Search Mailing List Archives

Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] [ISAtools] RE: Annotator query

Ray Fergerson ray.fergerson at
Thu Dec 13 10:56:11 PST 2012



I think that my example text was too short to get the idea across.  Here
is the situation. The ontology contains two distinct concepts (1)
"treatment" and (2) "compound treatment design". For the purposes of this
discussion, assume that neither term has any synonyms. The user passes in
to the Annotator some free text such as: 


"The patient was given a compound treatment: first we did treatment X and
then we did treatment Y".


The question which the Annotator is trying to answer is which concepts
from the ontology are present in this free text. The current answer, and I
believe the correct answer, is that the concept "treatment" appears three
times and the concept "compound treatment design" does not appear at all.
The Annotator only does a string comparison to extract concept names and
synonyms and the string "compound treatment design" does not appear in the
text. The annotator is not doing a "starts with" match. It is an exact
match only.


The only way that the free text above is going to produce an annotator
match to the "compound treatment design" concept is for this concept to
have  a synonym that appears exactly in the free text.   





From: Susanna-Assunta Sansone [mailto:sa.sansone at] 
Sent: Thursday, December 13, 2012 4:16 AM
To: Ray Fergerson
Cc: isatools at; 'Meng, Fan'; 'Eamonn Maguire'; 'Trish
Whetzel'; 'Dai, Manhong'; support at
Subject: Re: [ISAtools] RE: [bioontology-support] Annotator query


Hi Ray,


On 12/12/2012 21:55, Ray Fergerson wrote:



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.

I do not get this sorry. If what you say below (about the term has to be a
synonym to be found) is the case, then I do not believe that  "compound
treatment" is a  synonym of "treatment" that is why this is found and
"compound treatment design" is not.
If the Annotator is supposed to suggest terms you have to be able to find
both "treatment" and "compound treatment design" and then you leave the
user to choose which one is more relevant to their context.

My two cents,


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,
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 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

bioontology-support mailing list
bioontology-support at



ISA support team:
- Philippe Rocca-Serra
- Eamonn Maguire
- Alejandra Gonzalez-Beltran
- Susanna-Assunta Sansone


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <>

More information about the bioontology-support mailing list