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[bioontology-support] Annotator query

Eamonn Maguire eamonnmag at gmail.com
Wed Dec 12 09:48:17 PST 2012


Hi Trish, 

Thanks for your reply. It would be great if this feature were integrated in to the annotator. Some users have been asking us why the annotator doesn't find things they expect it to, so it's good to have a response to this. I understand why you do it the way you do but I'd assume that an indexing system such as Lucene could help improve the speed for these types of lookups.

Thanks again,

Eamonn

--
Eamonn Maguire
Oxford e-Research Centre & Computer Science Department
University of Oxford

7 Keble Road, Oxford, OX1 3QG
T: 01865 (2) 610788 M: 07526 924483






On Wednesday, 12 December 2012 at 17:45, Trish Whetzel wrote:

> Hi Eamonn, 
> 
> I am not aware of any parameters that can be altered with the Annotator to get a match based on the scenario below. The dictionary that the Annotator uses is based on the preferred names and synonyms of ontology terms and there has to be an exact match in the input text to the dictionary term to return a match .. good for speed of annotation but does not handle term variations in the matching step unless the variation is included in the ontology itself.
> 
> Last I talked with the developers of the entity recognizer that the Annotator uses, called Mgrep, they have developed some methods to account for term permutations and there was an interest to collect use cases to test further. I have included Fan Meng in this response in case this is of interest to pursue further.
> 
> Best,
> Trish 
> 
> 
> On Dec 12, 2012, at 4:17 AM, Eamonn Maguire wrote:
> > Hi all, 
> > 
> > I have a query about the annotator. 
> > 
> > It appears that if we search on something like "compound treatment", we don't get a hit for "compound treatment design" for instance from OBI/EFO. Do you have any idea about how we can get the search results to return a better match? Or if it's possible?
> > 
> > Many thanks,
> > 
> > Eamonn 
> > 
> > --
> > Eamonn Maguire
> > Oxford e-Research Centre & Computer Science Department
> > University of Oxford
> > 
> > 7 Keble Road, Oxford, OX1 3QG
> > T: 01865 (2) 610788 M: 07526 924483
> > 
> > 
> > 
> > 
> > 
> > _______________________________________________
> > bioontology-support mailing list
> > bioontology-support at lists.stanford.edu (mailto:bioontology-support at lists.stanford.edu)
> > https://mailman.stanford.edu/mailman/listinfo/bioontology-support
> 

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