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[bioontology-support] Questions about NCBO status and BioPortal

Jennifer Leigh Vendetti vendetti at stanford.edu
Wed Aug 7 12:47:40 PDT 2019


Hi Jeff,


On Aug 7, 2019, at 10:57 AM, Jeff Lerman <jeff.lerman at invitae.com<mailto:jeff.lerman at invitae.com>> wrote:

Got it, thanks.  Sounds like BioPortal lives on as an organization/team (https://www.bioontology.org/) as well as an application/toolset (https://bioportal.bioontology.org/) - is that (more or less) correct?


Yes, that’s correct.

In addition to our web application you listed above (http://bioportal.bioontology.org/), I would add a link to the BioPortal REST API documentation: http://data.bioontology.org/documentation. Our REST API is our most heavily used product offering.



Thanks also for the explanation of the relationship to OBO Foundry.  I’m sure some of the consequent details will become more clear as I browse some of the individual ontologies - e.g. I’m curious whether there are cases where a given ontology might be more current at BioPortal, though perhaps less in agreement with the unified model that OBO Foundry offers (if that makes sense).


I’m not sure I totally followed what you are asking here.

When end users upload ontologies to BioPortal, we give the option of specifying a URL that our system will check on a nightly basis for new versions. I’m not an expert on OBO Foundry processes, but it seems standard nowadays for their ontology files to reside in GitHub. We host many OBO Foundry ontologies in BioPortal that specify these pull URLs, so I expect that the versions we serve would be current with what OBO Foundry serves. That said, we also have end users that upload their ontology files manually when they want a new version to appear in BioPortal.

I believe there are also a number of differences in the metadata that we present about each ontology, versus what OBO Foundry presents.

Kind regards,
Jennifer

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