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[bioontology-support] BAO 1.6

Stephan Schurer PhD stephan.schurer at gmail.com
Fri Apr 20 14:55:05 PDT 2012


Ok - thanks for that info. That would not be idea.
I have one quick question. Is it possible to update the submitted file
later under the same version. Under the edit option it appears that one can
select and load another file. If that's possible It would solve the
problem. We could just upload and evaluate and if is something wrong we
re-upload. I mostly want to avoid wasting your time. If somebody sees a
small depiction error that is not a problem. We don't upload anything that
is insistent of wrong.
Thanks,
Stephan

On Fri, Apr 20, 2012 at 1:27 PM, Trish Whetzel <whetzel at stanford.edu> wrote:

> 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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