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[bioontology-support] ATC / bioportal

Jennifer Leigh Vendetti vendetti at stanford.edu
Mon Jan 9 09:03:07 PST 2017


Hello Olga,

On Jan 7, 2017, at 1:12 PM, Olga Ximena Giraldo <oxgiraldo at gmail.com<mailto:oxgiraldo at gmail.com>> wrote:

I would like to know who is the contact person for the WHO ATC ontology. the name in the bioportal page of the ontology is (https://bioportal.bioontology.org/ontologies/ATC), but his email is no longer active.


Apologies for that - we’ll get it sorted out and add a name with an active email address.



I am looking at the hierarchy and I see some discrepancies with the original who atc. In particular, "ergot" in the who atc has the same label for multiple concepts. This has been solved, somehow, by the version in bioportal by creating new categories.

Could somebody let me know how is transformed the who atc in owl and how is solved the problem -dealing with these kind of issues?


I can give you some high-level information about how we import ATC into BIoPortal, but I’m not sure I understand your question fully.

Roughly twice per year the UMLS [1] publishes a release of a group of ontologies, which we import into BioPortal.  ATC is one of the ontologies that’s pulled in when we do the UMLS imports.  According to the UMLS documentation, the 2016AA release includes version “ATC_2015_15_09_08” of ATC [2].  We are currently working toward importing the 2016AB UMLS release into BioPortal.  When that release is available, it will include version “ATC_2016_16_09_06” of ATC.

To perform the import, we have Python scripts that connect to a UMLS database and transforms the ontology content to RDF consumable by BioPortal.  The program that we use to do this is open source and available in our GitHub repository:

https://github.com/ncbo/umls2rdf

It’s unclear to me how you’re viewing / comparing the “original who atc” with the version in BioPortal, and also what you mean by creation of new categories?  Perhaps you’re referring to classes?

Kind regards,
Jennifer

[1] https://www.nlm.nih.gov/research/umls/
[2] http://wayback.archive-it.org/4253/20160415132921/https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/ATC/metadata.html


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