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[bioontology-support] Questions about NCBO status and BioPortal

John Graybeal jgraybeal at stanford.edu
Wed Aug 7 14:33:42 PDT 2019


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<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?

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


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Jeff Lerman
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On Tue, Aug 6, 2019 at 5:52 PM Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:
Hi Jeff,


On Aug 2, 2019, at 3:47 PM, Jeff Lerman <jeff.lerman at invitae.com<mailto: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

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========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
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