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[bioontology-support] [BioPortal] Feedback from mdebellis

Jennifer Leigh Vendetti vendetti at stanford.edu
Tue Apr 16 15:50:23 PDT 2019


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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