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[bioontology-support] BAO 1.6

Stephan Schurer PhD stephan.schurer at gmail.com
Tue Apr 17 05:27:01 PDT 2012


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****
>
> ** **
>
> ** **
>
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