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[bioontology-support] [BioPortal] Feedback from mdebellis

Jennifer Leigh Vendetti vendetti at stanford.edu
Wed Apr 17 18:09:55 PDT 2019


Hi Michael,

The BioPortal team develops the BioPortal application [1], REST API [2], and virtual appliance [3], which facilitate access to ontology data. However, we don’t author the ontologies we’re serving, nor do we participate in decision making processes for assigning licenses to ontologies. We simply abide by what the ontology authors / submitters give us in terms of license text.

I mentioned previously that we import SNOMED CT into BioPortal from the UMLS Metathesaurus (provided by the National Library of Medicine). The licensing terms for SNOMED CT in the context of the UMLS are described here in Appendix 2:

https://uts.nlm.nih.gov/license.html

The license text prohibits us from distributing SNOMED CT in any other form, hence we don’t provide a download link to the RDF representation that’s generated by our Python scripts.

Hope that explanation is helpful. If not, feel free to contact us with additional questions.

Kind regards,
Jennifer

[1] http://bioportal.bioontology.org/
[2] http://data.bioontology.org/
[3] https://www.bioontology.org/wiki/index.php/Category:NCBO_Virtual_Appliance



On Apr 16, 2019, at 6:00 PM, Michael DeBellis <mdebellissf at gmail.com<mailto:mdebellissf at gmail.com>> wrote:

Thanks Jennifer, to be honest I'm still kind of confused. If it's supposed to be an open standard that we want the healthcare community to adopt I don't get the issue with "licensing restrictions". Or maybe my understanding of what SNOMED is supposed to be is wrong. It seems to me you could just use a common open source copyleft license, I see that all the time, I used one on an ontology I developed and made available to the public a while back. But you also said that the OWL file could be generated which would solve the problem. I'm actually working on something else right now and was looking into this for a colleague and I forwarded your message on to him. Actually, I just noticed you are at Stanford, I was looking into this because someone asked about getting the OWL file for SNOMED on the Protege user support email list.  I will go back when I have more time and read those links and see if I can generate the OWL file. Thanks for your prompt response.

Michael

On Tue, Apr 16, 2019 at 3:50 PM Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:
Hi Michael,


On Apr 16, 2019, at 1:14 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: mdebellis

Email: mdebellissf at gmail.com<mailto:mdebellissf at gmail.com>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2Fontologies%2FSNOMEDCT

Feedback:

Hi, my email is mdebellissf at gmail.com<mailto:mdebellissf at gmail.com> I'm a retired computer scientist doing my own research on the Semantic Web. I've done a lot of work with healthcare in the past and want to download the OWL file for SNOMED-CT but I can't see where on the page one can download the actual OWL file. I can browse the various classes and properties but I want the actual file. Sorry, I'm probably missing something really obvious. Thanks in advance,



The short answer is that we don’t have a SNOMED CT OWL file.

We import the SNOMED CT ontology into BioPortal from the UMLS Metathesaurus [1]. We developed Python scripts [2] that convert from a UMLS database to an RDF file that we can load into our application. Due to licensing restrictions, we aren’t permitted to allow downloads of the SNOMED CT RDF file, though the SNOMED CT data is fully available from the BioPortal application and our REST API [3].

Alternatively, you may be interested to look at the announcement that came out in Nov. of 2018 that SNOMED CT will be offered in OWL [4]. I poked around in their FAQ and it appears that the OWL file is something you have to generate yourself [5], as it’s not included in their core distribution.

Hope that helps.

Kind regards,
Jennifer

[1] https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/
[2] https://github.com/ncbo/umls2rdf
[3] http://data.bioontology.org/ontologies/SNOMEDCT
[4] https://confluence.ihtsdotools.org/display/RMT/2018/11/28/ADVANCED+NOTICE%3A++Plan+for+the+transition+from+Stated+Relationships+to+OWL+files<https://confluence.ihtsdotools.org/display/RMT/2018/11/28/ADVANCED+NOTICE:++Plan+for+the+transition+from+Stated+Relationships+to+OWL+files>
[5] https://confluence.ihtsdotools.org/display/DOCTSG/9.2.6+SNOMED+CT+OWL+Distribution+FAQ


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