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[bioontology-support] Questions about NCBO status and BioPortal

Jeff Lerman jeff.lerman at invitae.com
Wed Aug 7 18:32:33 PDT 2019


Thanks Jennifer and John.  All that information is helpful, and I think I
now understand how the various entities relate to each other.  Also
interesting to know about the up-and-coming OntoPortal Alliance!

I’ll reach out when I have more questions.

Best,
—Jeff



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Jeff Lerman

AI Scientist

Mobile: 510-495-4621

www.invitae.com

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<https://www.linkedin.com/in/jefflerman/>


On Wed, Aug 7, 2019 at 2:33 PM John Graybeal <jgraybeal at stanford.edu> wrote:

> Jeff,
>
> The 'BioPortal organization/team' consists of both members of Stanford's
> Center for Biomedical Informatics Research (BMIR), the primary developers
> of BioPortal; and a number of collaborators, especially from the
> AgroPortal/SIFR community led by Clement Jonquet at Le Laboratoire
> d'Informatique, de Robotique et de Microélectronique de Montpellier (LIRMM)
> in France. Development is funded by grants and Stanford University's School
> of Medicine.
>
> There is a lot of information about BioPortal at the 'archival' Drupal
> site https://ncbo.bioontology.org; this also contains quite a lot of
> dated material (particularly about the originating National Center for
> Biomedical Ontologies, which as noted is no longer funded) that we have not
> had time to update.
>
> We are fostering an emerging community of BioPortal adopters called the
> OntoPortal Alliance (https://ontoportal.org), which brings together
> communities and individuals who are using a deployment of the BioPortal
> Virtual Appliance. This community is in the 'soft opening' phase (so we
> haven't started taking names!), but it represents the next level of
> sustainability for the BioPortal software.
>
> To your second question, there are a very few cases (one or two?) in which
> someone has asked for a different presentation of their OBO Library
> ontology to be provided on BioPortal (e.g., an OWL ontology on one, and an
> OBO ontology on the other). And at times, there are also new ontologies in
> the OBO Library that BIoPortal has not yet ingested. Other than those few
> cases, we work with the OBO Library community (with our thanks to Chris
> Mungall) to keep BioPortal in sync with the OBO Library content, so we
> generally encourage/ensure that those ontologies are automatically updated
> from the same source as the OBO Library uses. (Also I think there are a few
> acronym collisions, so BioPortal's version may have a different acronym
> than the OBO Library's version.)  If you find things out of sync, we would
> appreciate your letting us know.
>
> John
>
>
>
> On Aug 7, 2019, at 10:57 AM, Jeff Lerman <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?
>
> 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).
>
> Best,
> —Jeff
>
>
> [image: email_sig_logo_vert.png]
> Jeff Lerman
> AI Scientist
> Mobile: 510-495-4621
> www.invitae.com
> [image: email_sig_social_linkedin.png]
> <https://www.linkedin.com/in/jefflerman/>
>
>
> On Tue, Aug 6, 2019 at 5:52 PM Jennifer Leigh Vendetti <
> vendetti at stanford.edu> wrote:
>
>> Hi Jeff,
>>
>>
>> On Aug 2, 2019, at 3:47 PM, Jeff Lerman <jeff.lerman at invitae.com> wrote:
>>
>> Is NCBO still a going/funded entity?  I did see an (undated, but
>> apparently from January 2018
>> https://www.bioontology.org/mediawiki/index.php?title=Main_Page&diff=12957&oldid=12955)
>> mention on your wiki that NCBO’s funding has ended.  However, I see that
>> the email support list is still active, and many of the ontologies listed
>> at have been updated in 2019.  Is development at NCBO ongoing?
>>
>>
>>
>> Funding has concluded for the National Center for Biomedical Ontology.
>>
>> The BioPortal application, which was initially developed as part of NCBO,
>> continues to be funded and is actively developed / maintained.
>>
>>
>>
>> I’m also not completely clear on NCBO’s relationship with the OBO Foundry
>> - both appear to be efforts to provide a set of biomedical ontologies that
>> are coherent, in order to set a common language for describing biomedical
>> concepts.  Is there a relationship (formal or informal) between OBO Foundry
>> and NCBO (or NCBO’s efforts)?
>>
>>
>>
>> We have an informal relationship with the OBO Foundry community. On the
>> BioPortal side, we make an effort to include and serve all of the
>> ontologies that are part of the OBO Foundry. I would say the major
>> difference is that their set of ontologies is highly curated. You can’t
>> upload an ontology to the OBO Foundry without going through a review
>> process. This is in contrast to BioPortal, where anyone that has a
>> BioPortal account can upload their ontology.
>>
>> Kind regards,
>> Jennifer
>>
>> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
>
> ========================
> John Graybeal
> Technical Program Manager
> Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
> Stanford Center for Biomedical Informatics Research
> 650-736-1632
>
>
>
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