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Synchronising OMIM Included terms correctly #625

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matentzn opened this issue Aug 5, 2024 · 1 comment
Open
1 task

Synchronising OMIM Included terms correctly #625

matentzn opened this issue Aug 5, 2024 · 1 comment
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@twhetzel

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matentzn commented Aug 5, 2024 •
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I have added some draft instructions on how OMIM-included terms should (could) be handled as part of the Mondo ingest.

https://docs.google.com/document/d/17kKU1sCZJIckEI7NsAMTWTJzdt510Rv6NnEfydr8IrI/edit

I am not saying this has to be prioritised now, but I wanted to have a strategy in place for when the day comes!

As of 5th August 2024, there is no Mondo includedOMIM metadata on any synonym, only on xrefs.

  • We need to manually review what an OMIM-included xref in Mondo actually means. None of them have "exact", "related" or similar in the metadata it seems..

Current OMIM included xrefs in Mondo

MONDO ID OMIM xref Provenance
MONDO:0800425 OMIM:617347 MONDO:includedEntryInOMIM"
MONDO:0016607 OMIM:146300 Orphanet:247685/ntbt, Orphanet:247685, MONDO:includedEntryInOMIM"
MONDO:0800371 OMIM:617047 MONDO:includedEntryInOMIM"
MONDO:0800324 OMIM:601186 MONDO:includedEntryInOMIM"
MONDO:0800352 OMIM:613660 MONDO:includedEntryInOMIM"
MONDO:0013396 OMIM:613735 Orphanet:401986/e, Orphanet:401986, MONDO:includedEntryInOMIM, DOID:0060409"
MONDO:0800410 OMIM:266300 MONDO:includedEntryInOMIM"
MONDO:0800299 OMIM:218040 MONDO:includedEntryInOMIM"
MONDO:0018581 OMIM:184850 MONDO:includedEntryInOMIM"
MONDO:0100169 OMIM:139393 MONDO:includedEntryInOMIM"
MONDO:0800382 OMIM:613820 MONDO:includedEntryInOMIM"
MONDO:0015517 OMIM:607594 Orphanet:1572/e, Orphanet:1572, MONDO:includedEntryInOMIM, DOID:12177"
MONDO:0800313 OMIM:278760 MONDO:includedEntryInOMIM"
MONDO:0800376 OMIM:618857 MONDO:includedEntryInOMIM"
MONDO:0800374 OMIM:618782 MONDO:includedEntryInOMIM"
MONDO:0800199 OMIM:105830 MONDO:includedEntryInOMIM"
MONDO:0800413 OMIM:300615 MONDO:includedEntryInOMIM"
MONDO:0800364 OMIM:614859 MONDO:includedEntryInOMIM"
MONDO:0800271 OMIM:607682 MONDO:includedEntryInOMIM"
MONDO:0100181 OMIM:603165 MONDO:includedEntryInOMIM"
MONDO:0800358 OMIM:614332 MONDO:includedEntryInOMIM"
MONDO:0019806 OMIM:607485 MONDO:includedEntryInOMIM"
MONDO:0800198 OMIM:104000 MONDO:includedEntryInOMIM"
MONDO:0800347 OMIM:612158 MONDO:includedEntryInOMIM"
MONDO:0800431 OMIM:614546 MONDO:includedEntryInOMIM"
MONDO:0800298 OMIM:214110 MONDO:includedEntryInOMIM"
MONDO:0015339 OMIM:300100 Orphanet:139399/ntbt, Orphanet:139399, MONDO:includedEntryInOMIM"
MONDO:0100537 OMIM:217090 MONDO:includedEntryInOMIM"
MONDO:0100117 OMIM:115080 MONDO:includedEntryInOMIM"
MONDO:0700074 OMIM:231680 MONDO:includedEntryInOMIM"
MONDO:0800268 OMIM:606215 MONDO:includedEntryInOMIM"
MONDO:0800344 OMIM:610713 MONDO:includedEntryInOMIM"
MONDO:0800423 OMIM:601228 MONDO:includedEntryInOMIM"
MONDO:0800321 OMIM:306955 MONDO:includedEntryInOMIM"
MONDO:0800380 OMIM:202110 MONDO:includedEntryInOMIM"
MONDO:0800414 OMIM:609135 MONDO:includedEntryInOMIM"
MONDO:0800351 OMIM:613426 MONDO:includedEntryInOMIM"
MONDO:0100528 OMIM:616863 MONDO:includedEntryInOMIM"
MONDO:0800433 OMIM:604370 MONDO:includedEntryInOMIM"
MONDO:0800359 OMIM:614500 MONDO:includedEntryInOMIM"
MONDO:0011751 OMIM:606963 MONDO:includedEntryInOMIM"
MONDO:0019674 OMIM:174200 Orphanet:93335/ntbt, Orphanet:93335, MONDO:includedEntryInOMIM"
MONDO:0800279 OMIM:611942 MONDO:includedEntryInOMIM"
MONDO:0100538 OMIM:217090 MONDO:includedEntryInOMIM"
MONDO:0800426 OMIM:614371 MONDO:includedEntryInOMIM"
MONDO:0800197 OMIM:610024 MONDO:includedEntryInOMIM"
MONDO:0800287 OMIM:614671 MONDO:includedEntryInOMIM"
MONDO:0800339 OMIM:608390 MONDO:includedEntryInOMIM"
MONDO:0800319 OMIM:303700 MONDO:includedEntryInOMIM"
MONDO:0004975 OMIM:104300 MONDO:includedEntryInOMIM, EFO:0000249, DOID:10652"
MONDO:0800322 OMIM:600880 MONDO:includedEntryInOMIM"
MONDO:0800353 OMIM:613861 MONDO:includedEntryInOMIM"
MONDO:0800329 OMIM:604403 MONDO:includedEntryInOMIM"
MONDO:0800417 OMIM:608636 MONDO:includedEntryInOMIM"
MONDO:0800201 OMIM:109200 MONDO:includedEntryInOMIM"
MONDO:0800418 OMIM:604370 MONDO:includedEntryInOMIM"
MONDO:0800419 OMIM:612555 MONDO:includedEntryInOMIM"
MONDO:0006952 OMIM:133780 Orphanet:90050/ntbt, Orphanet:90050, MONDO:includedEntryInOMIM"
MONDO:0800375 OMIM:618856 MONDO:includedEntryInOMIM"
MONDO:0800370 OMIM:616553 MONDO:includedEntryInOMIM"
MONDO:0800346 OMIM:611878 MONDO:includedEntryInOMIM"
MONDO:0100536 OMIM:106600 MONDO:includedEntryInOMIM"
MONDO:0800429 OMIM:127700 MONDO:includedEntryInOMIM"
MONDO:0100173 OMIM:601626 MONDO:includedEntryInOMIM"
MONDO:0100206 OMIM:603932 MONDO:includedEntryInOMIM"
MONDO:0800340 OMIM:608516 MONDO:includedEntryInOMIM"
MONDO:0700076 OMIM:231680 MONDO:includedEntryInOMIM"
MONDO:0016605 OMIM:241500 Orphanet:247623/ntbt, Orphanet:247623, MONDO:includedEntryInOMIM"
MONDO:0800381 OMIM:40004 MONDO:includedEntryInOMIM"
MONDO:0800196 OMIM:613093 MONDO:includedEntryInOMIM"
MONDO:0800378 OMIM:202110 MONDO:includedEntryInOMIM"
MONDO:0800320 OMIM:304020 MONDO:includedEntryInOMIM"
MONDO:0800290 OMIM:151623 MONDO:includedEntryInOMIM"
MONDO:0800427 OMIM:614371 MONDO:includedEntryInOMIM"
MONDO:0800422 OMIM:215600 MONDO:includedEntryInOMIM"
MONDO:0800312 OMIM:278150 MONDO:includedEntryInOMIM"
MONDO:0800330 OMIM:604827 MONDO:includedEntryInOMIM"
MONDO:0100535 OMIM:106600 MONDO:includedEntryInOMIM"
MONDO:0800434 OMIM:612555 MONDO:includedEntryInOMIM"
MONDO:0800365 OMIM:614887 MONDO:includedEntryInOMIM"
MONDO:0800317 OMIM:300510 MONDO:includedEntryInOMIM"
MONDO:0010918 OMIM:600669 MONDO:includedEntryInOMIM"
MONDO:0800250 OMIM:300351 MONDO:includedEntryInOMIM"
MONDO:0800363 OMIM:614844 MONDO:includedEntryInOMIM"
MONDO:0800355 OMIM:613938 MONDO:includedEntryInOMIM"
MONDO:0100201 OMIM:603932 MONDO:includedEntryInOMIM"
MONDO:0800435 OMIM:613399 MONDO:includedEntryInOMIM"
MONDO:0800356 OMIM:614091 MONDO:includedEntryInOMIM"
MONDO:0800274 OMIM:611598 MONDO:includedEntryInOMIM"
MONDO:0800408 OMIM:277000 MONDO:includedEntryInOMIM"
MONDO:0800204 OMIM:126550 MONDO:includedEntryInOMIM"
MONDO:0800337 OMIM:607665 MONDO:includedEntryInOMIM"
MONDO:0800379 OMIM:202110 MONDO:includedEntryInOMIM"
MONDO:0800377 OMIM:615830 MONDO:includedEntryInOMIM"
MONDO:0800215 OMIM:148000 MONDO:includedEntryInOMIM"
MONDO:0800428 OMIM:614371 MONDO:includedEntryInOMIM"
MONDO:0800226 OMIM:185100 MONDO:includedEntryInOMIM"
MONDO:0800328 OMIM:604232 MONDO:includedEntryInOMIM"
MONDO:0019346 OMIM:256550 Orphanet:812/ntbt, Orphanet:812, MONDO:includedEntryInOMIM"
MONDO:0800222 OMIM:176780 MONDO:includedEntryInOMIM"
MONDO:0800209 OMIM:135700 MONDO:includedEntryInOMIM"
MONDO:0800366 OMIM:615190 MONDO:includedEntryInOMIM"
MONDO:0016008 OMIM:617955 MONDO:includedEntryInOMIM"
MONDO:0100168 OMIM:135290 MONDO:includedEntryInOMIM"
MONDO:0800350 OMIM:613424 MONDO:includedEntryInOMIM"
MONDO:0800349 OMIM:613120 MONDO:includedEntryInOMIM"
MONDO:0016281 OMIM:400045 Orphanet:2138/ntbt, Orphanet:2138, MONDO:includedEntryInOMIM"
MONDO:0800224 OMIM:183090 MONDO:includedEntryInOMIM"
MONDO:0800415 OMIM:208550 MONDO:includedEntryInOMIM"
MONDO:0800323 OMIM:600919 MONDO:includedEntryInOMIM"
MONDO:0800307 OMIM:256050 MONDO:includedEntryInOMIM"
MONDO:0020311 OMIM:607785 MONDO:includedEntryInOMIM"
MONDO:0020752 OMIM:254770 MONDO:includedEntryInOMIM"
MONDO:0007264 OMIM:115080 MONDO:includedEntryInOMIM, EFO:0004278"
MONDO:0800335 OMIM:607516 MONDO:includedEntryInOMIM"
MONDO:8000019 OMIM:193007 MONDO:includedEntryInOMIM, DOID:13941"
MONDO:0800210 OMIM:137750 MONDO:includedEntryInOMIM"
MONDO:0800354 OMIM:613863 MONDO:includedEntryInOMIM"
MONDO:0800318 OMIM:300696 MONDO:includedEntryInOMIM"
MONDO:0008274 OMIM:174800 MONDO:includedEntryInOMIM"
MONDO:0800331 OMIM:605899 MONDO:includedEntryInOMIM"
MONDO:0800348 OMIM:612712 MONDO:includedEntryInOMIM"
MONDO:0800314 OMIM:278780 MONDO:includedEntryInOMIM"
MONDO:0016202 OMIM:609508 Orphanet:209867/ntbt, Orphanet:209867, MONDO:includedEntryInOMIM"
MONDO:0800430 OMIM:127700 MONDO:includedEntryInOMIM"
MONDO:0100167 OMIM:606963 MONDO:includedEntryInOMIM"
MONDO:0700251 OMIM:225060 MONDO:includedEntryInOMIM"
MONDO:0800311 OMIM:277180 MONDO:includedEntryInOMIM"
MONDO:0700073 OMIM:231680 MONDO:includedEntryInOMIM"
MONDO:0800275 OMIM:611913 MONDO:includedEntryInOMIM"
MONDO:0100098 OMIM:233910 MONDO:includedEntryInOMIM"
MONDO:0800300 OMIM:227010 MONDO:includedEntryInOMIM"
MONDO:0800200 OMIM:108120 MONDO:includedEntryInOMIM"
MONDO:0018247 OMIM:300475 Orphanet:369942/ntbt, Orphanet:369942, MONDO:includedEntryInOMIM"
MONDO:0800302 OMIM:232240 MONDO:includedEntryInOMIM"
MONDO:0100568 OMIM:607948 MONDO:includedEntryInOMIM"
MONDO:0100560 OMIM:217090 MONDO:includedEntryInOMIM"
MONDO:0100050 OMIM:601067 MONDO:includedEntryInOMIM"
MONDO:0016718 OMIM:260500 Orphanet:251899/ntbt, Orphanet:251899, MONDO:includedEntryInOMIM"
MONDO:0800424 OMIM:601228 MONDO:includedEntryInOMIM"
MONDO:0100199 OMIM:137215 MONDO:includedEntryInOMIM"
MONDO:0800305 OMIM:254450 MONDO:includedEntryInOMIM"
MONDO:0010343 OMIM:300495 MONDO:includedEntryInOMIM"
MONDO:0800412 OMIM:273750 MONDO:includedEntryInOMIM"
MONDO:0800368 OMIM:615396 MONDO:includedEntryInOMIM"
MONDO:0800357 OMIM:614323 MONDO:includedEntryInOMIM"
MONDO:0800195 OMIM:231550 MONDO:includedEntryInOMIM"
MONDO:0800383 OMIM:614175 MONDO:includedEntryInOMIM"
MONDO:0800367 OMIM:615373 MONDO:includedEntryInOMIM"
MONDO:0800326 OMIM:602093 MONDO:includedEntryInOMIM"
MONDO:0800207 OMIM:133020 MONDO:includedEntryInOMIM"
MONDO:0100231 OMIM:607507 MONDO:includedEntryInOMIM"
MONDO:0800421 OMIM:115197 MONDO:includedEntryInOMIM"
MONDO:0004129 OMIM:105580 MONDO:includedEntryInOMIM"
MONDO:0800261 OMIM:601941 MONDO:includedEntryInOMIM"
MONDO:0800369 OMIM:615528 MONDO:includedEntryInOMIM"
MONDO:0800372 OMIM:617562 MONDO:includedEntryInOMIM"
MONDO:0027652 OMIM:274270 MONDO:includedEntryInOMIM"
MONDO:0100202 OMIM:603932 MONDO:includedEntryInOMIM"
MONDO:0800416 OMIM:209850 MONDO:includedEntryInOMIM"
MONDO:0800345 OMIM:611819 MONDO:includedEntryInOMIM"
MONDO:0800296 OMIM:193220 MONDO:includedEntryInOMIM"
MONDO:0019075 OMIM:601536 Orphanet:69737/ntbt, Orphanet:69737, MONDO:includedEntryInOMIM"
MONDO:0800304 OMIM:243000 MONDO:includedEntryInOMIM"
MONDO:0800308 OMIM:258900 MONDO:includedEntryInOMIM"
MONDO:0800420 OMIM:613399 MONDO:includedEntryInOMIM"
MONDO:0800310 OMIM:270960 MONDO:includedEntryInOMIM"
MONDO:0800432 OMIM:613444 MONDO:includedEntryInOMIM"
MONDO:0800206 OMIM:131750 MONDO:includedEntryInOMIM"
MONDO:0800291 OMIM:174700 MONDO:includedEntryInOMIM"
MONDO:0010340 OMIM:300425 MONDO:includedEntryInOMIM"
MONDO:0007127 OMIM:106400 Orphanet:2206/e, Orphanet:2206, MONDO:includedEntryInOMIM, DOID:6652"
MONDO:0011231 OMIM:602477 MONDO:includedEntryInOMIM"
MONDO:0008585 OMIM:189800 MONDO:includedEntryInOMIM"
MONDO:0800301 OMIM:229300 MONDO:includedEntryInOMIM"
MONDO:0800409 OMIM:603829 MONDO:includedEntryInOMIM"
MONDO:0027353 OMIM:613989 MONDO:includedEntryInOMIM, DOID:0070021"
MONDO:0019799 OMIM:176100 Orphanet:95159/ntbt, Orphanet:95159, MONDO:includedEntryInOMIM"

SPARQL to generate

SPARQL Query (click to expand) 
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX IAO: <http://purl.obolibrary.org/obo/IAO_>
PREFIX OMO: <http://purl.obolibrary.org/obo/OMO_>
PREFIX MONDO: <http://purl.obolibrary.org/obo/MONDO_>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
prefix oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>

# description: Checks if a proper obsolesence reason was documented for this class

SELECT ?entity ?xref (GROUP_CONCAT(DISTINCT STR(?other_source); separator=", ") as ?other_sources) WHERE {
  ?entity rdfs:label ?label .
  ?entity oboInOwl:hasDbXref ?xref .
  ?included_xref owl:annotatedSource ?entity ;
         owl:annotatedProperty oboInOwl:hasDbXref ;
         owl:annotatedTarget ?xref ;
         oboInOwl:source "MONDO:includedEntryInOMIM" .
  OPTIONAL {
    ?included_xref oboInOwl:source ?other_source .
  }
  FILTER (isIRI(?entity) && STRSTARTS(str(?entity), "http://purl.obolibrary.org/obo/MONDO_"))
} GROUP BY ?entity ?xref
@twhetzel
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OMIM Included entries were discussed in a Mondo Curation call and it was suggested that they be reviewed for how the two terms in an OMIM Included entry are related to each other and what the hierarchy should be and perhaps other changes. There may be some overlap with that work and what would be needed here so for now I'd like to pause on this here in mondo-ingest until the work in mondo happens.

Also, just to make it clear, the list of terms above are only the included term of an OMIM entry that contains an Included term. The "parent" of these OMIM Included terms only have a comment in the omim.owl representation, but there is nothing linking the two terms together in Mondo. Analysis of this was done here: Review Mondo and OMIM INCLUDED xref annotations

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