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[bioontology-support] STOP

Christie Frayser christieevemacmurray at hotmail.com
Fri Jun 28 10:29:47 PDT 2013






Many blessings,
Christie Frayser
"...and the angel said onto thee, I bring you great tidings of joy."


> From: bioontology-support-request at lists.stanford.edu
> Subject: bioontology-support Digest, Vol 62, Issue 28
> To: bioontology-support at lists.stanford.edu
> Date: Thu, 27 Jun 2013 17:28:29 -0700
> 
> Send bioontology-support mailing list submissions to
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> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of bioontology-support digest..."
> 
> 
> Today's Topics:
> 
>    1. Re: retrieving equivalent class descriptions (Ray Fergerson)
>    2. Re: FW: NCBO Virtual Appliance (Rekapalli, Hari)
>    3. Re: FW: NCBO Virtual Appliance (Ray Fergerson)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Thu, 27 Jun 2013 17:19:11 -0700 (PDT)
> From: "Ray Fergerson" <ray.fergerson at stanford.edu>
> To: "'Maxwell Neal'" <mneal at u.washington.edu>,
> 	<support at bioontology.org>
> Subject: Re: [bioontology-support] retrieving equivalent class
> 	descriptions
> Message-ID: <ebf03af6.000010a8.00000031 at BMIR-MSOB-245.stanford.edu>
> Content-Type: text/plain; charset="us-ascii"
> 
> Eventually yes, but not yet. The current beta SPARQL endpoint no longer
> updates with new ontologies. We are in the process of replacing this
> endpoint with another that will update but this is still at least a month
> away.
> 
>  
> 
> Ray
> 
>  
> 
> From: bioontology-support-bounces at lists.stanford.edu
> [mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of
> Maxwell Neal
> Sent: Thursday, June 27, 2013 12:16 PM
> To: support at bioontology.org
> Subject: [bioontology-support] retrieving equivalent class descriptions
> 
>  
> 
> Hi all,
> 
>  
> 
> I was wondering - if I include equivalent class expressions in an OWL
> ontology that I upload to BioPortal, are those expressions stored in the
> BioPortal RDF representation and accessible via the SPARQL service?
> 
>  
> 
> Many thanks!
> 
>  
> 
> M
> 
>  
> 
> ---------------------------------
> 
> Maxwell Neal
> 
>  
> 
> Post-doctoral researcher
> 
> Department of Bioengineering
> 
> University of Washington
> 
> mneal at uw.edu
> 
> ---------------------------------
> 
>  
> 
>  
> 
>  
> 
>  
> 
>  
> 
> 
> 
> 
> 
>  
> 
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> 
> ------------------------------
> 
> Message: 2
> Date: Fri, 28 Jun 2013 00:20:11 +0000
> From: "Rekapalli, Hari" <Hari.Rekapalli at ucsf.edu>
> To: "Ray Fergerson" <ray.fergerson at stanford.edu>,
> 	"support at bioontology.org" <support at bioontology.org>
> Subject: Re: [bioontology-support] FW: NCBO Virtual Appliance
> Message-ID:
> 	<00832D94C1562942AAB343A9EB3D0DFC24380CFC at ex04.net.ucsf.edu>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Hi Ray,
> Thanks for the info. What's considered large? I have about 30,000 patient discharge summary text records.
> 
> Best,
> Hari
> ________________________________
> From: Ray Fergerson [ray.fergerson at stanford.edu]
> Sent: Thursday, June 27, 2013 5:15 PM
> To: Rekapalli, Hari; support at bioontology.org
> Subject: RE: [bioontology-support] FW: NCBO Virtual Appliance
> 
> Hari,
> 
> You can use the REST access to the production version of the annotator for this as well. Instructions are available here:
> http://www.bioontology.org/wiki/index.php/Annotator_User_Guide
> 
> You can also do this sort of access with the VM as well (particularly if you have large data sets to process) but try out the production REST service first. If you need the VM then please contact me off list and we can get you set up.
> 
> Ray
> 
> From: bioontology-support-bounces at lists.stanford.edu [mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of Rekapalli, Hari
> Sent: Thursday, June 27, 2013 4:59 PM
> To: support at bioontology.org
> Subject: [bioontology-support] FW: NCBO Virtual Appliance
> 
> 
> ________________________________
> From: Rekapalli, Hari
> Sent: Thursday, June 27, 2013 4:56 PM
> To: whetzel at stanford.edu<mailto:whetzel at stanford.edu>
> Subject: NCBO Virtual Appliance
> Hi Trish,
> This is Hari Rekapalli, from UCSF. We met at the Hackathon a few months ago, hope you remember. I have a question for you. What's the best way to make use of the Annotator tool? I presume that you are no longer supporting the download version of it, and that you now have it rolled up into the Virtual Appliance. If this is the case, could you please let me know how do I go about downloading it? My username is 'rvharikrishna'. Once I have the appliance, I can run the REST queries locally with the source text as a param to get the SNOMED concepts as an output, right? Because that's what I am trying to do.
> 
> Thanks,
> Hari
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> 
> ------------------------------
> 
> Message: 3
> Date: Thu, 27 Jun 2013 17:28:17 -0700 (PDT)
> From: "Ray Fergerson" <ray.fergerson at stanford.edu>
> To: "'Rekapalli, Hari'" <Hari.Rekapalli at ucsf.edu>,
> 	<support at bioontology.org>
> Subject: Re: [bioontology-support] FW: NCBO Virtual Appliance
> Message-ID: <30228577.000010a8.00000033 at BMIR-MSOB-245.stanford.edu>
> Content-Type: text/plain; charset="us-ascii"
> 
> Probably should have said large or sensitive. You probably cannot send you
> patient records over the internet and thus need a VM. Will contact you
> privately about this.
> 
>  
> 
> Ray
> 
>  
> 
> From: Rekapalli, Hari [mailto:Hari.Rekapalli at ucsf.edu] 
> Sent: Thursday, June 27, 2013 5:20 PM
> To: Ray Fergerson; support at bioontology.org
> Subject: RE: [bioontology-support] FW: NCBO Virtual Appliance
> 
>  
> 
> Hi Ray,
> Thanks for the info. What's considered large? I have about 30,000 patient
> discharge summary text records.
> 
> Best,
> Hari
> 
>   _____  
> 
> From: Ray Fergerson [ray.fergerson at stanford.edu]
> Sent: Thursday, June 27, 2013 5:15 PM
> To: Rekapalli, Hari; support at bioontology.org
> Subject: RE: [bioontology-support] FW: NCBO Virtual Appliance
> 
> Hari,
> 
>  
> 
> You can use the REST access to the production version of the annotator for
> this as well. Instructions are available here:
> 
> http://www.bioontology.org/wiki/index.php/Annotator_User_Guide
> 
>  
> 
> You can also do this sort of access with the VM as well (particularly if
> you have large data sets to process) but try out the production REST
> service first. If you need the VM then please contact me off list and we
> can get you set up.
> 
>  
> 
> Ray 
> 
>  
> 
> From: bioontology-support-bounces at lists.stanford.edu
> [mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of
> Rekapalli, Hari
> Sent: Thursday, June 27, 2013 4:59 PM
> To: support at bioontology.org
> Subject: [bioontology-support] FW: NCBO Virtual Appliance
> 
>  
> 
>  
> 
>   _____  
> 
> From: Rekapalli, Hari
> Sent: Thursday, June 27, 2013 4:56 PM
> To: whetzel at stanford.edu
> Subject: NCBO Virtual Appliance 
> 
> Hi Trish,
> This is Hari Rekapalli, from UCSF. We met at the Hackathon a few months
> ago, hope you remember. I have a question for you. What's the best way to
> make use of the Annotator tool? I presume that you are no longer
> supporting the download version of it, and that you now have it rolled up
> into the Virtual Appliance. If this is the case, could you please let me
> know how do I go about downloading it? My username is 'rvharikrishna'.
> Once I have the appliance, I can run the REST queries locally with the
> source text as a param to get the SNOMED concepts as an output, right?
> Because that's what I am trying to do.
> 
> Thanks,
> Hari
> 
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> ------------------------------
> 
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> 
> End of bioontology-support Digest, Vol 62, Issue 28
> ***************************************************
 		 	   		  
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