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[bioontology-support] batch annotation extraction?

John Graybeal jgraybeal at stanford.edu
Tue Aug 4 16:51:13 PDT 2020


Hi Chris,

I will contact you off-thread to answer this question, since you're 'right next door' (metaphorically speaking).

I do not know of any existing tool that is exactly what you want, but I know we or others have written a script a few times to do what you want. (Depending on scope, the easiest thing might be to just manually run a command or use the UI.)

John

On Aug 4, 2020, at 2:09 PM, Christopher F. Beaulieu <beaulieu at stanford.edu<mailto:beaulieu at stanford.edu>> wrote:

Hi,

I have a need to try to match several very large lists of terms/short phrases with standardized annotations from the radiology RadLex ontology.

I can see how someone with programming expertise can work this out through the API or other resources on GitHub.   But what I wonder is if there is already an application
someone created out there for a similar task. Sorry but I am naive about programming but thought I’d check before enlisting a developer.

Ideally I’d like to provide a list and the return would be any matching RadLex terms with their RadLex ID’s as well.

thanks for any guidance,

Chris

*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
Christopher F. Beaulieu MD, PhD
Professor of Radiology
Associate Chair of Education
Stanford University Medical Center
300 Pasteur Dr., S-056
Stanford, CA  94305
beaulieu at stanford.edu<mailto:beaulieu at stanford.edu>
650-725-8018 (voice)
650-725-7296 (fax)


p.s. example list attached (the numbers are irrelevant)

<CHCO_iris diagnosis list copy test.txt>_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632  | ORCID  0000-0001-6875-5360



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