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[bioontology-support] Ontology version information

Laurel Cooper cooperl at science.oregonstate.edu
Thu Mar 3 17:26:45 PST 2011


Hi Trish,
Great talking with you, thanks for your help.
I was able to submit the new entry for the merged version.  The only 
issue is that came up is that on the metadata page, the
BioPortal PURL: http://purl.bioontology.org/ontology/PO (which is 
apparently auto-generated), takes you to the entry for the Plant Growth 
and Developmental Stage Ontology, v. 1.34.
Let me know if you sort out the issue with my user name and we can talk 
further about this other issue.
Thanks again,
Take care,
Laurel



On 3/3/2011 2:08 PM, Trish Whetzel wrote:
> Hi Laurel!
>
> Sorry about the delay in responding..I'm in a 3-week stretch of 
> offsite meetings. The information below regarding the header tags is 
> correct.
>
> Related to the new merged plant ontology file at:
> http://palea.cgrb.oregonstate.edu/viewsvn/Poc/tags/live/plant_ontology.obo?view=co 
> ,
> please create a new entry in BioPortal for this ontology. The 
> advantages of you registering the ontology is that you will be added 
> as the owner automatically and can then add the proper ontology metadata.
>
> Also, can you send me your BioPortal username and I can then add you 
> as the owner to the other plant ontologies? After your account is 
> linked as the owner, you will be able to update the ontology metadata.
>
> Best regards,
> Trish
>
>
> On Feb 21, 2011, at 12:22 PM, Laurel Cooper wrote:
>
>> Dear Trish,
>>
>> Thanks for getting in touch.  I am sure we can add that header tag in 
>> our next release.
>>
>> According to that page, the Header tags should appear in the 
>> following order:
>>
>>    1. format-version
>>    2. data-version
>>    3. date
>>    4. saved-by
>>    5. auto-generated-by
>>    6. import
>>    7. subsetdef
>>    8. synonymtypedef
>>    9. default-namespace
>>   10. remark
>>
>>  Correct?   Chris had requested we add an additional line "ontology: 
>> po",**so we have that**after the default namespace *
>>
>> *
>> I have had on my list to contact you about getting the version 
>> information updated on Bioportal.  As it still does not seem that the 
>> updated plant ontology file is available yet.
>> I had several email discussions with Paul Alexander since returning 
>> from PAG and our meeting there about getting the files and metadata 
>> updated.
>>
>> We have set up a stable URL for our live, updated version:  
>> http://palea.cgrb.oregonstate.edu/viewsvn/Poc/tags/live/plant_ontology.obo?view=co 
>>
>>  This link will always be the version of the file that is on our live 
>> site.  That is the merged file and is the one that should be linked to.
>>
>> I can send you more details of our discussions if you want or we can 
>> set up a time to have a brief skype.  I will subscribe to the email 
>> alerts,
>>
>> Thanks, Laurel
>>
>>
>> On 02/19/2011 11:28 PM, Trish Whetzel wrote:
>>> Hi Pankaj and Laurel,
>>>
>>> Since BioPortal (http://bioportal.bioontology.org/) is now able to load an ontology file given a URL vs. the previous method of connecting into a CVS/SVN repository, we are changing how we extract the ontology version information. For OBO format ontologies, we will extract this information from the property "data-version" based on the property description here:http://www.geneontology.org/GO.format.obo-1_4.shtml. For OWL ontologies, we will extract the version information from owl:versioninfo. In your next ontology release, can you include the version information in the ontology file?
>>>
>>> Also, is someone from your group subscribed to receive comments on your ontology via the email alert feature? To subscribe, please send email tosupport at bioontology.org  with the ontology name and email address to subscribe.
>>>
>>>
>>> Thanks!
>>> Trish
>>>
>>>
>>> Trish Whetzel, PhD
>>> Outreach Coordinator
>>> The National Center for Biomedical Ontology
>>> Ph: 650-721-2378
>>> whetzel at stanford.edu
>>> http://www.bioontology.org
>>>
>>>
>>>
>>>    
>>
>> -- 
>> **********************************************************
>> Laurel (Lol) Cooper, PhD
>> Coordinator, Plant Ontology Consortium
>> Dept. of Botany and Plant Pathology
>> Rm 3086, Cordley Hall
>> Oregon State University
>> Corvallis, OR 97331
>> Web:www.plantontology.org
>>
>> Phone:  541-737-5272
>> Fax:    541-737-3573
>>
>> ***********************************************************
>>
>

-- 
**********************************************************
Laurel (Lol) Cooper, PhD
Coordinator, Plant Ontology Consortium
Dept. of Botany and Plant Pathology
Rm 3086, Cordley Hall
Oregon State University
Corvallis, OR 97331
Web: www.plantontology.org

Phone:  541-737-5272
Fax:    541-737-3573

***********************************************************

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