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] Display error in BioPortal. Re: Automatic ontology pull

Yongqun He yongqunh at med.umich.edu
Mon Jan 18 15:50:52 PST 2010


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 <whetzel at stanford.edu> ( mailto: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


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



**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be 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/ )

 








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



**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20100118/55e65f6b/attachment.html>


More information about the bioontology-support mailing list