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Published 20 hours ago • verified publisher icon bridgedb

QC: test mapping files for expected databases

Open DeniseSl22 opened this issue 1 year ago • 3 comments

  • Based on the expected databases in a mapping file (which are different for GeneProtein/Metabolite/Etc.), there should be an output which databases should be present in the mapping files. @egonw @tabbassidaloii @DeniseSl22

DeniseSl22 avatar Mar 08 '23 10:03 DeniseSl22

expected databases in a mapping file

What do you mean with "expected" here? Expected by whom? Right now, the QC tool expects the same databases in the next release as the previous release. That is in the output.

You mean the BridgeDb Derby schema version, right?

egonw avatar Mar 17 '23 17:03 egonw

Well, apparently that is not a "foolproof" technique (as the issues with the GeneProtein Mapping files have shown). We know which databases we want to have represented in the mapping files, right? So, I think there should be a warning if one of those isn't there.... vs checking the content per database which is being done now.

DeniseSl22 avatar Mar 20 '23 08:03 DeniseSl22

When you compare with a previous database it already does report which databases are added or removed. That is separate from the differences.

What it does not do, is look at the attributes in both files.

egonw avatar Mar 20 '23 08:03 egonw