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[bioontology-support] AMIA workshop

Madani,Sina AHMadani at
Tue Dec 21 07:36:02 PST 2010

Hi Ray,

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?

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.

I was just able to add SNOMED to the annotation dictionary. It took 4 days for ncbo-appliance to process concepts and relationships and add it to the list of available terminologies for annotations. I am now working on the annotation service to accept incoming dictation notes. I haven't decided how I can make the best of the output results yet :)

Paul is a great help to me for operationalizing ncbo-appliance and services. I do really appreciate his and the support team's effort


From: Ray Fergerson [mailto:ray.fergerson at]
Sent: Monday, December 13, 2010 5:22 PM
To: Madani,Sina; 'Nigam Shah'
Cc: support at
Subject: RE: [bioontology-support] AMIA workshop


We removed the OWL export in part because the OWL that we generated was incorrect. The other reason for removing it (rather than fixing it) what that it seemed the other formats were  a more natural export mechanism for this information than OWL. People tend to deal with these sorts of "data" things with XML or RDF rather than OWL. In general we would like to "regularize" the export formats across the application to perhaps XML and RDF but we haven't done so yet.


From: bioontology-support-bounces at [mailto:bioontology-support-bounces at] On Behalf Of Madani,Sina
Sent: Monday, December 13, 2010 7:43 AM
To: Nigam Shah
Cc: support at
Subject: Re: [bioontology-support] AMIA workshop

Hi Nigam,
Thanks to Trish & Paul with their great help on setting up an instance of ncbo-appliance, I am closer to the point for using annotation service.
Looking at your slides, I see an "OWL" icon as one of the output formats for annotation results. When I did my quick sample test on few lines of text I saw only the first three formats: txt, csv, and xml formats. Is there a way to activate OWL output as well or is this an enhancement for future?

My plan is to run the annotation services on a corpus of millions of notes (perhaps only specific sections first) for local "Quality" ontology building purposes.


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From: Nigam Shah [mailto:nigam at]
Sent: Friday, November 19, 2010 12:15 PM
To: Madani,Sina
Cc: Ray Fergerson; support at
Subject: Re: AMIA workshop

Hi Sina,

It was good to meet you as well. I am copying Ray Fergerson, our project manager, who can direct you to getting a VM instance.

ps: I will be leaving for a month long trip to my home country, from Nov 26 - Dec 29 so might be unresponsive on email.

On Fri, Nov 19, 2010 at 6:48 AM, Madani,Sina <AHMadani at<mailto:AHMadani at>> wrote:
Hi Nigam,

It was very nice meeting you at AMIA. I really enjoyed your workshop presentation. We talked briefly about the possibility of a VM instance that Bioportal can provide for our institution note analysis purposes. I appreciate your help on this.


Sina Madani, MD MS
Data Integration & Modeling
MD Anderson Cancer Center
Phone : 713-563-1803

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