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[bioontology-support] Display error in BioPortal. Re: Automatic ontology pull

Trish Whetzel whetzel at stanford.edu
Mon Jan 18 15:59:13 PST 2010


Yes, each new version of VO will have a different ontology version
identifier.

Trish

From: Yongqun He [mailto:yongqunh at med.umich.edu] 
Sent: Monday, January 18, 2010 3:51 PM
To: Trish Whetzel
Cc: support at bioontology.org; Allen Xiang
Subject: Re: Display error in BioPortal. Re: Automatic ontology pull

 

Hi Trish,

 

The location of VO is in the VO SVN folder:

http://vaccineontology.svn.sourceforge.net/viewvc/vaccineontology/trunk/src/
ontology/

 

One more question: can the identifier 42178 change once a new VO version is
updated to BioPortal?  

 

Thanks!

Oliver

>>> Trish Whetzel <whetzel at stanford.edu> 1/18/2010 3:09 PM >>>

Can you send me the link for the location of VO in your repository?

 

The identifier 1172 is the ontology id also referred to as a virtual id
since when used in various web service calls it will retrieve information
from the most recent ontology version. This identifier can also be used to
link to BioPortal to display the latest version of an ontology. For example,
http://bioportal.bioontology.org/virtual/1172.   The identifier 42178
represents the ontology version id. 

 

Trish

 

 

On Jan 16, 2010, at 6:21 AM, Yongqun He wrote:





Hi Trish,

 

I just checked and was glad to find that VO is now automatically extracted
from SVN and displayed in BioPortal. 

http://bioportal.bioontology.org/visualize/42178

(redirected from http://bioportal.bioontology.org/virtual/1172 )

 

However, I found that the visualization has some error. Particularly, I
found the BFO upper level ontology is missing in the displayed structure. I
don't know why. 

 

Another question: the current VO site is located here:

http://bioportal.bioontology.org/ontologies/42178

VO's ID in BioPortal is 1172. I am wondering what is the difference between
1172 and 42178? Is the number 42178 temporary?

 

Thanks!

 

Oliver 

>>> Yongqun He 12/10/2009 5:36 PM >>>

Thanks, Allen.

 

Trish, it is not an issue from our side to use a SVN location. In that case,
let's use the svn location instead of the vo.owl release version in VIOLIN
website.

 

Thanks!

--Oliver

>>> Allen Zuoshuang Xiang <zxiang at med.umich.edu> 12/10/2009 5:09 PM >>>
I have updated ontologies.txt to use SVN URL.

Thanks,
Allen


On 12/10/2009 3:07 PM, Trish Whetzel wrote: 

Great! I would also like to talk to you about the location of the VO.owl
file in SVN. In order for the process, I was informed that the download URL
needs to be a SVN location as well. From our side, there are no issues with
daily updates to BioPortal. Would that be an issue from your side?

 

Trish

 

 

On Dec 10, 2009, at 12:44 PM, Allen Zuoshuang Xiang wrote:





Hi Trish,

I have updated the file and committed to the location you specified. 

Thanks,
Allen


On 12/10/2009 2:54 PM, Trish Whetzel wrote: 

PS - the file also needs to be in the SVN repository itself within the
checkout directory. Based on information sent earlier, this is specified as:

 /apps/bmir.apps/bioportal_resources/cvscheckout/Vaccine Ontology

 

So if the file can be added to at this location:
apps/bmir.apps/bioportal_resources/cvscheckout/Vaccine
Ontology/trunk/src/ontology/ontologies.txt that should be fine. 

 

Trish

 

 

Begin forwarded message:





From: Trish Whetzel <whetzel at stanford.edu>

Date: December 10, 2009 11:42:28 AM PST

To: Allen Zuoshuang Xiang <zxiang at med.umich.edu>

Subject: Re: Automatic ontology pull

 

Thanks Alan. Our developer reviewed the file and noticed one item with the
spacing for the contact field and suggested the following format, noting
differences between spaces and tabs:

contact<tab>AmphiAnat<space>mailing<space>list<tab>sbhdbe<tab>mst.edu<return
>

 

Also, the contact is intended to be an email address rather than a web site
URL. 

 

Trish

 

 

On Dec 10, 2009, at 11:14 AM, Allen Zuoshuang Xiang wrote:





Hi Trish,

The file is located at http://www.violinet.org/vo/bioportal_settings.txt

Thanks,
Allen



On 12/10/2009 12:57 PM, Yongqun He wrote: 

OK. I got you this time. 

Allen, can you please update the file and do what Trish suggests?

Thanks!
--Oliver

>>> Trish Whetzel  <mailto:whetzel at stanford.edu> <whetzel at stanford.edu>
12/10/2009 1:49 PM >>>

Sorry, I think that we have missed a connection. The metadata information
below (id, title, etc.) needs to be added to a text file, ensuring the
proper spacing with tabs etc, and uploaded to your server. Once the file is
on your server, if you can send us the full path to this file then we can
test out the process.

 

Trish 

 

 

On Dec 10, 2009, at 10:39 AM, Yongqun He wrote:





Hi Trish,

 

We uploaded our VO.owl file manually to the folder:

http://www.violinet.org/vo/VO.owl

So I guess that this is the full path. This file represents the most current
VO release version. Our VO is also deposited in OBO library which points to
the above file as well.  

 

I have another VO development version svn site:

http://vaccineontology.svn.sourceforge.net/viewvc/vaccineontology/trunk/src/
ontology/VO.owl

However, this VO document changes probably everyday. Therefore, we would not
recommend this site for your automatic update.

 

Thanks,

 

Oliver 



>>> Trish Whetzel <whetzel at stanford.edu> 12/10/2009 1:29 PM >>>

Thanks. Perhaps best to not include the additional commentary in the file,
e.g. the notes. 

 

Can you send the full path to where this file has been uploaded to your
server?

 

Trish

 

 

On Dec 10, 2009, at 9:23 AM, Yongqun He wrote:





Hi Trish,

 

Here it is:

 

------

 

id VO
title Vaccine Ontology
namespace VO
foundry NO (note: VO is listed in OBO libary:
http://www.obofoundry.org/cgi-bin/detail.cgi?id=vaccine)
status Production and review
download http://www.violinet.org/vo/VO.owl (NOTE: or use:
http://purl.obolibrary.org/obo/vo.owl , which points to the
http://www.violinet.org/vo/VO.owl)
source 
home Vaccine Ontology|http://www.violinet.org/vaccineontology/
documentation 
contact Yongqun Oliver He http://www.hegroup.org <http://www.hegroup.org/> 
format OWL
description A biomedical ontology in the vaccine domain
domain vaccine
subtypes_of 
patho_type 
granularity 
relevant_organism all possible organisms with the use of vaccines.

 

------

 

We don't know how to fill up some information so we leave them alone. Please
let us know if you need more information. Thanks,

 

Oliver



>>> Trish Whetzel <whetzel at stanford.edu> 12/9/2009 10:39 PM >>>
Hi Oliver,

I was informed that an ontology metadata file is also needed for the  
automatic ontology loading to BioPortal. I have attached a template  
for your use. Once this file is filled out and added to your  
repository, can you send us the full path to the file and we can begin  
the testing.

Thanks,
Trish

 

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Electronic Mail is not secure, may not be read every day, and should not be
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used for urgent or sensitive issues 

 

 

 

Trish Whetzel, PhD

Outreach Coordinator

The National Center for Biomedical Ontology

Ph: 650-721-2378

whetzel at stanford.edu

http://www.bioontology.org <http://www.bioontology.org/> 

 

 

 

 

 

 

 

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