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[bioontology-support] Feedback

Woodbridge, Mark R m.woodbridge at
Thu Apr 15 06:56:49 PDT 2010

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]
Sent: 15 April 2010 00:02
To: admin at
Cc: 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 wrote:

> Name : Mark Woodbridge
> Email : m.woodbridge at
> Comment:
> Hi,
> 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
> +
> bank
> &ontologiesToKeepInResult=42277&longestOnly=true&withSynonyms=false"
> -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.
> Mark.
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at

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