Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Proposal for cancer reclassification #7042

Merged
merged 5 commits into from
Jan 12, 2024
Merged

Proposal for cancer reclassification #7042

Changes from 1 commit
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
c8e2a20
Proposal for cancer reclassification
sabrinatoro Dec 14, 2023
f558d16
updated logical definition
sabrinatoro Dec 14, 2023
a3fdb2a
Merge branch 'master' into 231214-test
sabrinatoro Jan 12, 2024
62ba576
Update mondo-edit.obo
sabrinatoro Jan 12, 2024
bfe7947
Update mondo-edit.obo
sabrinatoro Jan 12, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
50 changes: 30 additions & 20 deletions src/ontology/mondo-edit.obo
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -90128,7 +90128,7 @@ xref: MESH:D006965 {source="MONDO:equivalentTo", source="EFO:0000536"}
xref: NCIT:C3113 {source="MONDO:equivalentTo", source="EFO:0000536", source="MONDO:exact-label-match"}
xref: SCTID:76197007 {source="EFO:0000536"}
xref: UMLS:C0020507 {source="MONDO:notFoundInDiseaseSubset", source="NCIT:C3113"}
is_a: MONDO:0045024 {source="MONDO:Redundant", source="MONDO:cjm"} ! cancer or benign tumor
is_a: MONDO:0045024 {source="MONDO:Redundant", source="MONDO:cjm"} ! cell proliferation disorder

[Term]
id: MONDO:0005044
Expand Down Expand Up @@ -91227,7 +91227,7 @@ xref: NCIT:C3340 {source="EFO:0000662", source="MONDO:equivalentTo", source="MON
xref: SCTID:41329004 {source="EFO:0000662"}
xref: SCTID:441456002 {source="EFO:0000662", source="MONDO:equivalentTo"}
xref: UMLS:C0032584 {source="NCIT:C3340", source="MONDO:notFoundInDiseaseSubset"}
is_a: MONDO:0045024 {source="https://github.com/monarch-initiative/mondo/issues/1014"} ! cancer or benign tumor
is_a: MONDO:0045024 {source="https://github.com/monarch-initiative/mondo/issues/1014"} ! cell proliferation disorder
relationship: excluded_subClassOf MONDO:0005070 {source="EFO:0000662"} ! neoplasm

[Term]
Expand Down Expand Up @@ -169796,7 +169796,7 @@ xref: UMLS:C1860850 {source="MONDO:equivalentTo", source="MONDO:ncbi_mim2gene_me
is_a: MONDO:0002051 {source="https://orcid.org/0000-0001-9310-0163", source="https://orcid.org/0000-0003-4830-7530"} ! integumentary system disorder
is_a: MONDO:0002531 {source="https://orcid.org/0000-0001-5208-3432"} ! skin neoplasm
is_a: MONDO:0003847 {source="https://orcid.org/0000-0001-5208-3432"} ! hereditary disease
is_a: MONDO:0045024 {source="https://orcid.org/0000-0001-9310-0163"} ! cancer or benign tumor
is_a: MONDO:0045024 {source="https://orcid.org/0000-0001-9310-0163"} ! cell proliferation disorder
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6739" xsd:anyURI
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6749" xsd:anyURI

Expand Down Expand Up @@ -247024,7 +247024,7 @@ xref: UMLS:C1857941 {source="MONDO:equivalentTo", source="MONDO:ncbi_mim2gene_me
is_a: MONDO:0000426 {source="DOID:0050693", source="MONDO:Redundant"} ! autosomal dominant disease
is_a: MONDO:0002254 {source="https://orcid.org/0000-0001-5208-3432"} ! syndromic disease
is_a: MONDO:0015356 {source="https://orcid.org/0000-0001-5208-3432"} ! hereditary neoplastic syndrome
is_a: MONDO:0045024 {source="https://orcid.org/0000-0001-9310-0163"} ! cancer or benign tumor
is_a: MONDO:0045024 {source="https://orcid.org/0000-0001-9310-0163"} ! cell proliferation disorder
relationship: excluded_subClassOf MONDO:0019300 {source="Orphanet:79493"} ! obsolete rare skin tumor or hamartoma
relationship: has_characteristic HP:0000006 {source="MONDO:HPOA", source="OMIM:605041", source="Orphanet:79493"} ! Autosomal dominant inheritance
relationship: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/2584 {source="MONDO:mim2gene_medgen"} ! CYLD
Expand Down Expand Up @@ -338475,7 +338475,7 @@ xref: UMLS:C0027672 {source="MONDO:equivalentTo", source="NCIT:C3266"}
xref: UMLS:CN199448 {source="MONDO:equivalentTo"}
xref: UMLS:CN882908 {source="MONDO:equivalentTo"}
is_a: MONDO:0003847 {source="MESH:D009386", source="MONDO:Redundant", source="NCIT:C3266", source="Orphanet:140162"} ! hereditary disease
is_a: MONDO:0021058 {source="NCIT:C54705", source="https://orcid.org/0000-0002-4036-287X"} ! neoplastic syndrome
is_a: MONDO:0021074 ! precancerous condition
relationship: excluded_subClassOf MONDO:0021058 {source="MONDO:Redundant", source="NCIT:C3266"} ! neoplastic syndrome
relationship: has_characteristic MONDO:0021136 {source="MONDO:0021198"} ! rare
relationship: has_characteristic MONDO:0021152 {source="https://github.com/monarch-initiative/mondo/issues/1520", source="https://orcid.org/0000-0001-5208-3432"} ! inherited
Expand Down Expand Up @@ -346300,7 +346300,7 @@ subset: rare
xref: GARD:20130 {source="Orphanet:171895"}
xref: Orphanet:171895 {source="MONDO:equivalentTo"}
is_a: MONDO:0005570 {source="https://orcid.org/0000-0001-5208-3432", source="https://orcid.org/0000-0001-9310-0163", source="https://orcid.org/0000-0002-5002-8648"} ! hematologic disorder
is_a: MONDO:0045024 {source="https://orcid.org/0000-0001-9310-0163", source="https://orcid.org/0000-0002-1216-4761"} ! cancer or benign tumor
is_a: MONDO:0045024 {source="https://orcid.org/0000-0001-9310-0163", source="https://orcid.org/0000-0002-1216-4761"} ! cell proliferation disorder
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6739" xsd:anyURI
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6746" xsd:anyURI

Expand All @@ -346316,7 +346316,7 @@ xref: GARD:20131 {source="Orphanet:171898"}
xref: Orphanet:171898 {source="MONDO:equivalentTo"}
is_a: MONDO:0002334 {source="https://orcid.org/0000-0001-5208-3432"} ! hematopoietic and lymphoid system neoplasm
is_a: MONDO:0005570 {source="https://orcid.org/0000-0001-9310-0163", source="https://orcid.org/0000-0002-5002-8648"} ! hematologic disorder
is_a: MONDO:0045024 {source="https://orcid.org/0000-0001-9310-0163", source="https://orcid.org/0000-0002-1216-4761"} ! cancer or benign tumor
is_a: MONDO:0045024 {source="https://orcid.org/0000-0001-9310-0163", source="https://orcid.org/0000-0002-1216-4761"} ! cell proliferation disorder
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6739" xsd:anyURI
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6746" xsd:anyURI

Expand Down Expand Up @@ -347505,7 +347505,7 @@ xref: Orphanet:178528 {source="MONDO:equivalentTo"}
xref: SCTID:765136002 {source="MONDO:equivalentTo"}
is_a: MONDO:0005570 {source="https://orcid.org/0000-0001-9310-0163"} ! hematologic disorder
is_a: MONDO:0015758 {source="https://orcid.org/0000-0001-5208-3432", source="https://orcid.org/0000-0002-5002-8648"} ! primary cutaneous T-cell lymphoma
is_a: MONDO:0045024 {source="https://orcid.org/0000-0001-9310-0163", source="https://orcid.org/0000-0002-1216-4761"} ! cancer or benign tumor
is_a: MONDO:0045024 {source="https://orcid.org/0000-0001-9310-0163", source="https://orcid.org/0000-0002-1216-4761"} ! cell proliferation disorder
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6739" xsd:anyURI
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6746" xsd:anyURI
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6749" xsd:anyURI
Expand All @@ -347524,7 +347524,7 @@ xref: ICD10CM:C84.4 {source="Orphanet:178533/ntbt", source="MONDO:relatedTo", so
xref: Orphanet:178533 {source="MONDO:equivalentTo"}
is_a: MONDO:0005570 {source="https://orcid.org/0000-0001-9310-0163"} ! hematologic disorder
is_a: MONDO:0015758 {source="https://orcid.org/0000-0001-5208-3432", source="https://orcid.org/0000-0002-5002-8648"} ! primary cutaneous T-cell lymphoma
is_a: MONDO:0045024 {source="https://orcid.org/0000-0001-9310-0163", source="https://orcid.org/0000-0002-1216-4761"} ! cancer or benign tumor
is_a: MONDO:0045024 {source="https://orcid.org/0000-0001-9310-0163", source="https://orcid.org/0000-0002-1216-4761"} ! cell proliferation disorder
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6739" xsd:anyURI
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6746" xsd:anyURI
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6749" xsd:anyURI
Expand Down Expand Up @@ -366071,7 +366071,7 @@ synonym: "leptomeningeal melanomatosis" BROAD [Orphanet:252031]
xref: GARD:20739 {source="Orphanet:252031"}
xref: Orphanet:252031 {source="MONDO:equivalentTo"}
is_a: MONDO:0016743 {source="https://orcid.org/0000-0001-5208-3432", source="https://orcid.org/0000-0002-4142-7153"} ! tumor of meninges
is_a: MONDO:0045024 {source="https://orcid.org/0000-0001-9310-0163", source="https://orcid.org/0000-0002-1216-4761"} ! cancer or benign tumor
is_a: MONDO:0045024 {source="https://orcid.org/0000-0001-9310-0163", source="https://orcid.org/0000-0002-1216-4761"} ! cell proliferation disorder
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6739" xsd:anyURI
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6752" xsd:anyURI

Expand Down Expand Up @@ -372020,7 +372020,7 @@ xref: Orphanet:2677 {source="MONDO:equivalentObsolete"}
xref: UMLS:C0027828 {source="MONDO:notFoundInDiseaseSubset", source="Orphanet:2677", source="Orphanet:2677/e"}
is_a: MONDO:0021193 {source="https://orcid.org/0000-0002-4142-7153"} ! neuroepithelial neoplasm
is_a: MONDO:0021248 {source="https://orcid.org/0000-0001-5208-3432"} ! nervous system neoplasm
is_a: MONDO:0045024 {source="https://orcid.org/0000-0001-9310-0163", source="https://orcid.org/0000-0002-1216-4761"} ! cancer or benign tumor
is_a: MONDO:0045024 {source="https://orcid.org/0000-0001-9310-0163", source="https://orcid.org/0000-0002-1216-4761"} ! cell proliferation disorder
property_value: confidence "0.012345679012345512" xsd:double
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6739" xsd:anyURI
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6752" xsd:anyURI
Expand Down Expand Up @@ -381517,7 +381517,7 @@ xref: UMLS:C1866398 {source="Orphanet:2969/e", source="MONDO:notFoundInDiseaseSu
is_a: MONDO:0002051 {source="https://orcid.org/0000-0001-9310-0163", source="https://orcid.org/0000-0003-4830-7530"} ! integumentary system disorder
is_a: MONDO:0003847 {source="https://orcid.org/0000-0002-5002-8648"} ! hereditary disease
is_a: MONDO:0017623 {source="NCIT:C179915", source="https://orcid.org/0000-0001-5208-3432"} ! PTEN hamartoma tumor syndrome
is_a: MONDO:0045024 {source="https://orcid.org/0000-0001-9310-0163"} ! cancer or benign tumor
is_a: MONDO:0045024 {source="https://orcid.org/0000-0001-9310-0163"} ! cell proliferation disorder
relationship: disease_shares_features_of MONDO:0008318 ! Proteus syndrome
property_value: confidence "1.14975845410628" xsd:double
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6739" xsd:anyURI
Expand Down Expand Up @@ -391327,7 +391327,7 @@ xref: UMLS:C4509837 {source="MONDO:equivalentObsolete"}
xref: UMLS:CN204388 {source="MONDO:equivalentTo"}
is_a: MONDO:0002051 {source="https://orcid.org/0000-0001-9310-0163", source="https://orcid.org/0000-0003-4830-7530"} ! integumentary system disorder
is_a: MONDO:0003847 {source="https://orcid.org/0000-0002-5002-8648"} ! hereditary disease
is_a: MONDO:0045024 {source="https://orcid.org/0000-0001-9310-0163"} ! cancer or benign tumor
is_a: MONDO:0045024 {source="https://orcid.org/0000-0001-9310-0163"} ! cell proliferation disorder
is_a: MONDO:0100118 {source="https://orcid.org/0000-0001-5208-3432"} ! hereditary skin disorder
relationship: excluded_subClassOf MONDO:0019300 {source="Orphanet:338"} ! obsolete rare skin tumor or hamartoma
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6739" xsd:anyURI
Expand Down Expand Up @@ -394137,7 +394137,7 @@ xref: ICD10CM:C63.7 {source="Orphanet:363478", source="Orphanet:363478/btnt"}
xref: ICD10CM:C63.8 {source="Orphanet:363478", source="Orphanet:363478/btnt"}
xref: Orphanet:363478 {source="MONDO:equivalentTo"}
is_a: MONDO:0005447 {source="https://orcid.org/0000-0001-5208-3432"} ! testicular cancer
is_a: MONDO:0045024 {source="https://orcid.org/0000-0001-9310-0163", source="https://orcid.org/0000-0002-1216-4761"} ! cancer or benign tumor
is_a: MONDO:0045024 {source="https://orcid.org/0000-0001-9310-0163", source="https://orcid.org/0000-0002-1216-4761"} ! cell proliferation disorder
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6739" xsd:anyURI

[Term]
Expand Down Expand Up @@ -422075,7 +422075,7 @@ xref: Orphanet:86885 {source="MONDO:equivalentTo"}
xref: UMLS:C0079774 {source="Orphanet:86885", source="MONDO:notFoundInDiseaseSubset", source="Orphanet:86885/e"}
is_a: MONDO:0005570 {source="https://orcid.org/0000-0001-9310-0163"} ! hematologic disorder
is_a: MONDO:0015758 {source="https://orcid.org/0000-0001-5208-3432", source="https://orcid.org/0000-0002-5002-8648"} ! primary cutaneous T-cell lymphoma
is_a: MONDO:0045024 {source="https://orcid.org/0000-0001-9310-0163", source="https://orcid.org/0000-0002-1216-4761"} ! cancer or benign tumor
is_a: MONDO:0045024 {source="https://orcid.org/0000-0001-9310-0163", source="https://orcid.org/0000-0002-1216-4761"} ! cell proliferation disorder
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6739" xsd:anyURI
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6746" xsd:anyURI
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6749" xsd:anyURI
Expand Down Expand Up @@ -448731,6 +448731,7 @@ xref: NCIT:C3311 {source="MONDO:equivalentTo"}
xref: SCTID:49783001 {source="MONDO:equivalentTo"}
xref: UMLS:C0030472 {source="MONDO:equivalentTo", source="NCIT:C3311"}
is_a: MONDO:0002254 {source="NCIT:C3311"} ! syndromic disease
is_a: MONDO:0045054 {source="https://orcid.org/0000-0002-4142-7153"} ! cancer-related condition

[Term]
id: MONDO:0021074
Expand All @@ -448744,7 +448745,7 @@ synonym: "premalignant state" EXACT [NCIT:C3341]
xref: MESH:D011230 {source="MONDO:equivalentTo"}
xref: NCIT:C3341 {source="MONDO:equivalentTo"}
xref: UMLS:C0032927 {source="NCIT:C3341", source="MONDO:notFoundInDiseaseSubset"}
is_a: MONDO:0045024 {source="MONDO:Redundant"} ! cancer or benign tumor
is_a: MONDO:0045024 {source="MONDO:Redundant"} ! cell proliferation disorder

[Term]
id: MONDO:0021075
Expand Down Expand Up @@ -464889,7 +464890,7 @@ name: neoplastic disease or syndrome
def: "Either an isolated neoplasm or a syndrome with neoplasm as a major feature." [MONDO:cjm]
synonym: "neoplastic disease" RELATED []
synonym: "neoplastic disorder" RELATED []
is_a: MONDO:0045024 {source="MONDO:Redundant"} ! cancer or benign tumor
is_a: MONDO:0045024 {source="MONDO:Redundant"} ! cell proliferation disorder
union_of: MONDO:0005070 ! neoplasm
union_of: MONDO:0021058 ! neoplastic syndrome

Expand Down Expand Up @@ -503877,10 +503878,11 @@ intersection_of: has_characteristic MONDO:0021141 ! acquired

[Term]
id: MONDO:0045024
name: cancer or benign tumor
name: cell proliferation disorder
def: "Any disorder that features disrupted cell proliferation. Includes hyperplasia, neoplastic syndrome and isolated neoplasm diseases as well as precancerous conditions." [MONDO:cjm]
subset: harrisons_view
subset: rare_grouping
synonym: "cancer or benign tumor" EXACT []
synonym: "cell proliferation disorder" EXACT [https://orcid.org/0000-0002-4142-7153]
synonym: "neoplasm" NARROW [https://www.cancer.gov/publications/dictionaries/cancer-terms/def/neoplasm]
intersection_of: MONDO:0700096 ! human disease
Expand Down Expand Up @@ -504170,7 +504172,7 @@ synonym: "problem/condition, cancer related" EXACT [NCIT:C8278]
synonym: "problem/condition, cancer-related" EXACT [NCIT:C8278]
xref: NCIT:C8278 {source="MONDO:equivalentTo"}
xref: UMLS:C0280950 {source="MONDO:equivalentTo"}
is_a: MONDO:0045024 {source="MONDO:Redundant"} ! cancer or benign tumor
is_a: MONDO:0045024 {source="MONDO:Redundant"} ! cell proliferation disorder

[Term]
id: MONDO:0045055
Expand Down Expand Up @@ -518110,6 +518112,14 @@ intersection_of: MONDO:0020120 ! skeletal muscle disorder
intersection_of: has_characteristic MONDO:0021152 ! inherited
property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/5658" xsd:anyURI

[Term]
id: MONDO:0700224
name: syndromic disorder of cell proliferation
is_a: MONDO:0045024 ! cell proliferation disorder
intersection_of: MONDO:0045024 ! cell proliferation disorder
intersection_of: has_characteristic MONDO:0021127 ! has a syndromic presentation
property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-4142-7153

[Term]
id: MONDO:0700225
name: hereditary gallbladder disorder
Expand Down Expand Up @@ -528851,7 +528861,7 @@ name: cancer or benign tumor, non-human animal
def: "Cancer or benign tumor that occurs in non-human animals." [MONDO:patterns/nonhuman_disease]
is_a: MONDO:0005583 ! non-human animal disease
intersection_of: MONDO:0005583 ! non-human animal disease
intersection_of: MONDO:0700097 MONDO:0045024 ! cross-species analog cancer or benign tumor
intersection_of: MONDO:0700097 MONDO:0045024 ! cross-species analog cell proliferation disorder

[Term]
id: MONDO:1011306
Expand Down
Loading