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[bioontology-support] Feedback

Nigam Shah nigam at
Wed May 6 16:58:53 PDT 2009

Dear Ian,

Attached is a paper that further describes what the annotator does. As
Natasha mentioned, the annotator finds exact matches to terms in
ontologies. "Parkinson" is not an ontology term and hence will not be
recognized as a disease term. This feature is crucial in preventing
false matches. e.g. "Helen Parkinson is a great person to work with"
in the annotator will NOT be tagged with Parkinson's disease.


On Wed, May 6, 2009 at 10:46 AM, Natasha Noy <noy at> wrote:
> Dear Ian,
> Thank you for trying it out. We should probably be more clear about the
> difference between the way the annotator and search work. We are still
> working out how best to present the different tools. Basically, for
> annotator, we are using a third-party software that looks for more or less
> exact matches of ontology terms and their synonyms in the text (doing only a
> bit of cleverness with stop words and such). We are currently using mgrep
> tool from University of Michigan [1]. We are also working on making this bit
> configurable and plugging in other term-extraction engines.
> So, there is no term "Parkinson" or "Parkinson's" in any of the ontologies,
> so the annotator doesn't find anything. If you put "Parkinson" in the search
> interface [2], you'll find all the concepts that you would expect. If you
> put "parkinson disease" in the annotator, you'll get what you expect as
> well. The annotator is not perfect, but it works reasonably well on texts of
> abstracts and such.
> I hope this at least explains the results that you are seeing. And thank you
> for the feedback! Please keep it coming.
> Natasha
> [1]
> [2]
> On May 6, 2009, at 12:47 AM, admin at wrote:
>> Name : Ian Donaldson
>> Email : ian.donaldson at
>> Comment:
>> I just tried your annotation service.
>> Try typing in a single word
>> Parkinsons
>> or
>> Parkinson's
>> The results are  disappointing. Is there a reference or any documentation
>> on what exactly the annotator is doing in order to recognize terms?
>> Ian
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at
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