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OntoZoo / ontobee

Ontobee is a linked data server for ontologies. See: http://www.ontobee.org.
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Issue with BFO_0000063 #96

Open mcourtot opened 7 years ago

mcourtot commented 7 years ago

Searching for 'precedes' in ontobee:

screen shot 2016-11-21 at 09 35 27

But the link towards BFO_0000063, http://www.ontobee.org/ontology/BFO?iri=http://purl.obolibrary.org/obo/BFO_0000063, returns a term not found.

cc @cmungall

yongqunh commented 7 years ago

It appears this term is hosted in RO: http://www.ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/BFO_0000063

I think we need to generate a library of special terms like this in order to properly dereference such terms.

Thanks, Oliver

From: Melanie Courtot [mailto:notifications@github.com] Sent: Monday, November 21, 2016 4:37 AM To: OntoZoo/ontobee Subject: [OntoZoo/ontobee] Issue with BFO_0000063 (#96)

Searching for 'precedes' in ontobee:

[screen shot 2016-11-21 at 09 35 27]https://cloud.githubusercontent.com/assets/2214135/20477536/f00e6f86-afcd-11e6-9421-9ed851bf1379.png

But the link towards BFO_0000063, http://www.ontobee.org/ontology/BFO?iri=http://purl.obolibrary.org/obo/BFO_0000063, returns a term not found.

cc @cmungallhttps://github.com/cmungall

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cmungall commented 7 years ago

Ontobee shouldn't hardcode assumptions about URIs.

The fact thathttp://purl.obolibrary.org/obo/BFO_0000063 does not resolve is nothing to do with ontobee, it's a purl.obolibrary issue. We had the correct redirect with OCLC, this was never ported to the new system.

yongqunh commented 7 years ago

OK. That’s good if the purl.obolibrary can solve the redirecting issue. Oliver

From: Chris Mungall [mailto:notifications@github.com] Sent: Monday, November 21, 2016 5:15 PM To: OntoZoo/ontobee Cc: He, Oliver; Comment Subject: Re: [OntoZoo/ontobee] Issue with BFO_0000063 (#96)

Ontobee shouldn't hardcode assumptions about URIs.

The fact thathttp://purl.obolibrary.org/obo/BFO_0000063 does not resolve is nothing to do with ontobee, it's a purl.obolibrary issue. We had the correct redirect with OCLC, this was never ported to the new system.

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mcourtot commented 7 years ago

@cmungall could you clarify?

http://purl.obolibrary.org/obo/BFO_0000063 redirects to http://www.ontobee.org/ontology/BFO?iri=http://purl.obolibrary.org/obo/BFO_0000063 which I believe is the right place.

cmungall commented 7 years ago

No, this is the right place: http://www.ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/BFO_0000063

cmungall commented 7 years ago

close this?

mcourtot commented 7 years ago

well it still doesn't resolve so I'd say no ;)

This raises 2 issues:

cmungall commented 7 years ago

https://github.com/oborel/obo-relations/wiki/ROAndBFO

cmungall commented 7 years ago

For the redirect you should be able to put something in bfo.yml in the purl github

mcourtot commented 7 years ago

This is really confusing - when OBI submitted relations to RO, we updated the prefix and obsoleted the OBI ones to get them RO IDs. Maybe slightly broader scope than the issue currently at hand, but I really think we ought to think about this in a general context and moving terms between ontologies. I agree with your comment above that the prefix should not dictate the master resource, and I thought we did create an AP a little while back specifically for this, though I don't find it in IAO. Something like "under authority of" - maybe we could have a configuration in Ontobee to read those APs and redirect accordingly? I agree we can do a one off specific redirect, but that doesn't seem very sustainable...

yongqunh commented 7 years ago

If needed, Ontobee can configure to make it read fine and redirect right. Let us know if this is allowed, and then we can do it.

cmungall commented 7 years ago

rdfs:isDefinedBy?