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OMOP Vocabularies as OWL

General
#1

Is anyone aware of recent efforts to represent OMOP Vocab data as OWL? I’m not finding much as i search through the forums.

Thank You!

#2

That subject pops up from time to time. Maybe not necessarily OWL, but as some kind of graph representation.

1 Like
#3

Hello @Tom_Walpole ,

We have SKOS representation of the OMOP vocabulary at MSK. I’d be happy to share our approach and, possibly, the vocabulary in SKOS. Please let me know if you are interested, and we can schedule a conversation.

Rimma

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#4

Thanks you guys - this is helpful! @rimma i’ll message you!

#5

Hello everyone,
I would be very interested as well @rimma. I’m working on a similar task to map SDTM to OMOP for a knowledge graph effort. Looking for ways to do so, e.g., owl, skos, rdf, etc. Thanks so much for your time and help.

Kind regards,
Jason

How to add a custom vocabulary to the OMOP vocabulary table?
#6

@Jason_B , @Tom_Walpole

I’d be happy to schedule sometime this or next week. Please let me know your availability at rimma.belenkaya@gmail.org

#7

Hey all, is there a public repository with code to compile OMOP concept and relation tables to SKOS or OWL?

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#8

Answering my own question, this was recently published in some paper report:

https://bitbucket.org/jibalamy/owlready2/src/master/pymedtermino2/omop_cdm/

I still think its worth exploring the creation of a metadamodel for OMOP that allows abstracting from the table form the current data model has, which also facilitates bindings into OWL/RDF. But for people that need something to work quickly, the above looks reasonable (have not tried it yet, just skimmed the paper).

#9

Thanks for the link @matentzn! As well as to whomever worked on this. The TIMS group is looking to potentially do this. Ill see if we can leverage this existing code.

t