snomed

[Alexander Garcia Castro]

Hi, I need to load snomed in tbc, any indications/instrcutions as to how can I do this? 

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Alexander Garcia
http://www.alexandergarcia.name/
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[nat...@topquadrant.com]

Hi Alex

What are the available formats ? Rdf, xml, csv ?

[David Price]

Snomed is not native RDF as far as I know, I think it uses its own ontology language syntax. 

I think the results are available as a tab-separated-file I think. Someone/something will have to translate that into RDF/OWL (e.g. Turtle file) before it can be imported into TB. My guess is there are already tools to do that and you just need to find and use one.

Cheers,

David

UK +44 7788 561308

US +1 336 283 0606

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[Paula Markes]

IHTSDO offers a script that will transform the SNOMED in the release files to OWL.  It was written by Kent Spackman, and is often referred to as the “Spackman Script”.  The Technical documentation guide provides some information on running it - http://ihtsdo.org/fileadmin/user_upload/doc/.  As you might suspect, SNOMED is very large and so you will need to make sure your hardware is appropriately sized to manage it.

-Paula

[Ankur Oberai]

I had a chance to play with the snomed data recently.

Snomed comes in a format called RF2. There is a pl script called tls2_StatedRelationshipsToOwlKRSS_INT_20160131.pl located in the snomed download zip at - SnomedCT_RF2Release_INT_20160131\SnomedCT_RF2Release_INT_20160131\Resources\StatedRelationshipsToOwlKRSS

There are instructions in this file on how to run this file and generate a .owl file. This can then be renamed to .rdf and opened in TBC.

The latest international version took TBC under 4 GB RAM to open.

Hope that helps.

Regards,

Ankur Oberai

Semantic Solutions Developer

TopQuadrant Inc.

[Irene Polikoff]

Several of our customers use SNOMED although I am not sure where they have obtained the RDF version – have they converted it themselves or is it available somewhere for download. I hope that one of these users is on the forum and may respond.

Once you have SNOMED in RDF, because it is large, the best way to open it in TBC is by streaming it into a TDB database. To do so, right click on a project, select Import > TopBraid Composer > Import RDF files into a new TDB and follow the rest of the wizard.

Irene Polikoff

[cbur...@healthwise.org]

Alex,

I don't know where to get the full U.S. version in an RDF format, but you can download the International version from Bioportal (looks like the latest available is the 2015AA release) in Turtle or CSV format:

http://bioportal.bioontology.org/ontologies/SNMI

Also, Tania Tudorache from Stanford has uploaded an OWL version of the SNOMED Anatomical Terms only, if that happens to be the module you're interested in: 

https://bioportal.bioontology.org/ontologies/SNOMED_ANATOMY

Depending on your coding abilities, you could also get it by using the UMLS2RDF Python scripts to convert the UMLS representation of SNOMED to an RDF format:

https://github.com/ncbo/umls2rdf

best,

Carl