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updated USI example to mzQC v1.0 #229

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merged 4 commits into from
Jul 29, 2024
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@cbielow cbielow commented Jul 10, 2024

  • added a few more references (for USI, and CV terms)
  • fixed links (ProteomicsDB keeps failing -- its their API according to their support team; PRIDE works ATM)
  • arranged columns in the CV Table as columns (would show as one row, which might confuse people)

The validator is still not entirely happy, but I think it needs an update of the CV:

    Metric use of severity 5 and message: Non-metric CV term used in metric context: accession = MS:4000068
    Metric value no-unit of severity 3 and message: Metric CV term used without value unit specification. accession(s) = MS:4000068

    Loading online vocabulary of severity 5 and message: Error loading the following online ontology referenced in mzQC file: could not find a parser to parse 'https://github.com/HUPO-PSI/psi-ms-CV/blob/master/psi-ms.obo'
    Loading online vocabulary of severity 5 and message: Error loading the following online ontology referenced in mzQC file: HTTP Error 404: Not Found

    Unknown CVTerm of severity 7 and message: CV term used without matching ontology entry: accession = MS:1001058
    Unknown CVTerm of severity 7 and message: CV term used without matching ontology entry: accession = MS:4000068

@mwalzer mwalzer mentioned this pull request Jul 23, 2024
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mwalzer commented Jul 23, 2024

mzQC should be good now, validator is not complaining anymore.
I used a new version of psi-ms and a 'stable' repo link to a release version of the UO github tree (unless they revise their git history, that link should work in the future)

This was linked to issues Jul 25, 2024
@bittremieux bittremieux merged commit 11bcff2 into HUPO-PSI:main Jul 29, 2024
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Update examples to mzQC v1.0 Remove QC CV from markup docs
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