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[bioontology-support] Annotator query

Dai, Manhong daimh at
Wed Dec 12 15:23:36 PST 2012

Hi Eamonn,

  I believe Ray and Fan answered your question. Actually this issue triggered me to ask you a question.

   If we add a spelling-check-like feature to mgrep, will this meet you need?

From: Ray Fergerson [ray.fergerson at]
Sent: Wednesday, December 12, 2012 4:55 PM
To: Meng, Fan; 'Eamonn Maguire'; 'Trish Whetzel'; Dai, Manhong
Cc: 'ISA Team'; support at
Subject: RE: [bioontology-support] Annotator query


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.


From: bioontology-support-bounces at [mailto:bioontology-support-bounces at] 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 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.



From: Eamonn Maguire [mailto:eamonnmag at]
Sent: Wednesday, December 12, 2012 12:48 PM
To: Trish Whetzel
Cc: Meng, Fan; support at<mailto:support at> 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 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.


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 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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