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sabrinatoro committed Nov 15, 2024
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36 changes: 36 additions & 0 deletions .github/workflows/synonyms.yaml
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name: Update Synonyms Evidence

on:
# schedule:
# - cron: '0 14 * * 1'
workflow_dispatch:

jobs:
build:
runs-on: ubuntu-latest
container: obolibrary/odkfull:v1.5.3

steps:
- name: Checkout main branch
uses: actions/checkout@v3

- name: Update Synonyms evidence
run: |
cd src/ontology
make GITHUB_ACTION=true IMP=false PAT=false update-synonyms-sync -B
- name: QC to ensure that nothing other than provenance has changed
run: cd src/ontology; make GITHUB_ACTION=true IMP=false PAT=false test -B
continue-on-error: true # Allow QC to fail but continue

- name: Create Pull Request
uses: peter-evans/create-pull-request@v5
with:
branch-suffix: short-commit-hash
labels: automated
body: "Update the confirmed synonyms axiom annotation."
title: "Monthly confirmed synonyms evidence update"
base: ${{ github.head_ref }}
branch: "confirmed_synonyms_evidence"
token: ${{ secrets.GH_TOKEN }}
#reviewers: "sabrinatoro"
52 changes: 34 additions & 18 deletions src/ontology/mondo-edit.obo
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Original file line number Diff line number Diff line change
Expand Up @@ -31155,11 +31155,15 @@ property_value: IAO:0000589 "bacteriuria (disease)" xsd:string
id: MONDO:0001883
name: blue toe syndrome
def: "A condition that is caused by recurring atheroembolism in the lower extremities. It is characterized by cyanotic discoloration of the toes, usually the first, fourth, and fifth toes. Discoloration may extend to the lateral aspect of the foot. Despite the gangrene-like appearance, blue toes may respond to conservative therapy without amputation." [MESH:D018438]
synonym: "purple toe syndrome" EXACT [https://orcid.org/0000-0002-0587-4693]
synonym: "trash foot" EXACT [https://orcid.org/0000-0002-0587-4693]
synonym: "warfarin blue toe syndrome" EXACT [https://orcid.org/0000-0002-0587-4693]
xref: DOID:14121 {source="MONDO:equivalentTo"}
xref: MEDGEN:66940 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"}
xref: MESH:D018438 {source="MONDO:equivalentTo", source="DOID:14121"}
xref: UMLS:C0242645 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:66940"}
is_a: MONDO:0005568 {source="DOID:14121", source="MESH:D018438"} ! cholesterol embolism
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8049" xsd:anyURI

[Term]
id: MONDO:0001884
Expand Down Expand Up @@ -108058,9 +108062,9 @@ def: "Blocking of a blood vessel by cholesterol-rich atheromatous deposits, gene
subset: otar {source="MONDO:OTAR"}
synonym: "atheroembolism" EXACT [DOID:1461]
synonym: "cholesterol crystal embolism" EXACT [DOID:1461]
synonym: "purple toe syndrome" EXACT [DOID:1461]
synonym: "trash foot" EXACT [DOID:1461]
synonym: "warfarin blue toe syndrome" EXACT [DOID:1461]
synonym: "purple toe syndrome" NARROW [DOID:1461]
synonym: "trash foot" NARROW [DOID:1461]
synonym: "warfarin blue toe syndrome" NARROW [DOID:1461]
xref: DOID:1461 {source="EFO:0005801", source="MONDO:equivalentTo"}
xref: EFO:0005801 {source="MONDO:equivalentTo", source="MONDO:EFO"}
xref: ICD10CM:I75 {source="DOID:1461"}
Expand All @@ -108073,6 +108077,7 @@ xref: SCTID:307406004 {source="EFO:0005801", source="MONDO:equivalentTo"}
xref: UMLS:C0149649 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:57437"}
is_a: MONDO:0005385 {source="DOID:1461", source="MESH:D017700/inferred"} ! vascular disorder
relationship: disease_has_location UBERON:0001981 {source="EFO:0000784"} ! blood vessel
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8049" xsd:anyURI

[Term]
id: MONDO:0005569
Expand Down Expand Up @@ -135967,7 +135972,7 @@ intersection_of: disease_has_location UBERON:0000079 ! male reproductive system
[Term]
id: MONDO:0006846
name: malignant hypertension
def: "Severe hypertension that is characterized by rapid onset of extremely high blood pressure." [NCIT:P378]
def: "Severe hypertension that is characterized by rapid onset of extremely high blood pressure and hypertension-mediated organ damage." [https://orcid.org/0000-0002-0587-4693, NCIT:P378, PMID:30165516, PMID:38658108]
subset: otar {source="MONDO:OTAR"}
synonym: "accelerated-malignant hypertension" EXACT [PMID:26658350]
synonym: "hypertensive emergency" EXACT [Wikipedia:Hypertensive_emergency]
Expand All @@ -135984,6 +135989,7 @@ xref: SCTID:286951002 {source="DOID:10824"}
xref: SCTID:70272006 {source="EFO:1001031", source="MONDO:equivalentTo", source="DOID:10824"}
xref: UMLS:C0020540 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:9374"}
is_a: MONDO:0005044 {source="DOID:10824", source="EFO:1001031", source="MESH:D006974"} ! hypertensive disorder
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8004" xsd:anyURI

[Term]
id: MONDO:0006847
Expand Down Expand Up @@ -251631,7 +251637,7 @@ property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/
[Term]
id: MONDO:0011182
name: trimethylaminuria
def: "A rare inborn error of metabolism characterized by the presence of large amounts of trimethylamine in urine, sweat, and breath, resulting in a fishy body odor in affected individuals." [Orphanet:468726]
def: "A rare inborn error of metabolism characterized by the presence of large amounts of trimethylamine in urine, sweat, and breath, resulting in a fishy body odor in affected individuals." [https://orcid.org/0000-0002-0587-4693]
subset: clingen {source="MONDO:CLINGEN"}
subset: inferred_rare
subset: otar {source="MONDO:OTAR"}
Expand All @@ -251657,6 +251663,7 @@ relationship: curated_content_resource https://search.clinicalgenome.org/kb/cond
relationship: disease_has_basis_in_disruption_of GO:0047865 {source="OMIM:602079"} ! dimethylglycine dehydrogenase activity
relationship: excluded_from_qc_check http://purl.obolibrary.org/obo/mondo/sparql/qc/general/qc-single-child.sparql
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/3448" xsd:anyURI
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8062" xsd:anyURI
property_value: IAO:0000589 "trimethylaminuria (disease)" xsd:string

[Term]
Expand Down Expand Up @@ -296553,7 +296560,7 @@ property_value: seeAlso "https://rarediseases.info.nih.gov/diseases/2578/guanidi
[Term]
id: MONDO:0013000
name: porphyria due to ALA dehydratase deficiency
def: "Porphyria of doss or deficiency of delta-aminolevulinic acid dehydratase (DALAD) is an extremely rare form of acute hepatic porphyria characterized by neuro-visceral attacks without cutaneous manifestations." [Orphanet:100924]
def: "An extremely rare form of acute hepatic porphyria characterized by neuro-visceral attacks without cutaneous manifestations." [https://clinicalgenome.org/affiliation/40097/, https://orcid.org/0000-0002-0587-4693]
subset: clingen {source="MONDO:CLINGEN"}
subset: gard_rare {source="GARD:16937", source="MONDO:GARD"}
subset: nord_rare {source="NORD:747", source="MONDO:NORD"}
Expand All @@ -296567,12 +296574,12 @@ synonym: "ALA dehydratase deficiency pophyria" RELATED [GARD:0004445]
synonym: "ALAD deficiency" RELATED [OMIM:612740]
synonym: "ALAD Porphyria" EXACT [NORD:747]
synonym: "ALAD porphyria" EXACT [Orphanet:100924]
synonym: "ALAD-related porphyria" EXACT CLINGEN_LABEL [https://clinicalgenome.org/affiliation/40097/]
synonym: "aminolevulinate dehydratase deficiency porphyria" RELATED [GARD:0004445]
synonym: "Delta-aminolevulinate dehydratase deficiency" RELATED [OMIM:612740]
synonym: "Doss porphyria" RELATED [OMIM:612740]
synonym: "Lead poisoning, susceptibility to" RELATED [OMIM:612740]
synonym: "porphobilinogen synthase deficiency" RELATED [OMIM:612740]
synonym: "porphyria due to ALA dehydratase deficiency" EXACT CLINGEN_LABEL []
synonym: "porphyria due to ALAD deficiency" EXACT [Orphanet:100924]
synonym: "porphyria due to delta-aminolevulinate dehydratase deficiency" EXACT [Orphanet:100924]
synonym: "porphyria of Doss" EXACT [Orphanet:100924]
Expand All @@ -296590,6 +296597,7 @@ xref: UMLS:C0268328 {source="MEDGEN:78659", source="MONDO:equivalentTo", source=
is_a: MONDO:0002520 {source="MESH:C562618", source="Orphanet:100924"} ! hepatic porphyria
relationship: curated_content_resource https://search.clinicalgenome.org/kb/conditions/MONDO:0013000 {source="MONDO:CLINGEN"}
relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/395 {source="MONDO:mim2gene_medgen"} ! ALAD
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8036" xsd:anyURI
property_value: seeAlso "https://rarediseases.info.nih.gov/diseases/4445/aminolevulinate-dehydratase-deficiency-porphyria" xsd:anyURI {source="GARD:0004445"}

[Term]
Expand Down Expand Up @@ -309904,7 +309912,7 @@ subset: ordo_malformation_syndrome {source="Orphanet:280576"}
subset: orphanet_rare {source="Orphanet:280576"}
subset: otar {source="MONDO:OTAR"}
subset: rare
synonym: "BANF1-related neurodevelopmental syndrome" EXACT CLINGEN_LABEL [https://search.clinicalgenome.org/CCID\:008387]
synonym: "BANF1-related neurodevelopmental syndrome" EXACT CLINGEN_LABEL []
synonym: "Nestor-Guillermo progeria syndrome" EXACT [MONDO:Lexical, OMIM:614008]
synonym: "NGPS" EXACT ABBREVIATION [MONDO:Lexical, OMIM:614008, Orphanet:280576]
synonym: "progeria syndrome, childhood-onset, with osteolysis" RELATED [OMIM:614008]
Expand Down Expand Up @@ -337384,7 +337392,7 @@ property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/
[Term]
id: MONDO:0014606
name: intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
def: "Intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome is a rare, genetic, syndromic intellectual disability disorder characterized by craniofacial dysmorphism (microcephaly, hypotonic facies, strabismus, long and flat malar region, posteriorly rotated ears, flat nasal bridge with broad nasal tip, short philtrum, thin vermillion border, open mouth with down-turned corners, high arched palate, pointed chin), global developmental delay, intellectual disability and variable neurobehavioral abnormalities (autism spectrum disorder, aggressivness, self injury). Additional features include vision abnormalities and variable sensorineural hearing loss, as well as short stature, hypotonia and gastrointestinal manifestations (e.g. poor feeding, gastroesophageal reflux, constipation)." [Orphanet:468678]
def: "Intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome is a rare, genetic, syndromic intellectual disability disorder characterized by craniofacial dysmorphism (microcephaly, hypotonic facies, strabismus, long and flat malar region, posteriorly rotated ears, flat nasal bridge with broad nasal tip, short philtrum, thin vermillion border, open mouth with down-turned corners, high arched palate, pointed chin), global developmental delay, intellectual disability and variable neurobehavioral abnormalities (autism spectrum disorder, aggressiveness, self injury). Additional features include vision abnormalities and variable sensorineural hearing loss, as well as short stature, hypotonia and gastrointestinal manifestations (e.g. poor feeding, gastroesophageal reflux, constipation)." [Orphanet:468678]
subset: clingen {source="MONDO:CLINGEN"}
subset: gard_rare {source="GARD:13774", source="MONDO:GARD"}
subset: nord_rare {source="MONDO:NORD"}
Expand Down Expand Up @@ -337417,6 +337425,7 @@ relationship: excluded_subClassOf MONDO:0015802 {source="DOID:0070067", source="
relationship: has_characteristic HP:0000006 ! Autosomal dominant inheritance
relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/18801 {source="MONDO:mim2gene_medgen"} ! POGZ
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/5588" xsd:anyURI
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7964" xsd:anyURI

[Term]
id: MONDO:0014607
Expand Down Expand Up @@ -372488,13 +372497,14 @@ subset: rare
synonym: "body of uterus squamous cell carcinoma" EXACT [MONDO:patterns/location]
synonym: "endometrial squamous cell carcinoma" RELATED [Orphanet:213716]
xref: GARD:20479 {source="MONDO:GARD"}
xref: ICD10CM:C50 {source="MONDO:relatedTo", source="Orphanet:213716/ntbt", source="Orphanet:213716"}
xref: ICD10CM:C54.1 {source="MONDO:relatedTo", source="Orphanet:213716/ntbt", source="Orphanet:213716"}
xref: MEDGEN:1633992 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"}
xref: Orphanet:213716 {source="MONDO:equivalentTo"}
xref: UMLS:C4707099 {source="MONDO:equivalentTo", source="MEDGEN:1633992", source="MONDO:MEDGEN"}
is_a: MONDO:0004992 {source="Orphanet:213716"} ! cancer
intersection_of: MONDO:0005096 ! squamous cell carcinoma
intersection_of: disease_has_location UBERON:0009853 ! body of uterus
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7998" xsd:anyURI

[Term]
id: MONDO:0016267
Expand All @@ -372508,13 +372518,14 @@ subset: rare
synonym: "body of uterus undifferentiated carcinoma" EXACT [MONDO:patterns/location]
synonym: "endometrial undifferentiated carcinoma" RELATED [Orphanet:213721]
xref: GARD:20480 {source="MONDO:GARD"}
xref: ICD10CM:C50 {source="Orphanet:213721/ntbt", source="MONDO:relatedTo", source="Orphanet:213721"}
xref: ICD10CM:C54.9 {source="Orphanet:213721/ntbt", source="MONDO:relatedTo", source="https://orcid.org/0000-0002-7347-2434", source="Orphanet:213721"}
xref: MEDGEN:1638762 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"}
xref: Orphanet:213721 {source="MONDO:equivalentTo"}
xref: UMLS:C4707822 {source="MEDGEN:1638762", source="MONDO:equivalentTo", source="MONDO:MEDGEN"}
is_a: MONDO:0004992 {source="Orphanet:213721"} ! cancer
intersection_of: MONDO:0005617 ! undifferentiated carcinoma
intersection_of: disease_has_location UBERON:0009853 ! body of uterus
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7998" xsd:anyURI

[Term]
id: MONDO:0016268
Expand Down Expand Up @@ -393832,7 +393843,7 @@ subset: otar {source="MONDO:OTAR"}
subset: rare
synonym: "ocular albinism" EXACT [MONDO:ambiguous]
synonym: "ocular albinism (disease)" EXACT [https://orcid.org/0000-0002-6601-2165]
synonym: "XLOA" EXACT ABBREVIATION [Orphanet:54]
synonym: "XLOA" NARROW ABBREVIATION [Orphanet:54]
xref: DOID:0050633 {source="MONDO:equivalentTo"}
xref: GARD:21124 {source="MONDO:GARD"}
xref: HP:0001107 {source="MONDO:otherHierarchy"}
Expand All @@ -393849,6 +393860,7 @@ xref: UMLS:C0078917 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source=
is_a: MONDO:0018134 {source="Orphanet:284804"} ! disorder of melanin metabolism
is_a: MONDO:0024458 {source="https://orcid.org/0000-0001-9310-0163"} ! disorder of visual system
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6745" xsd:anyURI
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7900" xsd:anyURI
property_value: IAO:0000589 "ocular albinism (disease)" xsd:string

[Term]
Expand Down Expand Up @@ -493060,7 +493072,7 @@ xref: NCIT:C4757 {source="MONDO:equivalentTo"}
xref: OMIM:608026 {source="MONDO:equivalentTo"}
xref: SCTID:38481006 {source="MONDO:equivalentTo"}
xref: UMLS:C0848548 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:167258"}
is_a: MONDO:0003847 {source="https://orcid.org/0000-0001-5208-3432"} ! hereditary disease
is_a: MONDO:0005240 {source="NCIT:C4757"} ! kidney disorder
intersection_of: MONDO:0005240 ! kidney disorder
intersection_of: disease_arises_from_feature MONDO:0005044 ! hypertensive disorder
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/3600" xsd:anyURI
Expand Down Expand Up @@ -533681,12 +533693,13 @@ property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/

[Term]
id: MONDO:0100010
name: tendinopathy
def: "Disorders that are causes by overuse of tendons." [PMID:19188560]
name: disease of the tendon
def: "A disease involving the tendon." [MONDO:patterns/location_top, PMID:19188560]
subset: otar {source="MONDO:OTAR"}
synonym: "disease of tendon" EXACT [MONDO:design_pattern, MONDO:patterns/location_top]
synonym: "disease or disorder of tendon" EXACT []
synonym: "disorder of tendon" EXACT [MONDO:design_pattern, MONDO:patterns/location_top]
synonym: "tendinopathy" EXACT [https://orcid.org/0000-0002-0587-4693]
synonym: "tendon disease" EXACT [MONDO:design_pattern]
synonym: "tendon disease or disorder" EXACT [MONDO:design_pattern, MONDO:patterns/location]
xref: EFO:1001434 {source="MONDO:equivalentTo", source="MONDO:EFO"}
Expand All @@ -533701,6 +533714,7 @@ intersection_of: disease_has_location UBERON:0000043 ! tendon
property_value: http://purl.org/dc/elements/1.1/date "2018-07-17T15:51:39Z" xsd:dateTime
property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0001-5208-3432
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/5537" xsd:anyURI
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/8042" xsd:anyURI

[Term]
id: MONDO:0100011
Expand All @@ -533709,7 +533723,7 @@ def: "The chronic degeneration of a tendon without inflammation." [PMID:27469590
xref: MEDGEN:293673 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"}
xref: SCTID:724152009 {source="MONDO:equivalentTo"}
xref: UMLS:C1568363 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:293673"}
is_a: MONDO:0100010 ! tendinopathy
is_a: MONDO:0100010 ! disease of the tendon
property_value: http://purl.org/dc/elements/1.1/date "2018-07-17T15:58:43Z" xsd:dateTime
property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0001-5208-3432

Expand Down Expand Up @@ -542406,15 +542420,17 @@ property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/

[Term]
id: MONDO:0100551
name: SPATA5L1-related complex neurodevelopmental disorder with motor features and hearing loss
def: "A neurodevelopmental disorder related to biallelic variants in SPATA5L1 and characterized by a spectrum of intellectual disability, hearing loss, and motor features including spasticity, dystonia, and/or hypotonia. Other phenotypic features commonly reported with the neurodevelopmental presentation include spasticity, focal or generalized epilepsy, and microcephaly." [https://clinicalgenome.org/affiliation/40006/]
name: AFG2B-related complex neurodevelopmental disorder with motor features and hearing loss
def: "A neurodevelopmental disorder related to biallelic variants in AFG2B and characterized by a spectrum of intellectual disability, hearing loss, and motor features including spasticity, dystonia, and/or hypotonia. Other phenotypic features commonly reported with the neurodevelopmental presentation include spasticity, focal or generalized epilepsy, and microcephaly." [https://clinicalgenome.org/affiliation/40006/, https://clinicalgenome.org/affiliation/40113/]
subset: inferred_rare
subset: rare
synonym: "AFG2B-related complex neurodevelopmental disorder with motor features and hearing loss" EXACT [https://orcid.org/0000-0001-5208-3432]
synonym: "SPATA5L1-related complex neurodevelopmental disorder with motor features and hearing loss" EXACT [https://clinicalgenome.org/affiliation/40006/]
is_a: MONDO:0100038 {source="https://clinicalgenome.org/affiliation/40006/"} ! complex neurodevelopmental disorder
relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/28762 {source="https://clinicalgenome.org/affiliation/40006/"} ! AFG2B
property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0001-5208-3432
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7317" xsd:anyURI
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/7975" xsd:anyURI

[Term]
id: MONDO:0100552
Expand Down
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