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

Madani,Sina AHMadani at mdanderson.org
Fri Dec 3 08:55:01 PST 2010


please ignore my question on "admin" page and page error. I figure out that the admin page is running under a different port, 8080"http://10.106.131.151:8080/bioportal_admin/", actually a separate war file. Perhaps the instruction on the wiki page needs updating :)

I am now stuck on how to parse the requested ontologies,  what is this "Ontology Version Ids" refer to? I tried both version and ontology id but didn't work

Thanks
Sina
[cid:image008.png at 01CB92D8.88EFCFC0]

From: Madani,Sina
Sent: Thursday, December 02, 2010 10:57 AM
To: 'Paul R Alexander'
Cc: 'support at bioontology.org'
Subject: RE: [bioontology-support] FW: BioPortal VM Image - access information

I forgot to ask whether "waiting to parse" means it's waiting for admin to trigger the parse or it will do it automatically. It's more than 2 hours that it shows this message
If the former is true, bioportal_admin page does not bring any page for manual start of parsing.

[cid:image001.png at 01CB92D7.EFB28870]

Thanks
Sina

From: Madani,Sina
Sent: Thursday, December 02, 2010 9:12 AM
To: 'Paul R Alexander'
Cc: support at bioontology.org
Subject: RE: [bioontology-support] FW: BioPortal VM Image - access information

Thanks! changing the hash worked. The instance is running in VMPlayer in Windows 7 environment.

I have some questions for you:

For RRF format terminologies, which RRF file I should use for upload (MRSAB, MRCONSO, or all of them)? For ICD9 below I just chose one and waiting for an error to happen.
How can I monitor the process except the fact that when it's loaded I get a status change.
How can I setup annotation services in admin GUI, if there is any, to process batch text file with no 300 words limit?
How can I delete a terminology?
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.

I tried using annotator user group to get my answers but it seems the group is not activated yet

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.

Sina

[cid:image002.jpg at 01CB92D7.EFB28870]

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

[cid:image003.png at 01CB92D7.EFB28870]

[cid:image004.jpg at 01CB92D7.EFB28870]


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


[cid:image005.jpg at 01CB92D7.EFB28870]


[cid:image006.png at 01CB92D7.EFB28870]



[cid:image007.png at 01CB92D7.EFB28870]



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/>









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