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[bioontology-support] [BioPortal] Feedback from Fred Trotter

Jennifer Leigh Vendetti vendetti at stanford.edu
Thu Nov 16 14:33:15 PST 2017


Hi Fred,


On Nov 16, 2017, at 12:55 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Fred Trotter

Email: fred.trotter at gmail.com<mailto:fred.trotter at gmail.com>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2F

Feedback:

Hi, your HCPCS ontology says that it has 5000+ classes
http://bioportal.bioontology.org/ontologies/HCPCS

But when you click "Classes" there is nothing there.

That cannot be right.

HCPCS is one of a small handful of ontologies in BioPortal with a “flat” model, meaning that the ontology has no (or very little) hierarchy. For flat ontologies we offer a search box, rather than a tree for navigating terms. On the classes page for HCPCS [1], you can start typing in the “Jump To:” text box in the upper left portion of the page.  BioPortal will then display a dropdown list of terms using autocomplete functionality based on the characters you type. You can select a class from the list and BioPortal will display the details in the right-hand side of the page. The classes are also available via our REST API [2].


Also, the "license" section of HCPCS code is set to be the same as UMLS. And indeed, HCPCS is available through UMLS. But it is also available directly from CMS under much less restrictive licensing. (UMLS licensing can require you to view to accept sub-licenses, which is onerous if all you want is HCPCS, etc)

https://www.cms.gov/Medicare/Coding/MedHCPCSGenInfo/index.html

I love the service, it is clearly the best of its kind. It would be cool if these bugs could be fixed.

I looked at the link you reference above, but it’s not obvious to me what formats they offer. I could only find a PDF document. BioPortal accepts ontology uploads in OWL, OBO, and SKOS format.

UMLS ontologies are a special case for us. We import them programmatically with a Python script that converts from UMLS Metathesaurus format to an RDF TTL file that's consumable by our application. If you’re aware of a version of HCPCS from CMS in a format that we currently handle, we could look at retrieving it from them and updating the license information.

Kind regards,
Jennifer

[1] http://bioportal.bioontology.org/ontologies/HCPCS/?p=classes
[2] http://data.bioontology.org/ontologies/HCPCS/classes
[3] https://github.com/ncbo/umls2rdf



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