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[bioontology-support] Annotator query

Eamonn Maguire eamonnmag at gmail.com
Wed Dec 12 09:50:48 PST 2012


Yes, this is an option, but speed has a significant part to play in the decision not to do this. If a user selects 20 terms to tag, running 20 bioportal searches won't be as quick as it would be by running on the annotator. For our users, we'd like to avoid this.  

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






On Wednesday, 12 December 2012 at 17:48, Paul R Alexander wrote:

> In the meantime, you could try running a search on BioPortal using your stub term, either across all the ontologies or just a subset you know to be relevant. The search service will do partial matching. If you take the preferred names and synonyms of the returned terms from the search call and appended those to the text you are annotating, it would give you an approximation of what you are asking for.
> 
> Paul
> 
> 
> On Dec 12, 2012, at 9:45 AM, Trish Whetzel <whetzel at stanford.edu (mailto:whetzel at stanford.edu)> 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
> > > 
> > > 
> > > 
> > > 
> > > 
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> > 
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