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] Which SNOMEDCT file is used to generate the ontology

Michael Dorf mdorf at stanford.edu
Fri Apr 12 11:17:17 PDT 2019


Hi Michael,

I am not the original creator of our UMLS import process, but just scanning the script, it’s possible to determine the tables used:

https://github.com/ncbo/umls2rdf/blob/master/umls2rdf.py#L478

The column identification is a bit more involved, as the info appears to be scattered throughout the script. These may be the areas to focus on:

https://github.com/ncbo/umls2rdf/blob/master/umls2rdf.py#L267
https://github.com/ncbo/umls2rdf/blob/master/umls2rdf.py#L125
https://github.com/ncbo/umls2rdf/blob/master/umls2rdf.py#L568

There is also a list of column constants at the top of the script that may provide some clues.

https://github.com/ncbo/umls2rdf/blob/master/umls2rdf.py#L45

Sorry, I couldn’t be of more help.

Michael


On Apr 11, 2019, at 8:08 PM, Michael Liu <megapode32559 at gmail.com<mailto:megapode32559 at gmail.com>> wrote:

Hi,

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

I downloaded the SNOMEDCT raw data from UMLS. But it has many tables
and the presentation is different from the above URL. Would you please
let me know what tables and columns in SNOMEDCT raw that you used to
create the view shown on the above URL? Thanks. Regards

--
Best wishes,
Michael
_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20190412/bdeba380/attachment.html>


More information about the bioontology-support mailing list