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FlyBase / flybase-controlled-vocabulary

The home of the FlyBase miscellaneous ontologies - incorporating the Drosophila Phenotype Ontology (see also FlyBase/drosophila-phenotype-ontology)
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Allow `property_value` tags in OBO files. #179

Closed gouttegd closed 2 years ago

gouttegd commented 2 years ago

Fix the OboModel.pm module to prevent it from emitting a warning upon reading a property_value tag. This tag is defined in the OBO Flatfile format specification and should therefore be considered valid.

Treating this tag as "unrecognized" is especially problematic now that we have switched metadata annotations from oboInOwl: to dcterms:, because dcterms: annotations are unknown in the OBO Flatfile format and therefore represented as generic property_value tags, instead of specific tags such as created_by or creation_date.

dosumis commented 2 years ago

Oh dear. Does that mean you're still using my ancient PERL scripts?! I'd assumed this was all superseded by ODK.

Clare72 commented 2 years ago

Nico set them up to run and make reports when we switched to ODK, so yes they are still in use.

gouttegd commented 2 years ago

As far as I know, there are still 3 Perl scripts (all dependant on OboModel.pm) that are used as part of the normal release process to generate reports: onto_metrics_calc.pm, chado_load_checks.pl, and obo_track_new.pl.

There’s also a audo_def_sub.pl script, but I believe this one is a remnant and is not actually used anymore.

Clare72 commented 2 years ago

audo_def_sub.pl - based on name, I think this used to make the auto-generated definitions. Nico's eq-writer.jar has replaced this one.