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[bioontology-support] BAO 1.6

Ray Fergerson ray.fergerson at
Tue Apr 17 00:57:55 PDT 2012


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.


From: Stephan Schurer PhD [mailto:stephan.schurer at]
Sent: Monday, April 16, 2012 6:27 AM
To: Trish Whetzel
Cc: Ray Fergerson; support at; 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


On Mon, Apr 16, 2012 at 5:48 AM, Trish Whetzel <whetzel at>

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?


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.


On Sun, Apr 15, 2012 at 9:20 AM, Trish Whetzel <whetzel at>

Hi Stephan,

Version 47196 is now removed.


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:

Thank you and sorry for the trouble.


On Wed, Apr 11, 2012 at 3:50 PM, Stephan Schurer PhD
<stephan.schurer at> 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.



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

---------- Forwarded message ----------
From: Stephan Schurer PhD <stephan.schurer at>
Date: Wed, Apr 11, 2012 at 3:25 PM
Subject: BAO 1.6
To: Trish Whetzel <whetzel at>
Cc: Uma Vempati <UVempati at>, Saminda Abeyruwan
<samindaa at>

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?



Trish Whetzel, PhD

Outreach Coordinator

The National Center for Biomedical Ontology

Ph: 650-721-2378

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