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[bioontology-support] Ontology version information

Trish Whetzel whetzel at stanford.edu
Fri Mar 4 11:27:29 PST 2011


Hi Ramona, 

Is the goal to have the Plant Ontology and the Plant structure and Plant growth and developmental stage ontologies all contain the same content? Or, do you plan to retire the Plant structure and Plant growth and developmental stage ontologies and ask your community to use the now merged Plant Ontology?

Trish


On Mar 4, 2011, at 10:17 AM, Walls, Ramona wrote:

> The new merged PO looks great on the BioPortal browser! Thanks! I notice that on the list of all ontologies, the plant structure and plant growth and developmental stage ontologies say they were uploaded in May 2010. There should be more recent versions of those as well, that match the merged version.
> 
> Ramona
> _____________________________
> Ramona Walls
> Post-doctoral Researcher/Plant Ontology Curator
> New York Botanical Garden
> 200th St. and Kazimiroff Blvd.
> Bronx, NY 10458
> (718)817-8173
> (516)885-8005
> 
> 
> 
> -----Original Message-----
> From: Trish Whetzel [mailto:whetzel at stanford.edu]
> Sent: Thu 3/3/2011 8:42 PM
> To: Laurel Cooper
> Cc: Pankaj Jaiswal; Walls, Ramona; support at bioontology.org Support
> Subject: Re: Ontology version information
> 
> Good to talk with you too! I've added you as the owner for the Plant growth and developmental stage  and Plant structure ontologies.
> 
> Also, I've re-directed the PURL to resolve to the new ontology you uploaded. It will resolve to the ontology tree hierarchy display with term details after the ontology parses.
> 
> Trish
> 
> 
> On Mar 3, 2011, at 5:26 PM, Laurel Cooper wrote:
> 
> > 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:
> >>> format-version
> >>> data-version
> >>> date
> >>> saved-by
> >>> auto-generated-by
> >>> import
> >>> subsetdef
> >>> synonymtypedef
> >>> default-namespace
> >>> 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 to support 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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