Open twhetzel opened 1 month ago
OMIM:101400
mimTitles.txt
Alternative Title(s); symbol(s)
:
MACULAR DYSTROPHY, CONCENTRIC ANNULAR, FORMERLY; MCDCA, FORMERLY;; MACULAR DYSTROPHY, BENIGN CONCENTRIC ANNULAR, FORMERLY; BCAMD, FORMERLY
OMIM:101400
mimTitles.txt
Included Title(s); symbols
:
SAETHRE-CHOTZEN SYNDROME WITH EYELID ANOMALIES, INCLUDED;; BLEPHAROPHIMOSIS, EPICANTHUS INVERSUS, AND PTOSIS 3, FORMERLY, INCLUDED; BPES3, FORMERLY, INCLUDED
I saw today that Sabrina said:
Mondo, we still keep this name as a synonym because users might still search using this name, but also it is the name used in older publications.
When the PR for #118 is complete, these will be added verbatim as synonyms.
Question:
, FORMERLY
from the title in the same way we are doing for , INCLUDED
?OMIM_CLASS mondo:omim_included SYNONYM
rdfs:comment "This term has one or more labels that end with ', INCLUDED'." ;
FYI I also updated examples above, showing how this looks for 1 case of "alternative titles", and 1 case of "included/other" titles.
- Do we want to remove , FORMERLY from the title in the same way we are doing for , INCLUDED?
yes please
- Unlike "included", we do want to add these as synonyms. However, do we also want to apply any of the same treatment we are giving to "included"?
No, I think keeping them as synonyms without any other information is good. It is possible that "previous name" in OMIM is still a current name in another group. So let's keep it simple and just add the "formerly" as simple synonym with no additional information
for the 'formerly' terms in Mondo, I think we usually deprecate them (although it does not seem like this is done consistently), for example:
[Term] id: MONDO:0003208 name: breast secretory carcinoma def: "A rare, low grade invasive adenocarcinoma of the breast characterized by the presence of cells that secrete milk-like material. Morphologically, it usually appears as a circumscribed lesion, composed of cystic spaces, tubular structures, and solid areas." [NCIT:C4189] synonym: "cystic hypersecretory breast carcinoma" EXACT [NCIT:C4189] synonym: "cystic hypersecretory carcinoma of breast" EXACT [NCIT:C4189] synonym: "cystic hypersecretory carcinoma of the breast" EXACT [NCIT:C4189] synonym: "infiltrating cystic hypersecretory duct breast carcinoma" EXACT [NCIT:C4189] synonym: "invasive cystic hypersecretory duct breast carcinoma" EXACT [NCIT:C4189] synonym: "JSCB" RELATED ABBREVIATION [ONCOTREE:JSCB] synonym: "juvenile breast carcinoma" EXACT [DOID:4922, NCIT:C4189] synonym: "juvenile carcinoma (formerly)" RELATED DEPRECATED [GARD:0009408] synonym: "juvenile carcinoma of breast" EXACT [NCIT:C4189] synonym: "juvenile carcinoma of the breast" EXACT [DOID:4922, NCIT:C4189] synonym: "juvenile carcinoma of the breast (morphologic abnormality)" EXACT [DOID:4922] synonym: "juvenile secretory breast carcinoma" EXACT [NCIT:C4189] synonym: "juvenile secretory carcinoma of breast" EXACT [DOID:4922, NCIT:C4189] synonym: "juvenile secretory carcinoma of the breast" EXACT [NCIT:C4189] synonym: "SBC" RELATED ABBREVIATION [GARD:0009408] synonym: "secretory breast carcinoma" EXACT [NCIT:C4189] synonym: "secretory carcinoma" EXACT [NCIT:C4189] synonym: "secretory carcinoma of breast" EXACT [NCIT:C4189] synonym: "secretory carcinoma of the breast" EXACT [NCIT:C4189] xref: DOID:4922 {source="MONDO:equivalentTo"} xref: ICDO:8502/3 {source="NCIT:C4189"} xref: ICDO:8508/3 {source="NCIT:C4189"} xref: MEDGEN:87226 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: MESH:C537535 {source="MONDO:equivalentTo", source="DOID:4922"} xref: NCIT:C4189 {source="MONDO:equivalentTo", source="DOID:4922"} xref: ONCOTREE:JSCB {source="MONDO:equivalentTo"} xref: SCTID:41919003 {source="DOID:4922"} xref: UMLS:C0334371 {source="MEDGEN:87226", source="MONDO:equivalentTo", source="MONDO:MEDGEN"} is_a: MONDO:0004988 {source="DOID:4922", source="MONDO:Redundant", source="NCIT:C4189/inferred"} ! breast adenocarcinoma is_a: MONDO:0005590 {source="NCIT:C4189"} ! breast ductal adenocarcinoma is_a: MONDO:0006256 {source="NCIT:C4189"} ! invasive breast carcinoma property_value: seeAlso "https://rarediseases.info.nih.gov/diseases/9408/secretory-breast-carcinoma" xsd:anyURI {source="GARD:0009408"}
[Term] id: MONDO:0007042 name: Saethre-Chotzen syndrome def: "Saethre-Chotzen syndrome (SCS) is an inherited craniosynostosis syndrome characterized by unilateral or bilateral coronal synostosis, facial asymmetry, ptosis, strabismus and small ears with prominent crus, among other less common manifestations." [Orphanet:794] comment: This term's classification was reviewed in the context of the Strategic Refinement project (2023) and was determined to be excluded from the 'disorder of visual system' (MONDO:0024458) ontology branch (https://orcid.org/0000-0001-9310-0163) subset: clingen {source="MONDO:CLINGEN"} subset: gard_rare {source="GARD:7598", source="MONDO:GARD"} subset: nord_rare {source="MONDO:NORD", source="NORD:1686"} subset: ordo_disorder {source="Orphanet:794"} subset: ordo_malformation_syndrome {source="Orphanet:794"} subset: orphanet_rare {source="Orphanet:794"} subset: otar {source="MONDO:OTAR"} subset: rare synonym: "acrocephalo-syndactyly, type 3" RELATED [GARD:0007598] synonym: "acrocephalosyndactyly type 3" EXACT [Orphanet:794] synonym: "acrocephalosyndactyly type III" RELATED [DOID:14768] synonym: "acrocephalosyndactyly, type 3" RELATED [OMIM:101400] synonym: "acrocephaly, skull asymmetry, and mild syndactyly" RELATED [OMIM:101400] synonym: "ACS 3" RELATED [OMIM:101400] synonym: "ACS3" EXACT ABBREVIATION [Orphanet:794] synonym: "blepharophimosis, epicanthus inversus, and ptosis 3" RELATED DEPRECATED [OMIM:101400] synonym: "blepharophimosis, epicanthus inversus, and ptosis 3, formerly" RELATED DEPRECATED [OMIM:101400] synonym: "blepharophimosis,epicanthus inversus, and ptosis 3 (formerly)" RELATED DEPRECATED [GARD:0007598] synonym: "Chotzen syndrome" RELATED [OMIM:101400] synonym: "Saethre Chotzen Syndrome" EXACT [NORD:1686] synonym: "Saethre-Chotzen syndrome" EXACT CLINGEN_LABEL [MONDO:Lexical, OMIM:101400] synonym: "Saethre-Chotzen syndrome with eyelid anomalies" RELATED [OMIM:101400] synonym: "Saethre-Chotzen syndrome with or without eyelid anomalies" EXACT [OMIM:101400, OMIM:genemap2] synonym: "SCS" EXACT ABBREVIATION [MONDO:Lexical, OMIM:101400, Orphanet:794] synonym: "type III Acrocephalosyndactyly" EXACT [NCIT:C75034] xref: DOID:14768 {source="MONDO:equivalentTo"} xref: GARD:7598 {source="MONDO:GARD"} xref: ICD10CM:Q87.0 {source="Orphanet:794/attributed", source="Orphanet:794/ntbt", source="Orphanet:794"} xref: icd11.foundation:2109857109 {source="MONDO:equivalentTo"} xref: MEDGEN:64221 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"} xref: MESH:D000168 {source="DOID:14768", source="MONDO:directSiblingOf"} xref: NANDO:2200848 {source="MONDO:NANDO", source="https://orcid.org/0000-0003-0011-764X", source="https://orcid.org/0000-0002-0170-9172"} xref: NCIT:C75034 {source="DOID:14768", source="MONDO:equivalentTo"} xref: NORD:1686 {source="MONDO:NORD"} xref: OMIM:101400 {source="DOID:14768", source="Orphanet:794/e", source="MONDO:equivalentTo", source="Orphanet:794"} xref: Orphanet:794 {source="MONDO:equivalentTo", source="OMIM:101400"} xref: SCTID:390726000 {source="DOID:14768"} xref: SCTID:390746005 {source="DOID:14768"} xref: SCTID:83015004 {source="DOID:14768", source="MONDO:equivalentTo"} xref: UMLS:C0175699 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:64221"} is_a: MONDO:0002254 {source="https://orcid.org/0000-0001-5208-3432"} ! syndromic disease is_a: MONDO:0015338 {source="PMID:31633310"} ! syndromic craniosynostosis is_a: MONDO:0019796 {source="DOID:14768", source="NCIT:C75034", source="Orphanet:794"} ! acrocephalosyndactyly relationship: curated_content_resource https://search.clinicalgenome.org/kb/conditions/MONDO:0007042 {source="MONDO:CLINGEN"} relationship: disease_has_feature HP:0000486 ! Strabismus relationship: excluded_subClassOf MONDO:0015368 {source="https://orcid.org/0000-0001-5208-3432"} ! obsolete neuro-ophthalmological disease property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/4521" xsd:anyURI property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/4948" xsd:anyURI property_value: IAO:0000233 "https://github.com/monarch-initiative/mondo/issues/6744" xsd:anyURI property_value: seeAlso "https://rarediseases.info.nih.gov/diseases/7598/saethre-chotzen-syndrome" xsd:anyURI {source="GARD:0007598"}
for the 'formerly' terms in Mondo, I think we usually deprecate them (although it does not seem like this is done consistently),
@nicolevasilevsky in the example you added I see both 'formerly' synonyms marked as RELATED DEPRECATED
. What is not done consistently?
not all of the synonyms that have (formerly) in the name have been deprecated, is what I meant. I think it makes sense to deprecate them all, as they are no longer used.
Ok, so any value found in a source, e.g. OMIM, that would be added as a synonym to the source and therefore added to MONDO as a synonym should have:
', formerly'
or 'formerly'
removed from the synonym value RELATED
and DEPRECATED
I see now an example of where this was not done (in addition to ~duplicate synonyms, which is a different problem):
id: MONDO:0021018
name: autosomal dominant limb-girdle muscular dystrophy type 1D (DNAJB6)
...
synonym: "autosomal dominant limb-girdle muscular dystrophy caused by mutation in DNAJB6" EXACT [MONDO:design_pattern]
synonym: "autosomal dominant limb-girdle muscular dystrophy type 1D" RELATED [Orphanet:34516]
synonym: "autosomal dominant limb-girdle muscular dystrophy type 1E" RELATED DEPRECATED [DOID:0110305]
synonym: "DNAJB6 autosomal dominant limb-girdle muscular dystrophy" EXACT [MONDO:design_pattern, MONDO:patterns/disease_series_by_gene]
synonym: "LGMD1D" EXACT ABBREVIATION [Orphanet:34516]
synonym: "LGMD1D (DNAJB6)" EXACT [https://orcid.org/0000-0002-6601-2165]
synonym: "LGMD1E" RELATED DEPRECATED [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4021627/, MONDO:Lexical, OMIM:603511]
synonym: "LGMD1E (Bushby and Beckmann, 2003)" RELATED DEPRECATED [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4021627/, OMIM:603511]
synonym: "limb-girdle muscular dystrophy type 1D" RELATED [GARD:0012528]
synonym: "muscular dystrophy limb-girdle type 1D" RELATED [DOID:0110305]
synonym: "muscular dystrophy limb-girdle type 1E" RELATED DEPRECATED [DOID:0110305]
synonym: "muscular dystrophy, limb-girdle, autosomal dominant 1" EXACT [OMIM:603511, OMIM:genemap2]
synonym: "muscular dystrophy, limb-girdle, type 1D" RELATED [OMIM:603511]
**synonym: "muscular dystrophy, limb-girdle, type 1D, formerly" RELATED [OMIM:603511]**
...
Overview
There are some OMIM entries where the values in "Alternative Titles; symbols" are marked as 'formerly'. In the curation call, these values were described as previous names/labels for the OMIM entry. We should discuss how this is being modeled in "omim.owl" and if/what changes are needed to properly represent these as synonyms in Mondo.
Examples: MONDO:0006493, MONDO:0005769
Handling this will be for the next phase of the Synonym Sync project.
See https://omim.org/entry/101000?search=FORMERLY&highlight=formerly
Sub-tasks