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[bioontology-support] Annotator query

Ray Fergerson ray.fergerson at stanford.edu
Wed Dec 12 13:55:12 PST 2012


Eamonn,



In OBI there are two terms “treatment” and “compound treatment design”. If 
the text that you supply is “compound treatment” then this results in a 
match on the first term but not the second.



This seems reasonable and it is difficult to see how it could work 
differently. If the ontology contained the term “hay fever” and you supplied 
the text “hay” I don’t think that you should expect a match. The annotator 
is not a search system, it is a term matching system. “hay” is not the same 
term as “hay fever”.



If “compound treatment” were a declared synonym of “compound treatment 
design” then it should be found. If it is really a synonym (unclear to me) 
but not declared to be one in the ontology that you are using then you could 
consider extending the ontology or contacting the authors and asking them to 
add a synonym.



Ray





From: bioontology-support-bounces at lists.stanford.edu 
[mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of Meng, 
Fan
Sent: Wednesday, December 12, 2012 12:49 PM
To: Eamonn Maguire; Trish Whetzel; Dai, Manhong
Cc: ISA Team; support at bioontology.org Support
Subject: Re: [bioontology-support] Annotator query



Hi Eamonn and Trish:



Thanks a lot for  your messages. If the terms “"compound treatment" 
and"compound treatment design" are both in an ontology, I believe mgrep will 
only give the longest match by default but list both terms as matches will 
be possible.

However, mgrep will not find them if none of them are in the ontologies you 
selected.



Manhong wrote the mgrep program and I believe it is possible to include that 
option although we may need to generate more complex dictionaries. Manhong 
can certainly provide better insights on this issue.



Best,



Fan



From: Eamonn Maguire [mailto:eamonnmag at gmail.com]
Sent: Wednesday, December 12, 2012 12:48 PM
To: Trish Whetzel
Cc: Meng, Fan; support at bioontology.org Support; ISA Team
Subject: Re: [bioontology-support] Annotator query



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

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