PURLs for some resources not resolving

[bgyori]

The following resources use PURLs as their default URI but these aren't resolving correctly:

• InterPro with pattern http://purl.obolibrary.org/obo/IPR_$1, e.g., http://purl.obolibrary.org/obo/IPR_IPR016380 resolves to http://www.berkeleybop.org/ontologies/IPR_IPR016380 yielding a 404 error
• LBO with pattern http://purl.obolibrary.org/obo/LBO_$1 e.g., http://purl.obolibrary.org/obo/LBO_0000487 resolves to http://www.berkeleybop.org/ontologies/LBO_0000487 yielding a 404 error
• PECO with pattern http://purl.obolibrary.org/obo/PECO_$1 e.g., http://purl.obolibrary.org/obo/PECO_0007114 resolves to https://ontobee.org/ontology/PECO?iri=http://purl.obolibrary.org/obo/PECO_0007114 yielding a Term Not Found error on Ontobee

@cmungall given the first two (InterPro and LBO) are related to berkeleybop.org, do you know what the issue could be? Who would be able to help with the Ontobee issue related to PECO?

[matentzn]

http://purl.obolibrary.org/obo/{X} redirects by default to http://www.berkeleybop.org/ontologies/ for historical reasons.

1. LBO and InterPro are both not OBO Foundry ontologies. Because of the above, their PURLs redirect to berkeley
2. PECO issue: https://github.com/Planteome/plant-experimental-conditions-ontology/issues/137. You can chime in there.

[bgyori]

Thanks @matentzn! Just to clarify: so LBO and InterPro are not expected to be resolvable through berkeleybop.org? In that case, we could use the BioPortal to resolve these since there are working URLs there.

[matentzn]

Thanks @matentzn! Just to clarify: so LBO and InterPro are not expected to be resolvable through berkeleybop.org? In that case, we could use the BioPortal to resolve these since there are working URLs there.

From the bioregistry perspective, you can, and should! But you won't be able to get the actual PURLs (http://purl.obolibrary.org/obo/{X}) to redirect.

So for the uri_prefix you can use Bioportal, put you should maintain the uri_prefix_rdf to be the http://purl.obolibrary.org/obo/{X}.

[bgyori]

These are fixed in #1119 with the approach of preserving rdf_uri_prefix PURLs while updating the uri_prefix to working resolver URLs.

[cmungall]

Interpro isn’t an ontology! It shoukd just resolve to the interpro site

On Tue, Jun 4, 2024 at 6:05 AM Benjamin M. Gyori @.***> wrote:

Thanks @matentzn https://github.com/matentzn! Just to clarify: so LBO and InterPro are not expected to be resolvable through berkeleybop.org? In that case, we could use the BioPortal to resolve these since there are working URLs there.

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