Search Mailing List Archives

Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] RRF conversion

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

Hi John,

Thank you!  We’ll give this a try.


From: John Graybeal <jgraybeal at>
Sent: Thursday, July 26, 2018 9:25 PM
To: Wynne, Robert (NIH/NCI) [C] <wynner at>
Cc: support at; Remennik, Lyubov (NIH/NCI) [E] <lyubov.remennik at>
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


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

bioontology-support mailing list
bioontology-support at<mailto:bioontology-support at>

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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <>

More information about the bioontology-support mailing list