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[bioontology-support] AMIA workshop

Nigam Shah nigam at
Tue Dec 21 20:33:56 PST 2010

> Thank you for the explanation. I apologize for my late response.
> On the same slide, MetaMap is shown near mgrep for annotation purposes. Can
> I download MetaMap and "switch" annotation services from mgrep to MetaMap?
Hi Sina,

Not easily .. we have a prototype underway where we are trying that out. See
the November 2009 prototype at
The main bottleneck right now is getting MetaMap installed with the ~200
ontology dictionary we have at NCBO. For smaller dictionaries, the prototype
does work.

We've stopped work on the prototype pending some upgrades to MetaMap coming
from NLM .. we can consider picking up this work if there is enough user
interest. We'd also welcome a user contribution along this line.

> Although Nigam told me in the workshop that he gets better results ( I read
> that paper as well) with mgrep compared to MetaMap, I was just curious to
> see if MetaMap is an option in ncbo-appliance.
Given our need for speed and high precision, we went to mgrep ... at the
expense of some recall. We have a number of projects underway to: 1)
quantify the recall hit we are taking; 2) experiment with hybrid annotators
(where the "easy" stuff gets done by mgrep and we use a smaller dictionary
with MetaMap for complex phrases); and 3) Provide users with a service to
create custom, "clean lexicons" which they can use with a concept recognizer
of their choice.

We have papers out on (1) and (3) ... setting up a hybrid annotator is on
hold (see above). We can share the prototype code we have with you if you
want to try and embed metamap as a "switch". It would be a very valuable
user contribution!

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