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Fix mismatched parentheses in QC check #7830

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merged 4 commits into from
Jun 27, 2024

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matentzn
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The src/sparql/qc/general/qc-xref-without-source.sparql check had mismatched parentheses which explained why almost no errors where caught correctly. Unfortunately, due to the enormous amount of NCIT and Orphanet errors, I had to drop these from the check..

Fixes #7824

Needs curation now, as more than 60 errors still present. the default solution is to simply delete all of these xrefs from Mondo!

The src/sparql/qc/general/qc-xref-without-source.sparql check had mismatched parentheses which explained why almost no errors where caught correctly. Unfortunately, due to the enormous amount of NCIT and Orphanet errors, I had to drop these from the check..
most of the x-ref had either no source at all, or had EFO as a source.
Almost all the x-ref removed are equivalent to another mondo term.
@sabrinatoro
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@matentzn could we remove all the NCIT and Orphanet computationally?
If you share a list, I can review a few of these to get a pattern of what we see (e.g. DOID were either without source or source from EFO), and if nothing looks suspicious, we could just remove these too.

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I reviewed the QC fails, and I approve this PR.
The PR can be merged once the QC have passed.
@matentzn Is there something else needed in this PR? or can we merge it?

@sabrinatoro sabrinatoro assigned matentzn and unassigned sabrinatoro Jun 26, 2024
@matentzn matentzn merged commit 6cf02c8 into master Jun 27, 2024
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@matentzn matentzn deleted the issue7824-fix-missing-source-xref branch June 27, 2024 07:13
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Issues with qc-xref-without-source.sparql
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