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[bioontology-support] AMIA workshop

Ray Fergerson ray.fergerson at
Mon Dec 13 15:22:02 PST 2010



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
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


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. 








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>

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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