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noy at stanford.edu
Wed May 6 10:46:20 PDT 2009
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 . We are
also working on making this bit configurable and plugging in other
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 , 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.
On May 6, 2009, at 12:47 AM, admin at bioontology.org wrote:
> Name : Ian Donaldson
> Email : ian.donaldson at biotek.uio.no
> I just tried your annotation service.
> Try typing in a single word
> The results are disappointing. Is there a reference or any
> documentation on what exactly the annotator is doing in order to
> recognize terms?
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