 - https://meshb.nlm.nih.gov/record/ui?ui=D040521 + MESH:D040521 https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D013131 + MESH:D013131 - https://meshb.nlm.nih.gov/record/ui?ui=D013131 + MESH:D013131 https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D005121 + MESH:D005121 - https://meshb.nlm.nih.gov/record/ui?ui=D005121 + MESH:D005121 https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D060910 + MESH:D060910 - https://meshb.nlm.nih.gov/record/ui?ui=D060910 + MESH:D060910 https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D065832 + MESH:D065832 - https://meshb.nlm.nih.gov/record/ui?ui=D065832 + MESH:D065832 https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D065839 + MESH:D065839 - https://meshb.nlm.nih.gov/record/ui?ui=D065839 + MESH:D065839 https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D045042 + MESH:D045042 - https://meshb.nlm.nih.gov/record/ui?ui=D045042 + MESH:D045042 https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D066268 + MESH:D066268 - https://meshb.nlm.nih.gov/record/ui?ui=D066268 + MESH:D066268 https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D065837 + MESH:D065837 - https://meshb.nlm.nih.gov/record/ui?ui=D065837 + MESH:D065837 https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D065846 + MESH:D065846 - https://meshb.nlm.nih.gov/record/ui?ui=D065846 + MESH:D065846 https://github.com/biopragmatics/biomappings - 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https://meshb.nlm.nih.gov/record/ui?ui=D066187 + MESH:D066187 - https://meshb.nlm.nih.gov/record/ui?ui=D066187 + MESH:D066187 https://github.com/biopragmatics/biomappings @@ -1997,12 +1997,12 @@ https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D065844 + MESH:D065844 - https://meshb.nlm.nih.gov/record/ui?ui=D065844 + MESH:D065844 https://github.com/biopragmatics/biomappings @@ -2029,75 +2029,75 @@ https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D020651 + MESH:D020651 - https://meshb.nlm.nih.gov/record/ui?ui=D020651 + MESH:D020651 https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D066274 + MESH:D066274 - https://meshb.nlm.nih.gov/record/ui?ui=D066274 + MESH:D066274 https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D018728 + MESH:D018728 - https://meshb.nlm.nih.gov/record/ui?ui=D018728 + MESH:D018728 https://github.com/biopragmatics/biomappings - 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https://meshb.nlm.nih.gov/record/ui?ui=D001016 + MESH:D001016 https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D000071596 + MESH:D000071596 - https://meshb.nlm.nih.gov/record/ui?ui=D000071596 + MESH:D000071596 https://github.com/biopragmatics/biomappings @@ -3794,34 +3794,34 @@ https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D000080886 + MESH:D000080886 - https://meshb.nlm.nih.gov/record/ui?ui=D000080886 + MESH:D000080886 https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D006722 + MESH:D006722 - https://meshb.nlm.nih.gov/record/ui?ui=D006722 + MESH:D006722 https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D000077502 + MESH:D000077502 - https://meshb.nlm.nih.gov/record/ui?ui=D000077502 + MESH:D000077502 https://github.com/biopragmatics/biomappings @@ -3838,33 +3838,33 @@ https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D009506 + MESH:D009506 - https://meshb.nlm.nih.gov/record/ui?ui=D009506 + MESH:D009506 https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D015452 + MESH:D015452 - https://meshb.nlm.nih.gov/record/ui?ui=D015452 + MESH:D015452 https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D002531 + MESH:D002531 - https://meshb.nlm.nih.gov/record/ui?ui=D002531 + MESH:D002531 https://github.com/biopragmatics/biomappings @@ -3902,23 +3902,23 @@ https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D008371 + MESH:D008371 - https://meshb.nlm.nih.gov/record/ui?ui=D008371 + MESH:D008371 https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D058729 + MESH:D058729 - https://meshb.nlm.nih.gov/record/ui?ui=D058729 + MESH:D058729 https://github.com/biopragmatics/biomappings @@ -3946,12 +3946,12 @@ https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=C067951 + MESH:C067951 - https://meshb.nlm.nih.gov/record/ui?ui=C067951 + MESH:C067951 https://github.com/biopragmatics/biomappings @@ -3979,12 +3979,12 @@ https://github.com/biopragmatics/biomappings - https://meshb.nlm.nih.gov/record/ui?ui=D013537 + MESH:D013537 - https://meshb.nlm.nih.gov/record/ui?ui=D013537 + MESH:D013537 https://github.com/biopragmatics/biomappings