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[bioontology-support] batch annotation extraction?

John Graybeal jgraybeal at
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.)


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


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,


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<mailto:beaulieu at>
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<mailto:bioontology-support at>

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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