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[bioontology-support] Something amiss in translation of WHOART

Ray Fergerson ray.fergerson at
Tue Apr 26 14:38:35 PDT 2011


Sorry that it took so long to get back to you on this. We spent a fair
amount of time investigating the problem and then another larger chunk of
time discussing what, if anything, to do about it.

First we completely agree that the results shown in BioPortal are
logically incorrect. We believe though that the original source had these
problems. It appears that logically different terms were assigned the same
code (making them effectively synonyms). We are unable to find a copy of
the original source independent of UMLS to verify this. Unfortunately UMLS
does not update this ontology and the version in UMLS is 10+ years old.

It appears that UMLS assigns different CUI's to these logically distinct
concepts even though they have the same code in the original source. This
appears to "fix" this problem, at least in the UMLS browser. Whether this
fix happens intentionally or not is unclear. All UMLS terminologies are
loaded into BioPortal using the underlying source codes rather than UMLS
CUI's. We believe that this is what people typically would want.
Unfortunately, in this instance, this means that BioPortal shows the "bad"
results from the original source.

Rather than focusing on fixing a 10 years old version of a vocabulary, if
we invested any additional effort in this project is would probably be in
writing a custom loader for the newer versions (assuming their licensing
is acceptable). This isn't a high priority item for us at the moment
though. If there is a big demand we would reconsider it.


> -----Original Message-----
> From: bioontology-support-bounces at
> [mailto:bioontology-support-bounces at] On Behalf Of
> Alan Ruttenberg
> Sent: Wednesday, April 06, 2011 7:46 PM
> To: support
> Subject: [bioontology-support] Something amiss in translation of WHOART
> 1 is not a synonym for 2 or 3.
> The subtypes are of 3.
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at

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