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[bioontology-support] Bad URIs used in Mappings for PR

Darren Natale dan5 at georgetown.edu
Tue Jun 8 15:16:31 PDT 2021


Dear BioPortal,

In looking at mappings between the PRotein Ontology and 
others--specifically those that were found by LOOM--I noticed that the 
URLs indicated for PR-defined entities are sometimes incorrect. For 
example, between PR and CIDO (Coronavirus Infectious Disease Ontology) 
there is a LOOM-based mapping for "PGR (human)" that, after removing the 
BioPortal additions to the URL, becomes:

in PR: http://purl.obolibrary.org/obo/HGNC_8910
in CIDO: http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=8910

What's interesting about this is that CIDO actually imports this very 
same class from PR. The only difference is that CIDO is getting the URI 
from the OWL version of PR, while the URI supplied by PR appears to be 
coming from a conversion of the OBO-file CURIE to a URI. Unfortunately, 
that CURIE-to-URI conversion fails to account for the idspace 
declaration in the OBO header:

idspace: HGNC http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=

I know that the conversion failure is not a BioPortal issue because we 
encounter the very same problem when we do the OBO-to-OWL conversion 
ourselves (I believe it is actually an OWLAPI issue). The difference is 
that we run a post-processing script to fix them.

I see two ways around the problem:

1) Use the OWL file http://purl.obolibrary.org/obo/pr.owl instead of the 
OBO file currently downloaded by BioPortal, or
2) Run the same converter we do (which I can supply if desired) to 
post-process the RDF/XML after BioPortal conversion.

I suspect method #1 will be much easier to implement, but I'm not able 
to make the change myself anymore (I'm not granted editing ability even 
after signing in and even though I'm the contact person for PR). I'm 
also not sure if this is best for users, who up to now have been 
downloading the reasoned OBO from BioPortal. Would they be forced to use 
the OWL version, or can BioPortal download both formats?

All advice welcome!

Best regards,
Darren Natale


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