Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] FW: BioPortal VM Image - access information

Paul R Alexander palexander at stanford.edu
Fri Dec 3 12:16:45 PST 2010


On 12/2/10 7:11 AM, Madani,Sina wrote:
> How can I monitor the process except the fact that when it's loaded I 
> get a status change.
I've started a FAQ page on our wiki which addresses this:
http://www.bioontology.org/wiki/index.php/Virtual_Appliance_FAQ

> How can I setup annotation services in admin GUI, if there is any, to 
> process batch text file with no 300 words limit?
>
There is no support for configuring the annotator via the admin GUI.

> How can I delete a terminology?
>
The admin interface has a feature for removing and/or deprecating 
ontologies. Deprecating them keeps a copy of the original file and a 
metadata record of that version. Removing them entirely wipes out any 
record of them.

> Is the OWL loader a general owl loader that you wrote or you are using 
> the owl loader that ships with LexEVS? I've heard that lexEVS owl 
> loader is customized toward loading NCI Thesaurus OWL file and may not 
> work on custom/local created OWL file that have restrictions within 
> classes.
>
The OWL loader uses Protege, which in turn uses the OWL API. It should 
handle general OWL ontologies but may encounter issues with features 
that are OWL2 only.

> I tried using annotator user group to get my answers but it seems the 
> group is not activated yet
>
Hm, perhaps Trish can look into this.

> Thanks again for your help. This is really great. We are using LexEVS 
> 5.1.4 with NCIT Browser for loading and visualizing our 
> internal/external terminologies but I found your interface much user 
> friendly.
>
I'm glad you like it, if you have any feedback we'd love to hear it.

Paul R Alexander
Web / UI Developer
NCBO BioPortal <http://bioportal.bioontology.org>
Stanford Center for Biomedical Informatics Research



> Sina
>
> *From:*Paul R Alexander [mailto:palexander at stanford.edu]
> *Sent:* Wednesday, December 01, 2010 5:30 PM
> *To:* Madani,Sina
> *Cc:* support at bioontology.org
> *Subject:* Re: [bioontology-support] FW: BioPortal VM Image - access 
> information
>
> Sina,
>
> The ncbo-appliance.ovf file does indeed have a different SHA1 hash 
> than what is listed in the manifest. I'm not sure how this could be, 
> but we haven't tested this on Windows so perhaps that is the cause.
>
> Could you try replacing something in the manifest file for me? I've 
> generated a new SHA1 hash based on the file you sent me, so switch:
> SHA1(ncbo-appliance.ovf)= 63ff730146c82b6ad680e92e523b8c8d38bf298c
> to
> SHA1(ncbo-appliance.ovf)= db622f8777c9b0a0c458d78565baf5900f091fdc
>
> And then run the utility again.
>
> Sorry for the trouble.
>
> Paul
>
>
> On 12/1/10 2:40 PM, Madani,Sina wrote:
>
> Nope, I just deleted all files, unzipped the tar file (using 7-zip), 
> and re-ran the tool but got the same error. I am downloading the tar 
> file again just in case it's related to download.
>
> I attached my manifest and ovf file in case it helps to troubleshoot
>
> Sina
>
> *From:*Paul R Alexander [mailto:palexander at stanford.edu]
> *Sent:* Wednesday, December 01, 2010 4:34 PM
> *To:* Madani,Sina
> *Cc:* support at bioontology.org <mailto:support at bioontology.org>
> *Subject:* Re: [bioontology-support] FW: BioPortal VM Image - access 
> information
>
> Did you alter the ncbo-appliance.ovf file at all? This would result in 
> the hash not matching what is in the manifest (a security precaution). 
> You could try decompressing the archive from scratch to make sure 
> nothing was modified.
>
> Paul
>
>
> On 12/1/10 2:31 PM, Madani,Sina wrote:
>
> Hi Paul,
>
> I wasn't running ovftool in the unzip directory. So I copied all the 
> unzipped appliance zipped file in the ovf tool program folder and ran 
> it again. This time I got below error.
>
> The second screenshot shows ovf tool directory with all 3 disk images, 
> their sizes and the manifest file content. Is it an indication of a 
> bad download?
>
> Thanks for the help
>
> Sina
>
> *From:*Paul R Alexander [mailto:palexander at stanford.edu]
> *Sent:* Wednesday, December 01, 2010 4:17 PM
> *To:* Madani,Sina
> *Cc:* support at bioontology.org <mailto:support at bioontology.org>
> *Subject:* Re: [bioontology-support] FW: BioPortal VM Image - access 
> information
>
> Sina,
>
> The OVF file won't open directly in the VMWare Player (as you 
> discovered) so the recommended route is to convert, just as you tried 
> to do. I'm wondering if you can see the file 
> (ncbo-appliance-disk3.vmx) in the same directory that you're running 
> the ovftool? Also, there should be a manifest file (ncbo-appliance.mf) 
> and it looks like that is missing too. You need to run ovftool in the 
> same directory as all of the files that were in the archive that you 
> downloaded.
>
> Paul R Alexander
> Web / UI Developer
> NCBO BioPortal <http://bioportal.bioontology.org>
> Stanford Center for Biomedical Informatics Research
>
>
> On 12/1/10 1:08 PM, Madani,Sina wrote:
>
> Hi Trish,
>
> I downloaded and unzipped the appliance file. I tried to open the 
> ncbo-appliance ovf file using vmware player but got the error shown 
> below. Then I tried converting it into a vmx file using ovf tool but 
> got error again (last screenshot). Any hint?
>
> Thanks
>
> Sina
>
> *From:*Trish Whetzel [mailto:whetzel at stanford.edu]
> *Sent:* Tuesday, November 23, 2010 4:00 PM
> *To:* Madani,Sina
> *Subject:* BioPortal VM Image - access information
>
> Thank you for providing the user metrics information. The VM image can 
> be downloaded from:
>
> http://www.bioontology.org/ncbo-appliance/ncbo-appliance-v0.1.tar
> and the documentation is at:
> http://www.bioontology.org/wiki/index.php/Category:NCBO_Virtual_Appliance
> If you have any questions with the installation, please email 
> support at bioontology.org <x-msg://7/support@bioontology.org>.
>
> Trish
>
> On Nov 22, 2010, at 12:22 PM, Madani,Sina wrote:
>
>
>
>
>
>
> Hi Trish,
>
> We previously tested MetaMap for analyzing our dictated notes but when 
> Nigam presented his talk about Mgrep and the fact that it can process 
> text files more accurately we decided to launch a local version of it 
> because we didn't want to send our patient dictation files over the 
> net to Bioportal text analysis services.
>
> The intended user at this moment is only I &  possibly Mike Riben. I 
> anticipate to run the instance for text processing of at least 5 
> million clinical dictated notes.
>
> Sina
>
> *From:*Trish Whetzel [mailto:whetzel at stanford.edu]
> *Sent:*Monday, November 22, 2010 1:59 PM
> *To:*Madani,Sina
> *Cc:*Ray Fergerson
> *Subject:*Re: AMIA workshop
>
> Hi Sina,
>
> The support forum that Ray mentioned is our mailing 
> list:support at bioontology.org <mailto:support at bioontology.org>.  Can 
> you provide a short description on how you plan to use the VM image 
> and the expected number of users? We are collecting additional user 
> metrics in response to queries from our Advisory Board.
>
> Thanks!
>
> Trish
>
> On Nov 22, 2010, at 6:25 AM, Madani,Sina wrote:
>
>
>
>
>
>
>
> Thank you Ray.
>
> What is the url for support forum?
>
> Sina
>
> *From:*Ray Fergerson [mailto:ray.fergerson at stanford.edu]
> *Sent:*Friday, November 19, 2010 4:16 PM
> *To:*'Nigam Shah'; Madani,Sina
> *Cc:*'Trish Whetzel'
> *Subject:*RE: AMIA workshop
>
> Sina,
>
> Happy to hear you are interested in the VM instance. Trish (copied) is 
> responsible for collecting the necessary information and providing you 
> with the link. She also monitors the support mailing list where you 
> should send any help requests.
>
> Ray
>
> *From:*Nigam Shah [mailto:nigam at stanford.edu]
> *Sent:*Friday, November 19, 2010 10:15 AM
> *To:*Madani,Sina
> *Cc:*Ray Fergerson;support at bioontology.org 
> <mailto:support at bioontology.org>
> *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.
>
> Regards,
>
> Nigam.
>
> 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 mdanderson.org 
> <mailto:AHMadani at mdanderson.org>> 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.
>
> Thanks
>
> Sina
>
> Sina Madani, MD MS
>
> Data Integration & Modeling
>
> MD Anderson Cancer Center
>
> Phone : 713-563-1803
>
> Trish Whetzel, PhD
>
> Outreach Coordinator
>
> The National Center for Biomedical Ontology
>
> Ph: 650-721-2378
>
> whetzel at stanford.edu <mailto:whetzel at stanford.edu>
>
> http://www.bioontology.org <http://www.bioontology.org/>
>
>   
>   
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu  <mailto:bioontology-support at lists.stanford.edu>
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20101203/a7c939a1/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: image/jpeg
Size: 82095 bytes
Desc: not available
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20101203/a7c939a1/attachment.jpe>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: image/png
Size: 4815 bytes
Desc: not available
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20101203/a7c939a1/attachment.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: image/jpeg
Size: 76691 bytes
Desc: not available
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20101203/a7c939a1/attachment-0001.jpe>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: image/jpeg
Size: 32359 bytes
Desc: not available
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20101203/a7c939a1/attachment-0002.jpe>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: image/png
Size: 7437 bytes
Desc: not available
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20101203/a7c939a1/attachment-0001.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: image/png
Size: 7757 bytes
Desc: not available
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20101203/a7c939a1/attachment-0002.png>


More information about the bioontology-support mailing list