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

Trish Whetzel whetzel at stanford.edu
Mon Jan 18 12:09:34 PST 2010


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

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