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[bioontology-support] RRF conversion

Wynne, Robert (NIH/NCI) [C] wynner at mail.nih.gov
Tue Jul 31 14:19:56 PDT 2018


Hi John,

Thank you!  We’ll give this a try.

Rob

From: John Graybeal <jgraybeal at stanford.edu>
Sent: Thursday, July 26, 2018 9:25 PM
To: Wynne, Robert (NIH/NCI) [C] <wynner at mail.nih.gov>
Cc: support at bioontology.org; Remennik, Lyubov (NIH/NCI) [E] <lyubov.remennik at nih.gov>
Subject: Re: [bioontology-support] RRF conversion

Hello Rob,

Our process is as follows:
1) download the UMLS full release in whatever format they provide
2) run Metamorphosys application which generates the RRF files and mysql load script
3) run the generated mysql load script to load data from RRF files
4) run our python umls2rdf script to generate TTL files

The only part of this you don't already have access to (if you're running the UMLS MetaMorphosys) is the umls2rdf script, which is in GitHub at https://github.com/ncbo/umls2rdf.

The

On Jul 26, 2018, at 7:47 AM, Wynne, Robert (NIH/NCI) [C] <wynner at mail.nih.gov<mailto:wynner at mail.nih.gov>> wrote:

Hi all,

We’re interested in converting an RRF subset from MetaMorphosys to something our Triplestore could consume (ttl/owl/rdf, etc).  Is a most recent script available for this?  Possibly in Github?

Thanks,
Rob
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========================
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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