Discuss how to handle "Alternative Titles; symbols" marked as 'formerly'

[twhetzel]

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

• Discuss how to handle at a high level
• Discuss implementation / questions
• Does , FORMERLY indicate owl:deprecated? #155
• Implementation
  • 'Formerly' titles/symbols: strip , FORMERLY #137
  • Alt. 'Formerly' titles/symbols: oio:exactSynonym & MONDO:omim_formerly #138

[joeflack4]

Examples

OMIM:153870
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

[joeflack4]

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:

• 1. Do we want to remove , FORMERLY from the title in the same way we are doing for , INCLUDED?
• 2. Unlike "included", we do want to add "formerly" cases as synonyms. However, do we also want to apply any of the same treatment we are giving to "included"? Replacing "included" below with "formerly" for these cases? i.e.:
  • i. Special annotation: OMIM_CLASS mondo:omim_included SYNONYM
  • ii. Comment entry: 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.

[sabrinatoro]

1. Do we want to remove , FORMERLY from the title in the same way we are doing for , INCLUDED?

yes please

2. 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

[nicolevasilevsky]

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 "monarch-initiative/mondo#4521" xsd:anyURI
property_value: IAO:0000233 "monarch-initiative/mondo#4948" xsd:anyURI
property_value: IAO:0000233 "monarch-initiative/mondo#6744" xsd:anyURI
property_value: seeAlso "https://rarediseases.info.nih.gov/diseases/7598/saethre-chotzen-syndrome" xsd:anyURI {source="GARD:0007598"}

[twhetzel]

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?

[nicolevasilevsky]

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.

[twhetzel]

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:

• the ', formerly' or 'formerly' removed from the synonym value
• be marked as both 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]**
...

[nicolevasilevsky]

from @sabrinatoro on Slack:

@nicole Vasilevsky it appears we are either in disagreement or we are talking about different things. (I know you are out, so hopefully you will see this "soon" 🙂 )
What should we do with the synonyms which are, at the source, "deprecated".
I think that we should keep them as exact synonyms, and only add a tag when the synonym is deprecated because it was offensive. The reason to not add a "deprecated" tag (imo) is because a deprecated synonym in one source might not be in another source, and it will be the name still used in the old literature. Also, it would be too much work to keep track of "deprecated in OMIM, but still active in Orphanet" (for example).
Your comments here (#120) mentioned that "we usually deprecate them" (ie add the annotation deprecated), "although it does not seem like this is done consistently". However, it is not clear from your comment whether you think that we should keep these tags moving forward.
Do you have an opinion on whether to tag the deprecated synonyms?
From my perspective, we should not (because of all the reasons above and because of easiness to consistently keep up to date), but I can be convinced otherwise (though I want to make sure that we have a plan for "deprecation in one source but not another).
Please let us know what you think.

[joeflack4]

Hey @nicolevasilevsky, I see the quote from Sabrina but I don't see your response?

Just throwing out there that in the synonym sync, we could theoretically only deprecate a synonym if all sources deprecate it, but I would guess that'd be a rare situation, and also not all of our sources are managed through the synonym sync (right now). Maybe will be after externally managed content is finished.

[nicolevasilevsky]

I haven't had a chance to respond yet, I'll read this more closely and respond shortly

[nicolevasilevsky]

@sabrinatoro just to clarify- the question is whether we should mark synonyms as DEPCRECATED if they are historic or no longer in use? And there is the question if a synonym is deprecated (or formerly) in OMIM but maybe it is still used by Orphanet in another terminology?

I don't really have a strong opinion on how to handle these, I am fine with whatever you all decide.

I was just making the point above that we have marked some (formerly) synonyms as DEPRECATED (because they are historic) but not all of them have been marked as such.

I think it's a good idea to make a decision about this and be consistent throughout (and be consistent if they are EXACT or RELATED).

Let me know if you have further questions for me. (Not sure if I answered everything?)

[sabrinatoro]

Thank you @nicolevasilevsky. You have answered everything.
I agree that we use DEPRECATED to indicate that a synonym is historic or no longer in use.
In this case, we have no indication (for the synonyms coming via the synonym synchronization) that the "formerly" synonyms fulfill these criteria (ie it is historic or no longer in use).

@joeflack4 and @twhetzel What I told you is still correct: bring these "formerly" synonyms as exact synonyms in Mondo.
We can reassess in the future if something changes in terms of the information we get from the sources.