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[bioontology-support] BAO 1.6

Trish Whetzel whetzel at stanford.edu
Fri Apr 20 10:27:38 PDT 2012


Hi Stephan, 

One note about changing the status to Private is that the BAO entry and all ontology versions of BAO (not just the one you want to review) will be made temporarily unavailable when the status is set to Private other than to those users you grant access to BAO. 

Trish 



On Apr 17, 2012, at 5:27 AM, Stephan Schurer PhD wrote:

> Hallo Ray,  This is very helpful. BAO IS OWL 2. We probably won't use the staging system, but uploading it as private makes sense for review.
> Thanks, -Stephan 
> 
> On Tue, Apr 17, 2012 at 3:57 AM, Ray Fergerson <ray.fergerson at stanford.edu> wrote:
> Stephan,
> 
>  
> 
> As Trish indicates there is no simple solution that always works. For OWL 1 ontologies the ontology should appear in BioPortal as it does in the latest Protégé 3.8.x. If it does not, then please report this as a bug. For OWL 2 ontologies we do some preprocessing to make it show up so you cannot really tell how it is going to look in BioPortal without loading it. The staging environment can be used if necessary but we discourage this because the environment is often taken down without notice. Also ontologies submitted to staging may disappear without notice at any time. Staging is a possibility though if you are aware of these limitations. Another possibility is to submit the ontology as private. Then only you will see it. You can make it public when you decide that it looks good.
> 
>  
> 
> Also as Trish indicates, in the coming year we will be changing the way ontologies are stored. When complete, the ontology hierarchy in BioPortal should look as it does in Protégé 4 since we will be using the same OWL library that Protégé 4 uses.
> 
>  
> 
> Sorry that this is so complicated. I hope that one of these solutions will work for you. We do not have the resources to setup and maintain another system just for this purpose.
> 
>  
> 
> Ray
> 
>  
> 
> From: Stephan Schurer PhD [mailto:stephan.schurer at gmail.com] 
> 
> Sent: Monday, April 16, 2012 6:27 AM
> To: Trish Whetzel
> Cc: Ray Fergerson; support at bioontology.org; Uma Vempati
> Subject: Re: BAO 1.6
> 
>  
> 
> Thanks. Please let us know. I hate to create more work for you to remove or change anything. Thanks so much for you help with correcting the recent version.
> 
> Stephan
> 
> On Mon, Apr 16, 2012 at 5:48 AM, Trish Whetzel <whetzel at stanford.edu> wrote:
> 
> Hi Stephan, 
> 
>  
> 
> As far as pre-viewing the ontology, in some cases we have loaded the ontology to the staging server. However, this is not the best solution overall.  Ray, do you have suggestions on more robust mechanisms to handle pre-viewing new ontology versions before the new version is made public or would you expect that as we move to the triple-store backend that this will become a non-issue?
> 
>  
> 
> Trish 
> 
>  
> 
>  
> 
> On Apr 16, 2012, at 2:14 AM, Stephan Schurer PhD wrote:
> 
> 
> 
> 
> Thank you! I need to find a better way to preview how the ontology gets displayed in the bioportal.
> 
> Stephan
> 
> On Sun, Apr 15, 2012 at 9:20 AM, Trish Whetzel <whetzel at stanford.edu> wrote:
> 
> Hi Stephan, 
> 
>  
> 
> Version 47196 is now removed.
> 
>  
> 
> Trish 
> 
>  
> 
>  
> 
> On Apr 12, 2012, at 8:55 PM, Stephan Schurer PhD wrote:
> 
> 
> 
> 
> Hallo, I uploaded a new version 1.6. Can you please delete the Bioportal entry BAO 1.6 uploaded 04/09/2012:
> 
> http://bioportal.bioontology.org/ontologies/1533
> 
> http://bioportal.bioontology.org/ontologies/47196?p=terms
> 
>  
> 
> Thank you and sorry for the trouble.
> 
>  
> 
> Stephan
> 
>  
> 
> On Wed, Apr 11, 2012 at 3:50 PM, Stephan Schurer PhD <stephan.schurer at gmail.com> wrote:
> 
> Dear BioPortal support,
> 
>  
> 
> I need to replace the BAO 1.6 version. We had two labels, but it looks bad when parsed in bioportal. Please see email below.
> 
> If you can delete version 1.6, I will upload again.
> 
>  
> 
> Thanks,
> 
>  
> 
> Stephan
> 
>  
> 
> P.S. Is there a good way to check prior to upload to the portal how the parsed ontology will show. There are always some subtle differences to Protege.
> 
>  
> 
>  
> 
> ---------- Forwarded message ----------
> From: Stephan Schurer PhD <stephan.schurer at gmail.com>
> Date: Wed, Apr 11, 2012 at 3:25 PM
> Subject: BAO 1.6
> To: Trish Whetzel <whetzel at stanford.edu>
> Cc: Uma Vempati <UVempati at med.miami.edu>, Saminda Abeyruwan <samindaa at gmail.com>
> 
> 
> Hallo Trish,
> 
>  
> 
> We just uploaded BAO 1.6 It processed fine, but I see one class that looks funny: 'bioassay component' / 'assay format' / {'cell based format', 'cell-based format'}
> 
> It appears that this is because there are two labels. Not sure how this happened, but we need to correct it.
> 
> Is there a way I can replace this version, or can you?
> 
>  
> 
> Thanks,
> 
>  
> 
> Stephan
> 
>  
> 
>  
> 
>  
> 
>  
> 
>  
> 
> Trish Whetzel, PhD
> 
> Outreach Coordinator
> 
> The National Center for Biomedical Ontology
> 
> Ph: 650-721-2378
> 
> http://www.bioontology.org
> 
>  
> 
> "Like" NCBO on Facebook: http://on.fb.me/bioontology
> 
>  
> 
> Follow NCBO on Twitter: http://twitter.com/#!/bioontology
> 
>  
> 
> Join in Discussions on LinkedIn: http://linkd.in/ncbo-group
> 
>  
> 
>  
> 
> 

Trish Whetzel, PhD
Outreach Coordinator
The National Center for Biomedical Ontology
Ph: 650-721-2378
http://www.bioontology.org

"Like" NCBO on Facebook: http://on.fb.me/bioontology

Follow NCBO on Twitter: http://twitter.com/#!/bioontology

Join in Discussions on LinkedIn: http://linkd.in/ncbo-group

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