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[bioontology-support] Question about processing UMLS ontologies

Michael Dorf mdorf at stanford.edu
Fri Feb 7 15:36:45 PST 2020


Hi Jahoon,

We have a script that converts the relational database representation of UMLS ontologies to RDF:

https://github.com/ncbo/umls2rdf

Once you’ve succeeded creating the Turtle files, you can try loading them into your appliance. Unfortunately, I am not in a position to offer a more detailed help on this process. We have our own internal way of loading UMLS ontologies into our repository that isn’t publicly available at the moment. Aside from the above process, we don’t publicly accept individual UMLS ontologies.

Sorry I couldn’t offer more help on this.

Michael


On Feb 7, 2020, at 3:15 PM, Koo, Jahoon <JAHOON.KOO at UCDENVER.EDU<mailto:JAHOON.KOO at UCDENVER.EDU>> wrote:

Hi BioPortal,

This is Jahoon, a student worker from Health Data Compass.

For my project, I have to migrate multiple UMLS ontologies from BioPortal into my virtual appliance.

On your wiki, it says “UMLS ontologies can be processed to work with our system by converting them to RDF. There is no automated way to do this and you must have your own UMLS MySQL installation and an OSX/Linux/Unix machine with 8GB+ of RAM in order for the conversion process to work. Once you have converted UMLS to RDF, you will get Turtle (.ttl) files that can be uploaded using the BioPortal Web UI”.

I would like to double check if there is no automated way to convert UMLS ontologies to RDF.
If not, I am wondering if there is an automated way to upload Turtle (.ttl) files to my virtual appliance without using the Web UI.

Respectfully,
Jahoon
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