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[bioontology-support] AMIA workshop

Madani,Sina AHMadani at
Wed Dec 22 06:50:36 PST 2010

From: Nigam Shah [mailto:nigam at]
Sent: Tuesday, December 21, 2010 10:34 PM
To: Madani,Sina
Cc: Ray Fergerson; support at; Paul R Alexander; Jin,Jeff; Riben,Michael Warren
Subject: Re: [bioontology-support] AMIA workshop

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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