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Add SPARQL test for taxon annotation property range #520

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dosumis opened this issue Jan 21, 2022 · 2 comments · Fixed by #527
Closed

Add SPARQL test for taxon annotation property range #520

dosumis opened this issue Jan 21, 2022 · 2 comments · Fixed by #527
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@dosumis
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dosumis commented Jan 21, 2022

never_in_taxon (RO_0002161) and present_in_taxon (RO_0002175) are annotation properties that require a taxon (NCBI taxon class) as a value. Ideally this range would be specified in RO, but limitations on specifying range for annotationProperties means there is no obvious way to do this. To compensate, we need a SPARQL check.

I think this should have two components:

  1. test that the value is an IRI
  2. cast to string and test that it begins with 'http://purl.obolibrary.org/obo/NCBITaxon_'
@matentzn
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For now, lets add this to Uberon - There are hundreds of SPARQL checks that we use across our projects, and we only want the very most general ones in ODK. Think of ODK SPARQL QC is those queries that are just an inch outside the criterion for ROBOT report.. Eventually, we want to find a better way to re-use and share SPARQL QC across repos, but for now, we can continue as we were I think.

@matentzn
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matentzn commented Jan 24, 2022

Ok, I changed my mind on this. Let's go ahead and add the check

@anitacaron after you made sure both tests work for Uberon, you can make a PR here and add them to the ODK template/src/sparql directory as well.

Before we make an ODK release, we also want #522.

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3 participants