include NCBO Bioportal as possible Ontology Browser, (and later the new OLS)

[proccaserra]

as per the discussion on OBO foundry operation call on August 11th, 2015.

[cmungall]

There is currently no way to do this globally as there is no deterministic procedure to translate an official OBO ontology id / IRI into a biioportal URL

In some cases we can guess:

• upcase(uberon) = http://bioportal.bioontology.org/ontologies/UBERON RESOLVES

But this doesn't always work. Consider the obo library ontology fbbt (which uses FBbt as a prefix)

This has the bioportal URL: http://bioportal.bioontology.org/ontologies/FB-BT

However, it's possible to do this on a per-ontology basis. I will demonstrate with fbbt

[cmungall]

@mmc46 @dosumis do you approve of the 3 browsing options I added here:
http://obofoundry.github.io/ontology/fbbt.html
(the 4 buttons on the main panel)

@proccaserra I'll leave this open pending decision / or until bioportal URLs have been added for all ontologies (click on the commit link above to see how I did this). Alternatively someone may want to reach out and figure out if they can resolve using our prefixes

[proccaserra]

@cmungall: +1 but should the OBOfoundry come with a specification/requirement for creating predictible variations (e.g. use lc(OBOFoundry ontology prefix) or uc(OBOFoundry ontology prefix) or concat(OBOF.OBOFoundry ontology prefix) ?
I presume Bioportal needs to deal with other prefixes which may collided with OBOF ones.

[dosumis]

On Aug 11, 2015, at 7:22 PM, Chris Mungall [email protected] wrote:

@mmc64 @dosumis do you approve of the 3 browsing options I added here:
http://obofoundry.github.io/ontology/fbbt.html
(the 4 buttons on the main panel)

Looks good to me.

Have sent pull request to update details:

master...dosumis:patch-1

Cheers,
David

@proccaserra I'll leave this open pending decision / or until bioportal URLs have been added for all ontologies. Alternatively someone may want to reach out and figure out if they can resolve using our prefixes

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[mmc46]

Looks good to me too. Thanks.

Marta

On 11 Aug 2015, at 20:01, David Osumi-Sutherland [email protected] wrote:

On Aug 11, 2015, at 7:22 PM, Chris Mungall [email protected] wrote:

@mmc64 @dosumis do you approve of the 3 browsing options I added here:
http://obofoundry.github.io/ontology/fbbt.html
(the 4 buttons on the main panel)

Looks good to me.

Have sent pull request to update details:

master...dosumis:patch-1

Cheers,
David

@proccaserra I'll leave this open pending decision / or until bioportal URLs have been added for all ontologies. Alternatively someone may want to reach out and figure out if they can resolve using our prefixes

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Reply to this email directly or view it on GitHub.

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Reply to this email directly or view it on GitHub.

[cmungall]

@proccaserra I think we would recommend that any external resource not introduce arbitrary changes - e.g introducing a dash; need to uniquify across broader set understood but ideally we'd all coordinate on this, with other stakeholders like identifiers.org too to avoid situations like what we have now with an OBO ontology called GEO that has nothing to do with the GEO (NCBI)

[cmungall]

@dosumis you needed to make one more click to make it a bona fide PR, no worries I did it and merged the changes in

[cmungall]

cc @graybeal

[nlharris]

What's the status of this?

[graybeal]

The mapping Jennifer mentions in #80 (comment) (and further documented in #80 (comment)) seems like the answer to the question above in #28 (comment). Yes?

[nlharris]

So can this ticket be closed?

[nlharris]

closing, please reopen or create a new ticket if there are still things to be done on this.