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Issues with qc-xref-without-source.sparql #7824

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sabrinatoro opened this issue Jun 19, 2024 · 1 comment · Fixed by #7830
Closed

Issues with qc-xref-without-source.sparql #7824

sabrinatoro opened this issue Jun 19, 2024 · 1 comment · Fixed by #7830
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@matentzn

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@sabrinatoro
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It looks like this QC (sparql/qc/general/qc-xref-without-source.sparql) has been implemented for all sources (OMIM, OMIMPS, Orphanet, DOID, NCIT).

  1. what happened to x-refs that did not have a "MONDO:" source?

  2. it looks like this QC does not report all errors. In the next comment, I added examples of terms for which there are xrefs without "MONDO:" source. We should also look at examples where Orphanet said that 1orphanet maps to multiple OMIM terms (we used to have a lot of these examples, but I cannot find any).

Notes:

  • we do remove all the x-refs that are not equivalent to the released version of Mondo. Mentioning this as it might have some sort of effect.
  • I noticed this QC when I curated an OMIM id without a "MONDO:" source in mondo-edit. This reported an error for this omim id
@sabrinatoro
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Examples of terms with x-ref (all from orphanet) without a "MONDO:" source. (note, I only added the "x-ref" annotations)

[Term]
id: MONDO:0100354
name: megacystis-microcolon-intestinal hypoperistalsis syndrome 1
xref: DOID:0060610 {source="MONDO:equivalentTo"}
xref: GARD:15195 {source="MONDO:GARD"}
xref: ICD10CM:Q43.8 {source="DOID:0060610", source="Orphanet:2241/attributed", source="Orphanet:2241/ntbt", source="Orphanet:2241"}
xref: MEDGEN:1778116 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"}
xref: MESH:C536138 {source="MONDO:equivalentTo", source="DOID:0060610"}
xref: NCIT:C98982 {source="MONDO:equivalentTo"}
xref: OMIM:249210 {source="Orphanet:2241/e", source="MONDO:equivalentTo", source="Orphanet:2241"}
xref: Orphanet:2241 {source="OMIM:249210", source="MONDO:equivalentTo", source="DOID:0060610"}
xref: Orphanet:2604 {source="OMIM:155310"}
xref: SCTID:253781004 {source="MONDO:equivalentTo"}
xref: UMLS:C5542316 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:1778116"}

[Term]
id: MONDO:0007062
name: adactylia, unilateral
xref: GARD:377 {source="MONDO:GARD"}
xref: ICD10CM:Q71.3 {source="Orphanet:973", source="Orphanet:973/attributed", source="Orphanet:973/ntbt"}
xref: MEDGEN:113098 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"}
xref: MESH:C562417 {source="MONDO:equivalentTo"}
xref: OMIM:102650 {source="Orphanet:973", source="GARD:0000377", source="MONDO:equivalentTo", source="Orphanet:973/e"}
xref: Orphanet:294990 {source="OMIM:102650"}
xref: Orphanet:973 {source="OMIM:102650", source="GARD:0000377", source="MONDO:equivalentTo"}
xref: UMLS:C0220660 {source="MEDGEN:113098", source="MONDO:equivalentTo", source="MONDO:MEDGEN"}

[Term]
id: MONDO:0015129
name: chronic primary adrenal insufficiency
xref: DOID:13774 {source="MONDO:equivalentTo"}
xref: GARD:19803 {source="MONDO:GARD"}
xref: ICD10CM:E27.1 {source="Orphanet:85138/ntbt", source="Orphanet:85138", source="DOID:13774"}
xref: ICD9:255.41 {source="MONDO:relatedTo", source="MONDO:i2s"}
xref: MedDRA:10001130 {source="Orphanet:85138", source="Orphanet:85138/e"}
xref: MEDGEN:1324 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"}
xref: MESH:D000224 {source="https://orcid.org/0000-0003-1967-3726", source="Orphanet:85138", source="MONDO:equivalentTo", source="Orphanet:85138/e", source="DOID:13774"}
xref: NANDO:1200411 {source="MONDO:NANDO", source="https://orcid.org/0000-0003-0011-764X", source="https://orcid.org/0000-0002-0170-9172"}
xref: NANDO:2200359 {source="MONDO:NANDO", source="https://orcid.org/0000-0003-0011-764X", source="https://orcid.org/0000-0002-0170-9172"}
xref: NANDO:2200360 {source="MONDO:NANDO", source="https://orcid.org/0000-0003-0011-764X", source="https://orcid.org/0000-0002-0170-9172"}
xref: NCIT:C113814
xref: NCIT:C26689 {source="MONDO:equivalentTo", source="DOID:13774"}
xref: OMIM:240200 {source="Orphanet:85138", source="MONDO:equivalentTo", source="Orphanet:85138/e", source="DOID:13774"}
xref: Orphanet:101959 {source="MONDO:equivalentTo"}
xref: Orphanet:85138 {source="OMIM:240200"}
xref: SCTID:111562000 {source="DOID:13774"}
xref: SCTID:154707007 {source="DOID:13774"}
xref: SCTID:267483004 {source="DOID:13774"}
xref: SCTID:363732003 {source="DOID:13774"}
xref: SCTID:367376006 {source="DOID:13774"}
xref: SCTID:373662000 {source="MONDO:equivalentTo", source="DOID:13774"}
xref: SCTID:68588005 {source="DOID:13774"}
xref: UMLS:C0001403 {source="MONDO:equivalentTo", source="MONDO:MEDGEN", source="MEDGEN:1324"}

[Term]
id: MONDO:0005045
name: hypertrophic cardiomyopathy
xref: DOID:11984 {source="MONDO:equivalentTo", source="EFO:0000538"}
xref: EFO:0000538 {source="MONDO:equivalentTo", source="MONDO:EFO"}
xref: HP:0001639 {source="MONDO:otherHierarchy", source="https://orcid.org/0000-0002-9584-9618"}
xref: ICD10CM:I42.1 {source="DOID:11984", source="MONDO:mondoIsBroaderThanSource"}
xref: ICD10CM:I42.2 {source="MONDO:relatedTo"}
xref: ICD9:425.1 {source="MONDO:mondoIsNarrowerThanSource", source="DOID:11984", source="EFO:0000538", source="https://orcid.org/0000-0002-9584-9618"}
xref: ICD9:425.11 {source="DOID:11984"}
xref: ICD9:425.4 {source="MONDO:relatedTo", source="MONDO:i2s"}
xref: MedDRA:10020871 {source="Orphanet:217569", source="Orphanet:217569/e"}
xref: MEDGEN:2881 {source="MONDO:equivalentTo", source="MONDO:MEDGEN"}
xref: MESH:D002312 {source="DOID:11984", source="Orphanet:217569", source="MONDO:equivalentTo", source="Orphanet:217569/e", source="EFO:0000538"}
xref: MESH:D024741 {source="DOID:11984"}
xref: NANDO:1200286 {source="MONDO:NANDO", source="https://orcid.org/0000-0003-0011-764X", source="https://orcid.org/0000-0002-0170-9172"}
xref: NANDO:1200288 {source="MONDO:NANDO", source="https://orcid.org/0000-0003-0011-764X", source="https://orcid.org/0000-0002-0170-9172"}
xref: NANDO:2100054 {source="MONDO:NANDO", source="https://orcid.org/0000-0003-0011-764X", source="https://orcid.org/0000-0002-0170-9172"}
xref: NANDO:2200229 {source="MONDO:NANDO", source="https://orcid.org/0000-0003-0011-764X", source="https://orcid.org/0000-0002-0170-9172"}
xref: NANDO:2201042 {source="MONDO:NANDO", source="https://orcid.org/0000-0003-0011-764X", source="https://orcid.org/0000-0002-0170-9172"}
xref: NCIT:C34449 {source="DOID:11984", source="MONDO:equivalentTo", source="EFO:0000538"}
xref: NCIT:C84773 {source="DOID:11984"}
xref: OMIMPS:192600 {source="DOID:11984"}

@matentzn matentzn mentioned this issue Jun 20, 2024
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Fix mismatched parentheses in QC check monarch-initiative/mondo
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@matentzn @sabrinatoro