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[bioontology-support] batch annotation extraction?

John Graybeal jgraybeal at stanford.edu
Wed Aug 5 18:09:23 PDT 2020


I don't know what limits it has, but OntoMaton may be just the ticket. See https://github.com/ISA-tools/OntoMaton and the paper at https://academic.oup.com/bioinformatics/article/29/4/525/198710 for details.

Other possibilities are RightField<https://academic.oup.com/bioinformatics/article/27/14/2021/194783>, and Table2Annotation<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7362945/>. I found these by searching for "display bioportal annotator results in excel", but I'm sorry that I don't have experience with them 'in the wild'. Others on the list may be able to provide insight.

John

On Aug 5, 2020, at 8:07 AM, Christopher F. Beaulieu <beaulieu at stanford.edu<mailto:beaulieu at stanford.edu>> wrote:

Thank you John.

There are thousands of entries so automation would be key.


Chris

On Aug 4, 2020, at 4:51 PM, John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>> wrote:

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





========================
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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