Multiple synonyms with only capitalization differences

[joeflack4]

Overview

There are cases where a Mondo term has 2+ synonyms that differ only in capitalization. This shouldn't happen. We need to merge these into a single synonym declaration.

Examples

1. Capitalized word(s). No acronyms.

id: MONDO:0005764
synonym: "follicular Dendritic cell sarcoma" EXACT [DOID:6262, NCIT:C9281]
synonym: "follicular dendritic cell sarcoma" EXACT [MONDO:patterns/location]

2. Abbreviation

id: MONDO:0010916
name: polycystic kidney disease 3 with or without polycystic liver disease
synonym: "PKD3" EXACT ABBREVIATION [MONDO:Lexical, OMIM:600666]
synonym: "Pkd3" EXACT [DOID:0110860]

3. Acronym within multi-word synonym

id: MONDO:0011225
name: severe combined immunodeficiency due to DCLRE1C deficiency
synonym: "SCID due to ARTEMIS deficiency" EXACT [Orphanet:275]
synonym: "SCID due to artemis deficiency" EXACT [DOID:0090012]

Additional info

Context in which this has come up:

• Bug: Synonym Sync: Duplicate rows mondo-ingest#720
• mondo-ingest meeting notes 2024/12/16

[matentzn]

Possible QC query:

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
PREFIX MONDO: <http://purl.obolibrary.org/obo/MONDO_>

SELECT DISTINCT ?mondo_id ?label ?synonym1 ?synonym2 WHERE {
  VALUES ?synonym_type { oboInOwl:hasExactSynonym oboInOwl:hasRelatedSynonym oboInOwl:hasBroadSynonym oboInOwl:hasNarrowSynonym }
  
  ?mondo_id rdfs:subClassOf <http://purl.obolibrary.org/obo/MONDO_0000001> ;
            rdfs:label ?label ;
            ?synonym_type ?synonym1;
            ?synonym_type ?synonym2 .
  
  FILTER (lcase(str(?synonym1)) = lcase(str(?synonym2)) && ?synonym1 != ?synonym2)
}

Over 2000 hits: https://api.triplydb.com/s/qXVEsJ27J