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[bioontology-support] Feedback

Natasha Noy noy at stanford.edu
Wed May 6 10:46:20 PDT 2009


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] http://www.biomedcentral.com/1471-2105/10/S2/S1#B15
[2] http://bioportal.bioontology.org/search

On May 6, 2009, at 12:47 AM, admin at bioontology.org wrote:

> Name : Ian Donaldson
>
> Email : ian.donaldson at biotek.uio.no
>
> 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 lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support




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