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[bioontology-support] ATC / bioportal

Olga Ximena Giraldo oxgiraldo at gmail.com
Mon Jan 9 20:38:01 PST 2017


Thanks Jennifer.



If I understand correctly you do not take care of converting (transforming)
the original WHO ATC vocabulary into an RDF file. Instead, you just take
whatever UMLS has and that is what you transform to RDF. Right?



The original WHO ATC, as available at [1]  does not have the classes “Ergot
alkaloid oxytocics” and “Porstaglandins, Oxytocics”

while the one in bioportal does have these two classes [2], [3].



I would like to know what other differences in the hierarchy are there
between the original WHO ATC (14 main groups) and that in bioportal (17
main groups) [4].


thanks in advance,


[1] https://www.whocc.no/atc_ddd_index/

[2]
http://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FUATC%2FG02AB

[3]
http://bioportal.bioontology.org/ontologies/ATC/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FUATC%2FG02AD

[4] http://bioportal.bioontology.org/ontologies/ATC?p=classes&conceptid=root



On Mon, Jan 9, 2017 at 12:03 PM, Jennifer Leigh Vendetti <
vendetti at stanford.edu> wrote:

> Hello Olga,
>
> On Jan 7, 2017, at 1:12 PM, Olga Ximena Giraldo <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 bioontology.org/ontologies/ATC), but his email is no longer active.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
>
>
>


-- 
Olga Ximena Giraldo
http://oxgiraldo.wordpress.com
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