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[bioontology-support] Feedback

Woodbridge, Mark R m.woodbridge at
Thu Apr 15 08:54:25 PDT 2010

Hi Trish,

longestOnly isn't quite what I want - I would like a response only if there is an exact match e.g. 'river bank' should return a match but 'river bark' should return no matches. Using longestOnly in this case would return 'river' as a match. However, as I explained, I can get the functionality I need by looking at the indexes given in the response. I just thought it might be useful to provide such a parameter for users who want to check if a provided term is present in an ontology.

Thanks for looking into the definition field. It would be very useful to allow our users to interactively disambiguate multiple matches by looking at the definitions.


From: Trish Whetzel [whetzel at]
Sent: 15 April 2010 16:52
To: Woodbridge, Mark R
Cc: Natasha Noy; bioontology-support at
Subject: Re: [bioontology-support] Feedback

Hi Mark,

We'll check into why the definition field is empty. As for returning only the term 'river bank', that is possible by setting the parameter 'longestOnly' to true. More details on all parameters for the Annotator are described here:


On Apr 15, 2010, at 6:56 AM, Woodbridge, Mark R wrote:

Hi Natasha,

Many thanks. It works perfectly now! There are a couple of extra features that would make the Annotator ideal for our usage scenario - I don't know if whether these are currently possible, or whether you have considered adding them:

- Optionally including term definitions in the response alongside the fullId and synonyms. I noticed that you do have a <definitions> element but it seems to be empty.

- Exact matches. In some cases I would like to submit a term (e.g. 'river bank') and only get a response if that terms exists in the specified ontology. (Though I can easily work round this by looking at the 'from' and 'to' indexes in the response and checking whether they span the whole input).

Many thanks for your help,


Mark Woodbridge
CISBIC Data Management
Imperial College London

From: Natasha Noy [noy at<mailto:noy at>]
Sent: 15 April 2010 00:02
To: admin at<mailto:admin at>
Cc: bioontology-support at<mailto:bioontology-support at>; Woodbridge, Mark R
Subject: Re: [bioontology-support] Feedback

Thank you, Mark, for bringing this up to our attention. There were
some problems on our server that we have now fixed.

Please try it out and do not hesitate to let us know if you see more

Thank you for your feedback!


On Apr 14, 2010, at 4:08 AM, admin at<mailto:admin at> wrote:

Name : Mark Woodbridge

Email : m.woodbridge at<mailto:m.woodbridge at>


I'm trying to use the Annotator to identify ontology terms in free
text. I'm not sure whether it is suitable for this use case, but I
started with something simple:

curl -d "textToAnnotate=river
-s ""

i.e. I would like to search the Environment Ontology for "river
bank" (ENVO:00000143). This seems to return "bar" (a synonym which I
tried to exclude using the withSynonyms parameter) and "bank" but
not "river bank".

Am I doing something wrong? Any help would be greatly appreciated.

bioontology-support mailing list
bioontology-support at<mailto:bioontology-support at>
bioontology-support mailing list
bioontology-support at<mailto:bioontology-support at>

Trish Whetzel, PhD
Outreach Coordinator
The National Center for Biomedical Ontology
Ph: 650-721-2378
whetzel at<mailto:whetzel at>

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