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

Meng, Fan mengf at
Thu Dec 13 11:14:29 PST 2012

Hi all:

I completely agree with Ray's explanations. If a word or phrase is part of a concept but itself is not defined as a synonym of the concept or a different concepts,  Annotator will not identify that word or phrase as a match.  The only correct way for Annotator to find "compound treatment" is to define it as a synonym to "compound treatment design" in the ontology or define it as a new concept.

While we can modify the program to do partial match and to indicate the full concept string associated with the partial match, the result will likely be very messy.  In the example we discussed, "compound treatment", "treatment design", "compound", "treatment", "design" can be different concepts as well as be associated with many different concepts. Even if we limit the length of the partial phrase to be at least two words, "compound treatment" and  "treatment design" in this example are likely represent different concepts.



From: Ray Fergerson [mailto:ray.fergerson at]
Sent: Thursday, December 13, 2012 1:56 PM
To: 'Susanna-Assunta Sansone'
Cc: isatools at; Meng, Fan; 'Eamonn Maguire'; 'Trish Whetzel'; Dai, Manhong; support at
Subject: RE: [ISAtools] RE: [bioontology-support] Annotator query


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<mailto:isatools at>; 'Meng, Fan'; 'Eamonn Maguire'; 'Trish Whetzel'; 'Dai, Manhong'; support at<mailto: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> [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<mailto: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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ISA support team:
- Philippe Rocca-Serra
- Eamonn Maguire
- Alejandra Gonzalez-Beltran
- Susanna-Assunta Sansone

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